diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 0dd4d79..4f7bf47 100644 Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index f9df1a3..ceec537 100644 Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index b0bfb11..5125166 100644 Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 7a226ee..7385545 100644 Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index c51b90a..48f2cdb 100644 Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png index a89aab3..d373ebf 100644 Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ diff --git a/articles/ar-grid.html b/articles/ar-grid.html index fb2a2e0..fb3e720 100644 --- a/articles/ar-grid.html +++ b/articles/ar-grid.html @@ -206,23 +206,23 @@

Create A&R grid gt::gt() |> gt::fmt_markdown(columns = gt::everything()) |> gt::tab_options(table.font.size = 15) -
- diff --git a/favicon-16x16.png b/favicon-16x16.png index 058f621..04c18f7 100644 Binary files a/favicon-16x16.png and b/favicon-16x16.png differ diff --git a/favicon-32x32.png b/favicon-32x32.png index 9f3e72d..abb6a13 100644 Binary files a/favicon-32x32.png and b/favicon-32x32.png differ diff --git a/pkgdown.yml b/pkgdown.yml index a2298f6..2a0a201 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -7,7 +7,7 @@ articles: component: component.html metalite: metalite.html mockup-table: mockup-table.html -last_built: 2024-01-16T02:42Z +last_built: 2024-02-07T18:07Z urls: reference: https://merck.github.io/metalite/reference article: https://merck.github.io/metalite/articles diff --git a/reference/meta_inherit.html b/reference/meta_inherit.html index 973f40a..7f90913 100644 --- a/reference/meta_inherit.html +++ b/reference/meta_inherit.html @@ -90,8 +90,10 @@

Value

Examples

- 
meta_adam(population = r2rtf::r2rtf_adsl,
-          observation = r2rtf::r2rtf_adae) |>
+    
meta_adam(
+  population = r2rtf::r2rtf_adsl,
+  observation = r2rtf::r2rtf_adae
+) |>
   meta_inherit(meta_example(), c("apat", "wk12", "ae_summary"))
 #> ADaM metadata: 
 #>    .$data_population 	Population data with 254 subjects 
diff --git a/search.json b/search.json
index d93a451..3843df5 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C)     This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see .   Copyright (C)    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to Variable Mapping","text":"design abstraction variable mapping enhance robustness metadata information. goal follow dependency inversion principle software design. design inspired ggplot2::aes(). typical analysis, require developer provide variable names : name: reference name key link components. Subject identifier (id): typically using USUBJID ADaM data. Treatment group (group): typically using TRTXX ADaM data. variables (var): additional variables required analysis. subset: subset expression define analysis. Typically using analysis flag XXFL ADaM data. label: natural language describe purpose adam_mapping object.","code":""},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"example-1-all-participants-as-treated-apat","dir":"Articles","previous_headings":"","what":"Example 1: All Participants as Treated (apat)","title":"Introduction to Variable Mapping","text":"example, define adam_mapping APaT population. example illustrate use case decouple variable name ADSL based data_mapping abstract layer. defined variable mapping, development standard function can rely abstraction. long study team provide proper data associate adam_mapping, standard function can used. R, abstraction named list can accessed .$subset assigned <-. goal summarize var group within population defined subset. can write R scripts abstract layer using base R tidy evaluation .","code":"x <- adam_mapping(   name = \"apat\",   id = \"USUBJID\",   group = \"TRT01A\",   subset = TRTFL == \"Y\",   label = \"All Participants as Treated\" )  x #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> \"TRT01A\" #> * `var`    -> NULL #> * `subset` -> TRTFL == \"Y\" #> * `label`  -> \"All Participants as Treated\" x$subset #> TRTFL == \"Y\" x$var <- \"AGE\" x$subset <- quote(SAFFL == \"Y\") # using quote for an expression x #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> \"TRT01A\" #> * `var`    -> \"AGE\" #> * `subset` -> SAFFL == \"Y\" #> * `label`  -> \"All Participants as Treated\""},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"base-r","dir":"Articles","previous_headings":"Example 1: All Participants as Treated (apat)","what":"Base R","title":"Introduction to Variable Mapping","text":"Reference: eval expression.","code":"df <- r2rtf::r2rtf_adsl ana <- df[eval(x$subset, df), ]  split(ana, ana[[x$group]]) |>   sapply(function(y) mean(y[[x$var]])) #>              Placebo Xanomeline High Dose  Xanomeline Low Dose  #>             75.20930             74.38095             75.66667"},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"tidy-evaluation","dir":"Articles","previous_headings":"Example 1: All Participants as Treated (apat)","what":"Tidy evaluation","title":"Introduction to Variable Mapping","text":"Reference: Programming dplyr. using adam_mapping abstract layer, creates additional challenges develop R program, yet can reduce maintenance future.","code":"library(dplyr) df |>   dplyr::filter(!!x$subset) |>   dplyr::group_by(.data[[x$group]]) |>   dplyr::summarise(mean = mean(.data[[x$var]]))"},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"example-2-serious-adverse-events-ser","dir":"Articles","previous_headings":"","what":"Example 2: Serious adverse events (ser)","title":"Introduction to Variable Mapping","text":"example, define adam_mapping serious adverse events (AE). example illustrate use case inherit default values defined metalite. organization conventions define different analysis terms. can define default values commonly used analysis terms. example, define default adam_mapping object . real example can found metalite:::default_parameter_ae. default values, user can reduce input still allow override default values required. Assuming user define adam_mapping study, study require footnote explain meaning serious adverse events. merge user defined default adam_mapping objects. (always left join) can keep user defined variables. add default subset variable, defined user. Note: adam_mapping object also allow user define variables. example, added footnote variable.","code":"ser_default <- adam_mapping(   name = \"ser\",   label = \"serious adverse events\",   subset = quote(AESER == \"Y\") )  ser_default #> ADaM mapping:  #> * `name`   -> \"ser\" #> * `id`     -> NULL #> * `group`  -> NULL #> * `var`    -> NULL #> * `subset` -> AESER == \"Y\" #> * `label`  -> \"serious adverse events\" ser_user <- adam_mapping(   name = \"ser\",   id = \"USUBJID\",   group = \"TRT01A\",   label = \"serious{^a} adverse events\",   footnote = \"{^a} this is a footnote\" ) ser_user #> ADaM mapping:  #> * `name`     -> \"ser\" #> * `id`       -> \"USUBJID\" #> * `group`    -> \"TRT01A\" #> * `var`      -> NULL #> * `subset`   -> NULL #> * `label`    -> \"serious{^a} adverse events\" #> * `footnote` -> \"{^a} this is a footnote\" merge(ser_user, ser_default) #> ADaM mapping:  #> * `name`     -> \"ser\" #> * `id`       -> \"USUBJID\" #> * `group`    -> \"TRT01A\" #> * `var`      -> NULL #> * `subset`   -> AESER == \"Y\" #> * `label`    -> \"serious{^a} adverse events\" #> * `footnote` -> \"{^a} this is a footnote\""},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Create AR Grid","text":"document, illustrate create &R grid metalite.","code":""},{"path":[]},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-1-input-the-population-and-observation-datasets","dir":"Articles","previous_headings":"Build metadata","what":"Step 1: input the population and observation datasets","title":"Create AR Grid","text":"","code":"metadata <- meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae )"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-2-create-statistical-analysis-plans","dir":"Articles","previous_headings":"Build metadata","what":"Step 2: create statistical analysis plans","title":"Create AR Grid","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" ) |>   add_plan(     analysis = \"ae_specific\", population = \"apat\",     observation = c(\"wk12\", \"wk24\"),     parameter = c(\"any\", \"aeosi\", \"rel\", \"ser\")   )"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-3-feed-in-the-analysis-plan-to-the-existing-metadata","dir":"Articles","previous_headings":"Build metadata","what":"Step 3: feed in the analysis plan to the existing metadata","title":"Create AR Grid","text":"","code":"metadata <- metadata |> define_plan(plan)"},{"path":[]},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-4-1-define-the-key-words-in-population-observation","dir":"Articles","previous_headings":"Build metadata","what":"Step 4.1: define the key words in population & observation","title":"Create AR Grid","text":"","code":"metadata <- metadata |>   define_population(     name = \"apat\",     group = \"TRT01A\",     subset = SAFFL == \"Y\"   ) |>   define_observation(     name = \"wk12\",     group = \"TRTA\",     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) |>   define_observation(     name = \"wk24\",     group = \"TRTA\",     subset = AOCC01FL == \"Y\", # just for demo, another flag shall be used.     label = \"Weeks 0 to 24\"   )"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-4-2-define-the-key-words-in-the-analysis-plans","dir":"Articles","previous_headings":"Build metadata","what":"Step 4.2 define the key words in the analysis plans","title":"Create AR Grid","text":"","code":"metadata <- metadata |>   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) |>   define_parameter(     name = \"aeosi\",     subset = AEOSI == \"Y\",     label = \"adverse events of special interest\"   ) |>   define_analysis(     name = \"ae_summary\",     title = \"Summary of Adverse Events\"   ) |>   define_analysis(     name = \"ae_specific\",     title = \"Summary of Specific Adverse Events\"   )"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-5-build-the-metadata","dir":"Articles","previous_headings":"Build metadata","what":"Step 5: build the metadata","title":"Create AR Grid","text":"","code":"metadata <- metadata |> meta_build()"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"create-ar-grid","dir":"Articles","previous_headings":"","what":"Create A&R grid","title":"Create AR Grid","text":"Summary Adverse EventsWeeks 0 12All Participants Treated ae0summary0wk12.rtf ae_summary Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ Summary Adverse EventsWeeks 0 24All Participants Treated ae0summary0wk24.rtf ae_summary Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ Summary Specific Adverse EventsWeeks 0 12All Participants Treated ae0specific0wk120any.rtf ae_specific Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ Summary Specific Adverse EventsWeeks 0 24All Participants Treated ae0specific0wk240any.rtf ae_specific Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ Summary Specific Adverse EventsWeeks 0 12All Participants Treated ae0specific0wk120aeosi.rtf ae_specific Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ AEOSI == ‘Y’ Summary Specific Adverse EventsWeeks 0 24All Participants Treated ae0specific0wk240aeosi.rtf ae_specific Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ AEOSI == ‘Y’ Summary Specific Adverse EventsWeeks 0 12All Participants Treated ae0specific0wk120rel.rtf ae_specific Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ AEREL %% c(‘POSSIBLE’, ‘PROBABLE’) Summary Specific Adverse EventsWeeks 0 24All Participants Treated ae0specific0wk240rel.rtf ae_specific Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ AEREL %% c(‘POSSIBLE’, ‘PROBABLE’) Summary Specific Adverse EventsWeeks 0 12All Participants Treated ae0specific0wk120ser.rtf ae_specific Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ AESER == ‘Y’ Summary Specific Adverse EventsWeeks 0 24All Participants Treated ae0specific0wk240ser.rtf ae_specific Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ AESER == ‘Y’","code":"ar_grid <- data.frame(   title = spec_title(metadata),   filename = spec_filename(metadata),   function_name = metadata$plan$analysis,   population = spec_analysis_population(metadata) ) ar_grid |>   mutate(across(everything(), ~ gsub(\"\\n\", \"
\", .x))) |>   gt::gt() |>   gt::fmt_markdown(columns = gt::everything()) |>   gt::tab_options(table.font.size = 15)"},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-adam-mapping","dir":"Articles","previous_headings":"","what":"Collect ADaM mapping","title":"Collect Components","text":"object meta organized list ADaM mapping objects. example, can directly access ADaM mapping object list. created helper function help access components component name. example, can collect apat component meta name using collect_adam_mapping(). Collect ADaM mapping participants treated. can collect ADaM mapping serious adverse events parameter meta$parameter$ser. can collect ADaM mapping AE summary analysis method meta$analysis$ae_summary.","code":"meta$population$apat #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> \"TRTA\" #> * `var`    -> NULL #> * `subset` -> SAFFL == \"Y\" #> * `label`  -> \"All Participants as Treated\" collect_adam_mapping(meta, name = \"apat\") #> ADaM mapping:  #> * `name`      -> \"apat\" #> * `id`        -> \"USUBJID\" #> * `group`     -> \"TRTA\" #> * `var`       -> NULL #> * `subset`    -> SAFFL == \"Y\" #> * `label`     -> \"All Participants as Treated\" #> * `.location` -> \"population\" collect_adam_mapping(meta, name = \"ser\") #> ADaM mapping:  #> * `name`      -> \"ser\" #> * `id`        -> NULL #> * `group`     -> NULL #> * `var`       -> \"AEDECOD\" #> * `subset`    -> AESER == \"Y\" #> * `label`     -> \"serious adverse events\" #> * `soc`       -> \"AEBODSYS\" #> * `seq`       -> 401 #> * `term1`     -> \"Serious\" #> * `term2`     -> \"\" #> * `summ_row`  -> \"with serious adverse events\" #> * `.location` -> \"parameter\" collect_adam_mapping(meta, name = \"ae_summary\") #> ADaM mapping:  #> * `name`      -> \"ae_summary\" #> * `id`        -> NULL #> * `group`     -> NULL #> * `var`       -> NULL #> * `subset`    -> NULL #> * `label`     -> \"Table: adverse event summary\" #> * `title`     -> \"Summary of Adverse Events\" #> * `.location` -> \"analysis\""},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-population","dir":"Articles","previous_headings":"","what":"Collect population","title":"Collect Components","text":"developing tools, developer also need access subset condition population. can access information list Equivalently, can also use collect_population() collect definition population. example, can collect subset condition apat using collect_population(), can find subset condition multiple levels. example, can collect analysis population definition apat population, wk12 observation ser parameters.","code":"meta$population$apat$subset #> SAFFL == \"Y\" collect_population(meta, population = \"apat\") #> $population #> [1] \"SAFFL == 'Y'\" collect_population(meta,   population = \"apat\",   observation = \"wk12\",   parameter = \"ser\" ) #> $population #> [1] \"SAFFL == 'Y'\" #>  #> $observation #> [1] \"SAFFL == 'Y'\" #>  #> $parameter #> [1] \"AESER == 'Y'\""},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-population-records","dir":"Articles","previous_headings":"","what":"Collect population records","title":"Collect Components","text":"User may want identify records belong analysis population. can use collect_population_index() show population record index. example, user get index population data set apat participants treated. Alternatively, people may want know ID subjects population. case, collect_population_id() can used collect ID - > USUBJID apat population. can directly collect observations using collect_population_record(). default, key variables used id, group, subset displayed. example shows collect population record population data set participants treated display default variables. example show add variables population data set display. can also add add multiple additional variable display","code":"population_index <- collect_population_index(meta, \"apat\") head(collect_population_index(meta, \"apat\")) #> [1] 1 2 3 4 5 6 population_id <- collect_population_id(meta, \"apat\") head(collect_population_id(meta, \"apat\")) #> [1] \"01-701-1015\" \"01-701-1023\" \"01-701-1028\" \"01-701-1033\" \"01-701-1034\" #> [6] \"01-701-1047\" head(collect_population_record(meta, \"apat\")) #>       USUBJID                 TRTA SAFFL #> 1 01-701-1015              Placebo     Y #> 2 01-701-1023              Placebo     Y #> 3 01-701-1028 Xanomeline High Dose     Y #> 4 01-701-1033  Xanomeline Low Dose     Y #> 5 01-701-1034 Xanomeline High Dose     Y #> 6 01-701-1047              Placebo     Y head(collect_population_record(meta, \"apat\", var = \"AGE\")) #>       USUBJID                 TRTA SAFFL AGE #> 1 01-701-1015              Placebo     Y  63 #> 2 01-701-1023              Placebo     Y  64 #> 3 01-701-1028 Xanomeline High Dose     Y  71 #> 4 01-701-1033  Xanomeline Low Dose     Y  74 #> 5 01-701-1034 Xanomeline High Dose     Y  77 #> 6 01-701-1047              Placebo     Y  85 head(collect_population_record(meta, \"apat\", var = c(\"AGE\", \"TRT01P\"))) #>       USUBJID                 TRTA SAFFL AGE               TRT01P #> 1 01-701-1015              Placebo     Y  63              Placebo #> 2 01-701-1023              Placebo     Y  64              Placebo #> 3 01-701-1028 Xanomeline High Dose     Y  71 Xanomeline High Dose #> 4 01-701-1033  Xanomeline Low Dose     Y  74  Xanomeline Low Dose #> 5 01-701-1034 Xanomeline High Dose     Y  77 Xanomeline High Dose #> 6 01-701-1047              Placebo     Y  85              Placebo"},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-observation-record","dir":"Articles","previous_headings":"","what":"Collect observation record","title":"Collect Components","text":"Similarly can collect observation records examples . example shows collect observation record index observation data set serious AE weeks 0 12 using collect_observation_index() can also directly collect records using collect_observation_record(). default, key variables used id, group, subset displayed. example shows collect observation record observation data set participants treated 0 12 week serious AE display default variables. example show add variables observation data set display.","code":"collect_observation_index(meta, \"apat\", \"wk12\", \"ser\") #> [1]  689 1131 1173 collect_observation_record(meta, \"apat\", \"wk12\", \"ser\") #>          USUBJID                 TRTA #> 689  01-709-1424 Xanomeline High Dose #> 1131 01-718-1170  Xanomeline Low Dose #> 1173 01-718-1371 Xanomeline High Dose #>                                             AEDECOD SAFFL AESER #> 689                                         SYNCOPE     Y     Y #> 1131                                        SYNCOPE     Y     Y #> 1173 PARTIAL SEIZURES WITH SECONDARY GENERALISATION     Y     Y collect_observation_record(meta, \"apat\", \"wk12\", \"ser\", var = \"AEDECOD\") #>          USUBJID                 TRTA #> 689  01-709-1424 Xanomeline High Dose #> 1131 01-718-1170  Xanomeline Low Dose #> 1173 01-718-1371 Xanomeline High Dose #>                                             AEDECOD SAFFL AESER #> 689                                         SYNCOPE     Y     Y #> 1131                                        SYNCOPE     Y     Y #> 1173 PARTIAL SEIZURES WITH SECONDARY GENERALISATION     Y     Y"},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-specifications","dir":"Articles","previous_headings":"","what":"Collect specifications","title":"Collect Components","text":"also provided helper functions collect commonly used items Developer can collect table title analysis function meta information using collect_title(). Developer can collect specification data set name using collect_dataname(). show data set name population observation.","code":"collect_title(meta, \"apat\", \"wk12\", \"ser\", \"ae_summary\") #> [1] \"Summary of Adverse Events\"   \"Weeks 0 to 12\"               #> [3] \"All Participants as Treated\" collect_dataname(meta) #>  population observation  #>      \"adsl\"      \"adae\""},{"path":"https://merck.github.io/metalite/articles/metalite.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to metalite","text":"purpose metalite unify data structure saving metadata information clinical analysis & reporting (&R), leveraging Analysis Data Model (ADaM) datasets consistent accurate metadata representation. metalite framework designed : Standardize function input analysis reporting. Enable use pipes (|>). Reduce manual steps maintain SDLC documentation. Ensure consistency analysis specification, mock, results. built metalite following principles: Automation: prefer function call checklist. example, enter data source one time AE analysis. End--end: cover steps software development lifecycle (SDLC) define delivery.","code":""},{"path":"https://merck.github.io/metalite/articles/metalite.html","id":"use-cases","dir":"Articles","previous_headings":"","what":"Use cases","title":"Introduction to metalite","text":"metalite package offers foundation simplify tool development create standard engineering workflows. example, metalite can used : Standardize input output &R functions. Create analysis reporting planning grid. Create mock table. Create validate &R results. Trace analysis records. metalite needs work R packages complete work. idea illustrated diagram .","code":""},{"path":"https://merck.github.io/metalite/articles/metalite.html","id":"mental-model","dir":"Articles","previous_headings":"","what":"Mental model","title":"Introduction to metalite","text":"typical analysis reporting based ADaM data contain three layers. Data Analysis plan Analysis metadata design metalite align layers using meta_adam define_xxx functions.","code":""},{"path":"https://merck.github.io/metalite/articles/metalite.html","id":"example-adverse-events-analysis","dir":"Articles","previous_headings":"Mental model","what":"Example: adverse events analysis","title":"Introduction to metalite","text":"use simplified adverse events analysis example illustrate mental model. Observation level: ADAE Population level: ADSL typical adverse events analysis, AE records saved ADAE (observation level) population information saved ADSL (population level). demo ADaM datasets r2rtf package, can construct object using meta_adam(). &R grid validation tracker mock table also need understand analysis plan adverse events analysis. Specifically, details table, listing figure (TLF) use two helper functions (plan() add_plan()) create analysis plan. analysis plan data frame indicate specification TLF. code , construct 10 TLFs based different combination analysis function, population, observation parameter. , can define analysis plan using define_plan(). population (define_population()): e.g.: name = \"apat\", group = \"TRT01A\", subset = SAFFL == \"Y\" observation (define_observation()): e.g.: name = \"wk12\", group = \"TRTA\", subset = SAFFL == \"Y\", label = \"Weeks 0 12\" parameter (define_parameter()): e.g.: name = \"ser\", subset = AESER == \"Y\", label = \"serious adverse events\" analysis (define_analysis()): AE summary, Specific AE table, Rainfall plot (static interactive), Volcano plot, etc. details needs defined metadata information. example, select APaT population ADSL dataset. achieved defining population. defined built-information follows &R conventions. , programs know meaning apat . project specific information still needs provided study team group variable name subset flag condition. Similarly, can define meta information analysis observation, parameter function. also use meta_build() add default values name specified. metalite, saved demo meta_example() illustrate different use cases. developer, can reuse meta information development. also allow developers standardize input functions. plan$analysis analysis name. meta columns plan() function arguments","code":"meta_adam(   observation = r2rtf_adae,   population = r2rtf_adsl ) #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" ) |>   add_plan(     analysis = \"ae_specific\", population = \"apat\",     observation = c(\"wk12\", \"wk24\"),     parameter = c(\"any\", \"aeosi\", \"rel\", \"ser\")   )  plan #>    mock    analysis population observation   parameter #> 1     1  ae_summary       apat        wk12 any;rel;ser #> 2     1  ae_summary       apat        wk24 any;rel;ser #> 3     2 ae_specific       apat        wk12         any #> 4     2 ae_specific       apat        wk24         any #> 5     2 ae_specific       apat        wk12       aeosi #> 6     2 ae_specific       apat        wk24       aeosi #> 7     2 ae_specific       apat        wk12         rel #> 8     2 ae_specific       apat        wk24         rel #> 9     2 ae_specific       apat        wk12         ser #> 10    2 ae_specific       apat        wk24         ser meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae ) |>   define_plan(plan) #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 10 plans meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae ) |>   define_plan(plan) |>   define_population(name = \"apat\") #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id group var subset                         label #> 1 'apat' 'USUBJID'                  'All Participants as Treated' meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae ) |>   define_plan(plan) |>   define_population(     name = \"apat\",     group = \"TRT01A\",     subset = SAFFL == \"Y\"   ) #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id    group var       subset                         label #> 1 'apat' 'USUBJID' 'TRT01A'     SAFFL == 'Y' 'All Participants as Treated' meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae ) |>   define_plan(plan = plan) |>   define_population(     name = \"apat\",     group = \"TRT01A\",     subset = SAFFL == \"Y\"   ) |>   define_observation(     name = \"wk12\",     group = \"TRTA\",     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) |>   define_observation(     name = \"wk24\",     group = \"TRTA\",     subset = AOCC01FL == \"Y\", # just for demo, another flag shall be used.     label = \"Weeks 0 to 24\"   ) |>   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) |>   define_parameter(     name = \"aeosi\",     subset = AEOSI == \"Y\",     label = \"adverse events of special interest\"   ) |>   define_analysis(     name = \"ae_summary\",     title = \"Summary of Adverse Events\"   ) |>   meta_build() #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id    group var       subset                         label #> 1 'apat' 'USUBJID' 'TRT01A'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' ae_summary(   meta,   population,   observation,   parameter, ... )"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"overview-of-the-example-we-used","dir":"Articles","previous_headings":"","what":"Overview of the example we used","title":"Create Mockup Table Based on Metadata","text":"example, available datasets adae adsl, available r2rtf package, .e., r2rtf::r2rtf_adae r2rtf::r2rtf_adsl. two datasets, objective conduct two adverse event (AE) analysis: (1) AE summary analysis (3) specific AE analysis. population two analysis participants treated (APaT). Besides, one observations two analysis: weeks 0-12. analysis, interested three types AEs: (1) AEs, (2) series AEs, (3) drug-related AEs. Please note example servers illustration purpose, instead comprehensive production ready work. users interested AE analysis AE categories, get types populations/observations, modification code vignette needed.","code":""},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"prepare-the-metadata","dir":"Articles","previous_headings":"","what":"Prepare the metadata","title":"Create Mockup Table Based on Metadata","text":"section, introduce steps prepare metadata used aforementioned two AE analysis.","code":""},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"step-1-define-the-metadata","dir":"Articles","previous_headings":"Prepare the metadata","what":"Step 1: Define the metadata","title":"Create Mockup Table Based on Metadata","text":"define metadata, users need specify population observations datasets. example, observation dataset comes r2rtf::r2rtf_adae population dataset comes r2rtf::r2rtf_adsl. define metadata meta_adam() follows, users can specify observation dataset name population dataset name.","code":"adae <- r2rtf::r2rtf_adae adsl <- r2rtf::r2rtf_adsl |> rename(TRTA = TRT01A) meta <- meta_adam(   observation = adae,   population = adsl )"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"step-2-define-the-analysis-plan","dir":"Articles","previous_headings":"Prepare the metadata","what":"Step 2: Define the analysis plan","title":"Create Mockup Table Based on Metadata","text":"start mockup tables, begin defining mockup analysis plan. define analysis plan, use plan() add_plan() add details per one mockup analysis. Recall example, 2 analysis plans: AE summary; Specific AE analysis. AE summary analysis, define analysis = \"ae_summary\". Similarly define proper population, observation parameter key words population = \"apat\": Participants Treated (APaT). observation = \"wk12\": Weeks 0-12 analyses. parameter = \";rel;ser\": table cover “”, “drug related” “serious” adverse events. AE specific analysis, users can follow similar logic AE summary. , can define analysis plan total 2 mockup generate 4 TLFs. , use incorporate defined plan metadata using define_plan(), .e.,","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = \"wk12\", parameter = \"any;rel;ser\" ) |>   add_plan(     analysis = \"ae_specific\", population = \"apat\",     observation = \"wk12\",     parameter = c(\"any\", \"rel\", \"ser\")   ) plan #>   mock    analysis population observation   parameter #> 1    1  ae_summary       apat        wk12 any;rel;ser #> 2    2 ae_specific       apat        wk12         any #> 3    2 ae_specific       apat        wk12         rel #> 4    2 ae_specific       apat        wk12         ser meta <- meta |> define_plan(plan)"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"step-3-define-the-keywords","dir":"Articles","previous_headings":"Prepare the metadata","what":"Step 3: Define the keywords","title":"Create Mockup Table Based on Metadata","text":"defining overview analysis plan, begin define meaning key words. Define keywords population: following code define keywords \"apat\", population keywords APaT population. also cover key information group variable, group order, etc… Define keywords observation: following code define keywords \"wk12\", observation keywords Weeks 0-12 observations. Define keywords analysis plans: Note analysis plan, 5 keywords: \"\": parameter keywords adverse events. \"rel\": parameter keywords drug-related adverse events. \"ser\": parameter keywords serious adverse events. \"ae_summary\": analysis keywords AE summary analysis. \"ae_specific\": analysis keywords specific AE analysis. first three keywords, can define define_parameter() follows. can add (1) endnotes, (2) labels, (3) criterion filter, etc. last two keywords, can define define_analysis(). vignette, present mockup table AE summary. users interested specific AE analysis, please define keywords \"ae_specific\" define_analysis(name = \"ae_specific\", title = ...).","code":"meta <- meta |>   define_population(     name = \"apat\",     group = \"TRTA\",     group_order = c(       \"High Dose\" = \"Xanomeline High Dose\",       \"Placebo\" = \"Placebo\"     ),     subset = SAFFL == \"Y\"   ) meta <- meta |>   define_observation(     name = \"wk12\",     group = \"TRTA\",     ae_var = \"AEDECOD\",     var = c(\"AEREL\", \"AESER\"),     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) meta <- meta |>   define_parameter(     name = \"any\",     end_notes = c()   ) |>   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\"),     label = \"drug-realted adverse events\"   ) |>   define_parameter(     name = \"ser\",     subset = AESER == \"Y\",     label = \"serious adverse events\",     end_notes = c(\"Serious adverse events up to 90 days of last dose are included.\")   ) meta <- meta |>   define_analysis(     name = \"ae_summary\",     title = \"Summary of Adverse Events\"   )"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"step-4-build-and-review-the-metadata","dir":"Articles","previous_headings":"Prepare the metadata","what":"Step 4: Build and review the metadata","title":"Create Mockup Table Based on Metadata","text":"keywords, datasets, analysis plan defined, users can build metadata compose information. entire metadata built, users can review analysis plan entire meta ","code":"meta <- meta |> meta_build() meta$plan #>   mock    analysis population observation   parameter #> 1    1  ae_summary       apat        wk12 any;rel;ser #> 2    2 ae_specific       apat        wk12         any #> 3    2 ae_specific       apat        wk12         rel #> 4    2 ae_specific       apat        wk12         ser meta #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 4 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>                     group_order #> 1 Xanomeline High Dose, Placebo #>  #>  #>   Analysis observation type: #>     name        id  group          var       subset           label    ae_var #> 1 'wk12' 'USUBJID' 'TRTA' AEREL, AESER SAFFL == 'Y' 'Weeks 0 to 12' 'AEDECOD' #>  #>  #>   Analysis parameter type: #>    name                         label                               subset #> 1 'any'          'any adverse events'                                      #> 2 'rel' 'drug-realted adverse events' AEREL %in% c('POSSIBLE', 'PROBABLE') #> 3 'ser'      'serious adverse events'                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event'"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"add-components-of-mockup-table","dir":"Articles","previous_headings":"","what":"Add components of mockup table","title":"Create Mockup Table Based on Metadata","text":"Based mockup table, specify additional parameters required function define next section. mockup = TRUE create mockup analysis. output_report define output path based analysis keywords. plan updated, can construct call program. also provide global argument data source. pending effort define ae_summary() ae_specific() function can generate mock tables based inputs.","code":"meta$plan <- meta$plan |>   mutate(     mockup = TRUE,     output_report = paste0(\"./tlf/mock-\", analysis, \".rtf\")   ) meta$plan #>   mock    analysis population observation   parameter mockup #> 1    1  ae_summary       apat        wk12 any;rel;ser   TRUE #> 2    2 ae_specific       apat        wk12         any   TRUE #> 3    2 ae_specific       apat        wk12         rel   TRUE #> 4    2 ae_specific       apat        wk12         ser   TRUE #>                output_report #> 1  ./tlf/mock-ae_summary.rtf #> 2 ./tlf/mock-ae_specific.rtf #> 3 ./tlf/mock-ae_specific.rtf #> 4 ./tlf/mock-ae_specific.rtf spec_call_program(meta,   data_source = \"[adam-adsl; adae]\" ) #> [1] \"ae_summary(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any;rel;ser', mockup = TRUE, output_report = './tlf/mock-ae_summary.rtf', data_source = '[adam-adsl; adae]')\" #> [2] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any', mockup = TRUE, output_report = './tlf/mock-ae_specific.rtf', data_source = '[adam-adsl; adae]')\"       #> [3] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'rel', mockup = TRUE, output_report = './tlf/mock-ae_specific.rtf', data_source = '[adam-adsl; adae]')\"       #> [4] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'ser', mockup = TRUE, output_report = './tlf/mock-ae_specific.rtf', data_source = '[adam-adsl; adae]')\""},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"create-functions","dir":"Articles","previous_headings":"","what":"Create functions","title":"Create Mockup Table Based on Metadata","text":"Let’s create simplified version ae_summary() illustrate idea. illustration purposes, create mock table first row.","code":"ae_summary <- function(meta,                        population,                        observation,                        parameter,                        mockup,                        output_report,                        data_source,                        ...) {   # Identify parameter keywords   para_list <- unlist(strsplit(parameter, \";\"))    # Row label   ae_label <- vapply(para_list,     FUN = function(x) {       collect_adam_mapping(meta, x)$label     },     FUN.VALUE = character(1)   )    # Get treatment grouping order   trt_order <- eval(collect_adam_mapping(meta, population)$group_order)    # Get the title/endnotes of TLF   title_text <- collect_title(     meta = meta,     population = population,     observation = observation,     parameter = parameter, analysis = \"ae_summary\"   )   title_text[2] <- \"{Week}\"    # Logic to create mockup table   if (mockup) {     # Generate RTF     x <- tibble::tibble(       ae_label = ae_label,       n_1 = rep(\"x\", length(ae_label)),       n_2 = rep(\"x\", length(ae_label)), # no display_total/CI       pct_1 = rep(\"x.xx\", length(ae_label)),       pct_2 = rep(\"x.xx\", length(ae_label))     ) |>       dplyr::select(ae_label, n_1, pct_1, n_2, pct_2, everything()) |>       # r2rtf::rtf_title(rtf_mock_color(title_text)) |>       r2rtf::rtf_title(title_text) |>       r2rtf::rtf_colheader(paste0(\" | \", paste(names(trt_order), collapse = \" | \"), \" \"),         col_rel_width = c(3, rep(2, length(trt_order)))       ) |>       r2rtf::rtf_colheader(\" | n | (%) | n | (%) \",         border_top = c(\"\", rep(\"single\", 2 * length(trt_order))),         border_bottom = \"single\",         border_left = c(\"single\", rep(c(\"single\", \"\"), length(trt_order))),         col_rel_width = c(3, rep(1, 2 * length(trt_order)))       ) |>       r2rtf::rtf_body(         col_rel_width = c(3, rep(1, 2 * length(trt_order))),         border_left = c(\"single\", rep(c(\"single\", \"\"), length(trt_order))),         text_justification = c(\"l\", rep(\"c\", 2 * length(trt_order)))       ) |>       r2rtf::rtf_source(data_source)      # Require r2rtf to use color     attr(x, \"page\")$use_color <- TRUE      # Save RTF to a path     if (!is.null(output_report)) {       x |>         r2rtf::rtf_encode() |>         r2rtf::write_rtf(output_report)     }   }    if (!mockup) {     # Logic to perform actual AE summary table.     # Omit here   }    output_report } meta_run(meta,   i = 1,   data_source = \"[adam-adsl; adae]\" ) #> $`ae_summary(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any;rel;ser', mockup = TRUE, output_report = './tlf/mock-ae_summary.rtf', data_source = '[adam-adsl; adae]')` #> [1] \"./tlf/mock-ae_summary.rtf\""},{"path":[]},{"path":"https://merck.github.io/metalite/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yilong Zhang. Author. Yujie Zhao. Author, maintainer. Nan Xiao. Author. Benjamin Wang. Contributor. Brian Lang. Contributor. Howard Baek. Contributor. Ruchitbhai Patel. Contributor. Madhusudhan Ginnaram. Contributor. Sarad Nepal. Contributor. Venkatesh Burla. Contributor. Merck Sharp & Dohme Corp. Copyright holder.","code":""},{"path":"https://merck.github.io/metalite/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhang Y, Zhao Y, Xiao N (2024). metalite: ADaM Metadata Structure. R package version 0.1.3, https://github.com/Merck/metalite, https://merck.github.io/metalite/.","code":"@Manual{,   title = {metalite: ADaM Metadata Structure},   author = {Yilong Zhang and Yujie Zhao and Nan Xiao},   year = {2024},   note = {R package version 0.1.3, https://github.com/Merck/metalite},   url = {https://merck.github.io/metalite/}, }"},{"path":"https://merck.github.io/metalite/index.html","id":"metalite-","dir":"","previous_headings":"","what":"ADaM Metadata Structure","title":"ADaM Metadata Structure","text":"Unified representation metadata structure clinical analysis & reporting (&R) leveraging Analysis Data Model (ADaM) datasets.","code":""},{"path":"https://merck.github.io/metalite/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"ADaM Metadata Structure","text":"easiest way get metalite install CRAN: Alternatively, use new feature get bug fix, can install development version metalite GitHub:","code":"install.packages(\"metalite\") # install.packages(\"remotes\") remotes::install_github(\"Merck/metalite\")"},{"path":"https://merck.github.io/metalite/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"ADaM Metadata Structure","text":"metalite framework designed : Standardize function input analysis reporting. Separate analysis logic data source. Enable use pipes (|>). Reduce manual steps develop maintain documentation clinical trial development. Ensure consistency analysis specification, mock, results.","code":""},{"path":"https://merck.github.io/metalite/index.html","id":"use-cases","dir":"","previous_headings":"","what":"Use cases","title":"ADaM Metadata Structure","text":"metalite package offers foundation simplify tool development create standard engineering workflows. example, metalite can used : Standardize input output &R functions. Create analysis reporting planning grid. Create mock table. Create validate &R results. Trace analysis records. Note: metalite low-level R package needs work R packages complete work. idea illustrated diagram .","code":""},{"path":"https://merck.github.io/metalite/index.html","id":"design-principles","dir":"","previous_headings":"","what":"Design principles","title":"ADaM Metadata Structure","text":"built metalite following principles: Automation: prefer function call checklist. example, enter data source one time AE analysis. End--end: cover steps software development lifecycle (SDLC) define delivery.","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Construct ADaM mappings — adam_mapping","title":"Construct ADaM mappings — adam_mapping","text":"ADaM mappings describe variables meta information ADaM data mapped standardized term.","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Construct ADaM mappings — adam_mapping","text":"","code":"adam_mapping(   name,   id = NULL,   group = NULL,   var = NULL,   subset = NULL,   label = NULL,   ... )"},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Construct ADaM mappings — adam_mapping","text":"name character value term name. term name used key link information. id character value subject identifier variable name ADaM dataset. group character vector group variable names ADaM dataset. var character vector useful variable names ADaM dataset. subset expression identify analysis records. See base::subset(). label character value analysis label. ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Construct ADaM mappings — adam_mapping","text":"list class adam_mapping. Components list either quosures constants.","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Construct ADaM mappings — adam_mapping","text":"design inspired ggplot2::aes().","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Construct ADaM mappings — adam_mapping","text":"","code":"adam_mapping(   name = \"apat\",   id = \"USUBJID\",   group = \"TRT01A\",   subset = TRTFL == \"Y\",   label = \"All Participants as Treated\" ) #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> \"TRT01A\" #> * `var`    -> NULL #> * `subset` -> TRTFL == \"Y\" #> * `label`  -> \"All Participants as Treated\""},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":null,"dir":"Reference","previous_headings":"","what":"Add additional analysis plan — add_plan","title":"Add additional analysis plan — add_plan","text":"Add additional analysis plan","code":""},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add additional analysis plan — add_plan","text":"","code":"add_plan(plan, analysis, population, observation, parameter, ...)"},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add additional analysis plan — add_plan","text":"plan meta_plan object. analysis character value analysis term name. term name used key link information. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. ... Additional arguments.","code":""},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add additional analysis plan — add_plan","text":"data frame containing analysis plans new plans added.","code":""},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add additional analysis plan — add_plan","text":"","code":"plan(\"ae_summary\",   population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel\" ) |>   add_plan(\"ae_specific\",     population = \"apat\",     observation = c(\"wk12\", \"wk24\"), parameter = c(\"any\", \"rel\")   ) #>   mock    analysis population observation parameter #> 1    1  ae_summary       apat        wk12   any;rel #> 2    1  ae_summary       apat        wk24   any;rel #> 3    2 ae_specific       apat        wk12       any #> 4    2 ae_specific       apat        wk24       any #> 5    2 ae_specific       apat        wk12       rel #> 6    2 ae_specific       apat        wk24       rel"},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to assign labels to a data frame — assign_label","title":"A function to assign labels to a data frame — assign_label","text":"function assign labels data frame","code":""},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to assign labels to a data frame — assign_label","text":"","code":"assign_label(data, var = names(data), label = names(data))"},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to assign labels to a data frame — assign_label","text":"data data frame. var variables assign labels. label labels assigned.","code":""},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to assign labels to a data frame — assign_label","text":"data frame labels updated.","code":""},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A function to assign labels to a data frame — assign_label","text":"Case 1: variable's label already define original data frame redefined assign_label(...), original labels kept. Case 2: variable's label already define original data frame re-defined assign_label(...), labels re-defined. Case 3: variable's label define original data frame defined assign_label(...), labels added. Case 4: variable's label define original data frame, neither defined assign_label(...), labels variable name .","code":""},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A function to assign labels to a data frame — assign_label","text":"","code":"assign_label(r2rtf::r2rtf_adae) |> head() #>        STUDYID SITEID     USUBJID    TRTA TRTAN AGE AGEGR1 AGEGR1N  RACE RACEN #> 1 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 2 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 3 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 4 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #> 5 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #> 6 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #>   SEX SAFFL     TRTSDT     TRTEDT      ASTDT ASTDTF ASTDY      AENDT AENDY #> 1   F     Y 2014-01-02 2014-07-02 2014-01-03            2           NA #> 2   F     Y 2014-01-02 2014-07-02 2014-01-03            2           NA #> 3   F     Y 2014-01-02 2014-07-02 2014-01-09            8 2014-01-11    10 #> 4   M     Y 2012-08-05 2012-09-01 2012-08-07            3 2012-08-30    26 #> 5   M     Y 2012-08-05 2012-09-01 2012-08-07            3           NA #> 6   M     Y 2012-08-05 2012-09-01 2012-08-26           22           NA #>   ADURN ADURU                               AETERM                    AELLT #> 1    NA                  APPLICATION SITE ERYTHEMA APPLICATION SITE REDNESS #> 2    NA                  APPLICATION SITE PRURITUS APPLICATION SITE ITCHING #> 3     3   DAY                            DIARRHOEA                 DIARRHEA #> 4    24   DAY                             ERYTHEMA                 ERYTHEMA #> 5    NA                                   ERYTHEMA       LOCALIZED ERYTHEMA #> 6    NA       ATRIOVENTRICULAR BLOCK SECOND DEGREE   AV BLOCK SECOND DEGREE #>   AELLTCD                              AEDECOD AEPTCD    AEHLT AEHLTCD #> 1      NA            APPLICATION SITE ERYTHEMA     NA HLT_0617      NA #> 2      NA            APPLICATION SITE PRURITUS     NA HLT_0317      NA #> 3      NA                            DIARRHOEA     NA HLT_0148      NA #> 4      NA                             ERYTHEMA     NA HLT_0284      NA #> 5      NA                             ERYTHEMA     NA HLT_0284      NA #> 6      NA ATRIOVENTRICULAR BLOCK SECOND DEGREE     NA HLT_0415      NA #>      AEHLGT AEHLGTCD                                             AEBODSYS #> 1 HLGT_0152       NA GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS #> 2 HLGT_0338       NA GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS #> 3 HLGT_0588       NA                           GASTROINTESTINAL DISORDERS #> 4 HLGT_0192       NA               SKIN AND SUBCUTANEOUS TISSUE DISORDERS #> 5 HLGT_0192       NA               SKIN AND SUBCUTANEOUS TISSUE DISORDERS #> 6 HLGT_0086       NA                                    CARDIAC DISORDERS #>                                                  AESOC AESOCCD    AESEV AESER #> 1 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS      NA     MILD     N #> 2 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS      NA     MILD     N #> 3                           GASTROINTESTINAL DISORDERS      NA     MILD     N #> 4               SKIN AND SUBCUTANEOUS TISSUE DISORDERS      NA     MILD     N #> 5               SKIN AND SUBCUTANEOUS TISSUE DISORDERS      NA MODERATE     N #> 6                                    CARDIAC DISORDERS      NA     MILD     N #>   AESCAN AESCONG AESDISAB AESDTH AESHOSP AESLIFE AESOD    AEREL AEACN #> 1      N       N        N      N       N       N     N PROBABLE       #> 2      N       N        N      N       N       N     N PROBABLE       #> 3      N       N        N      N       N       N     N   REMOTE       #> 4      N       N        N      N       N       N     N POSSIBLE       #> 5      N       N        N      N       N       N     N PROBABLE       #> 6      N       N        N      N       N       N     N POSSIBLE       #>                        AEOUT AESEQ TRTEMFL AOCCFL AOCCSFL AOCCPFL AOCC02FL #> 1 NOT RECOVERED/NOT RESOLVED     1       Y      Y       Y       Y          #> 2 NOT RECOVERED/NOT RESOLVED     2       Y                      Y          #> 3         RECOVERED/RESOLVED     3       Y              Y       Y          #> 4 NOT RECOVERED/NOT RESOLVED     1       Y      Y       Y       Y          #> 5 NOT RECOVERED/NOT RESOLVED     2       Y                                 #> 6 NOT RECOVERED/NOT RESOLVED     3       Y              Y       Y          #>   AOCC03FL AOCC04FL             CQ01NAM AOCC01FL #> 1                   DERMATOLOGIC EVENTS        Y #> 2                   DERMATOLOGIC EVENTS          #> 3                                                #> 4                   DERMATOLOGIC EVENTS        Y #> 5                   DERMATOLOGIC EVENTS          #> 6                                                assign_label(   r2rtf::r2rtf_adae,   var = \"USUBJID\",   label = \"Unique subject identifier\" ) |> head() #>        STUDYID SITEID     USUBJID    TRTA TRTAN AGE AGEGR1 AGEGR1N  RACE RACEN #> 1 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 2 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 3 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 4 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #> 5 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #> 6 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #>   SEX SAFFL     TRTSDT     TRTEDT      ASTDT ASTDTF ASTDY      AENDT AENDY #> 1   F     Y 2014-01-02 2014-07-02 2014-01-03            2           NA #> 2   F     Y 2014-01-02 2014-07-02 2014-01-03            2           NA #> 3   F     Y 2014-01-02 2014-07-02 2014-01-09            8 2014-01-11    10 #> 4   M     Y 2012-08-05 2012-09-01 2012-08-07            3 2012-08-30    26 #> 5   M     Y 2012-08-05 2012-09-01 2012-08-07            3           NA #> 6   M     Y 2012-08-05 2012-09-01 2012-08-26           22           NA #>   ADURN ADURU                               AETERM                    AELLT #> 1    NA                  APPLICATION SITE ERYTHEMA APPLICATION SITE REDNESS #> 2    NA                  APPLICATION SITE PRURITUS APPLICATION SITE ITCHING #> 3     3   DAY                            DIARRHOEA                 DIARRHEA #> 4    24   DAY                             ERYTHEMA                 ERYTHEMA #> 5    NA                                   ERYTHEMA       LOCALIZED ERYTHEMA #> 6    NA       ATRIOVENTRICULAR BLOCK SECOND DEGREE   AV BLOCK SECOND DEGREE #>   AELLTCD                              AEDECOD AEPTCD    AEHLT AEHLTCD #> 1      NA            APPLICATION SITE ERYTHEMA     NA HLT_0617      NA #> 2      NA            APPLICATION SITE PRURITUS     NA HLT_0317      NA #> 3      NA                            DIARRHOEA     NA HLT_0148      NA #> 4      NA                             ERYTHEMA     NA HLT_0284      NA #> 5      NA                             ERYTHEMA     NA HLT_0284      NA #> 6      NA ATRIOVENTRICULAR BLOCK SECOND DEGREE     NA HLT_0415      NA #>      AEHLGT AEHLGTCD                                             AEBODSYS #> 1 HLGT_0152       NA GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS #> 2 HLGT_0338       NA GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS #> 3 HLGT_0588       NA                           GASTROINTESTINAL DISORDERS #> 4 HLGT_0192       NA               SKIN AND SUBCUTANEOUS TISSUE DISORDERS #> 5 HLGT_0192       NA               SKIN AND SUBCUTANEOUS TISSUE DISORDERS #> 6 HLGT_0086       NA                                    CARDIAC DISORDERS #>                                                  AESOC AESOCCD    AESEV AESER #> 1 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS      NA     MILD     N #> 2 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS      NA     MILD     N #> 3                           GASTROINTESTINAL DISORDERS      NA     MILD     N #> 4               SKIN AND SUBCUTANEOUS TISSUE DISORDERS      NA     MILD     N #> 5               SKIN AND SUBCUTANEOUS TISSUE DISORDERS      NA MODERATE     N #> 6                                    CARDIAC DISORDERS      NA     MILD     N #>   AESCAN AESCONG AESDISAB AESDTH AESHOSP AESLIFE AESOD    AEREL AEACN #> 1      N       N        N      N       N       N     N PROBABLE       #> 2      N       N        N      N       N       N     N PROBABLE       #> 3      N       N        N      N       N       N     N   REMOTE       #> 4      N       N        N      N       N       N     N POSSIBLE       #> 5      N       N        N      N       N       N     N PROBABLE       #> 6      N       N        N      N       N       N     N POSSIBLE       #>                        AEOUT AESEQ TRTEMFL AOCCFL AOCCSFL AOCCPFL AOCC02FL #> 1 NOT RECOVERED/NOT RESOLVED     1       Y      Y       Y       Y          #> 2 NOT RECOVERED/NOT RESOLVED     2       Y                      Y          #> 3         RECOVERED/RESOLVED     3       Y              Y       Y          #> 4 NOT RECOVERED/NOT RESOLVED     1       Y      Y       Y       Y          #> 5 NOT RECOVERED/NOT RESOLVED     2       Y                                 #> 6 NOT RECOVERED/NOT RESOLVED     3       Y              Y       Y          #>   AOCC03FL AOCC04FL             CQ01NAM AOCC01FL #> 1                   DERMATOLOGIC EVENTS        Y #> 2                   DERMATOLOGIC EVENTS          #> 3                                                #> 4                   DERMATOLOGIC EVENTS        Y #> 5                   DERMATOLOGIC EVENTS          #> 6"},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"Collect adam_mapping meta_adam name","code":""},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"","code":"collect_adam_mapping(meta, name)"},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"meta meta_adam object. name keyword value.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"adam_mapping class object containing definition search variable name.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"","code":"meta <- meta_example() collect_adam_mapping(meta, \"apat\") #> ADaM mapping:  #> * `name`      -> \"apat\" #> * `id`        -> \"USUBJID\" #> * `group`     -> \"TRTA\" #> * `var`       -> NULL #> * `subset`    -> SAFFL == \"Y\" #> * `label`     -> \"All Participants as Treated\" #> * `.location` -> \"population\""},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect specification for dataset name — collect_dataname","title":"Collect specification for dataset name — collect_dataname","text":"Collect specification dataset name","code":""},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect specification for dataset name — collect_dataname","text":"","code":"collect_dataname(meta)"},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect specification for dataset name — collect_dataname","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect specification for dataset name — collect_dataname","text":"vector character strings containing name population/observation.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect specification for dataset name — collect_dataname","text":"","code":"meta <- meta_example() collect_dataname(meta) #>  population observation  #>      \"adsl\"      \"adae\""},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect number of subjects and its subset condition — collect_n_subject","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"Collect number subjects subset condition","code":""},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"","code":"collect_n_subject(   meta,   population,   parameter,   listing = FALSE,   histogram = FALSE,   var_listing = NULL,   remove_blank_group = FALSE,   type = \"Subjects\",   use_na = c(\"ifany\", \"no\", \"always\"),   display_total = TRUE )"},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"meta meta_adam object. population character value population term name. term name used key link information. parameter character value parameter term name. term name used key link information. listing logical value display drill listing per row. histogram logical value display histogram group. var_listing character vector additional variables included listing. remove_blank_group logical value remove group missing value parameter. type character value control title name, e.g., Subjects Records. use_na character value whether include NA values table. See useNA argument base::table() details. display_total logical value display total column.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"list containing number subjects subset condition.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"","code":"suppressWarnings(   meta <- meta_example() |>     define_parameter(name = \"sex\", var = \"SEX\", label = \"Sex\") ) collect_n_subject(meta, \"apat\", \"sex\") #> $table #>                 name     Placebo Xanomeline Low Dose Xanomeline High Dose #> 1 Number of Subjects          86                  84                   84 #> 2                Sex                                          #> 3 Subjects with Data          86                  84                   84 #> 4                  F 53 ( 61.6%)         50 ( 59.5%)          40 ( 47.6%) #> 5                  M 33 ( 38.4%)         34 ( 40.5%)          44 ( 52.4%) #>          Total #> 1          254 #> 2          #> 3          254 #> 4 143 ( 56.3%) #> 5 111 ( 43.7%) #>  #> $n #>                 name Placebo Xanomeline Low Dose Xanomeline High Dose Total #> 1 Number of Subjects      86                  84                   84   254 #>  #> $subset #>                 name                                           Placebo #> 1 Number of Subjects           TRUE & TRTA == 'Placebo' & SAFFL == 'Y' #> 2 Subjects with Data (! is.na(SEX)) & TRTA == 'Placebo' & SAFFL == 'Y' #> 3                    is.na(SEX) & TRTA == 'Placebo' & SAFFL == 'Y' #> 4                  F     SEX == 'F' & TRTA == 'Placebo' & SAFFL == 'Y' #> 5                  M     SEX == 'M' & TRTA == 'Placebo' & SAFFL == 'Y' #>                                             Xanomeline Low Dose #> 1           TRUE & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #> 2 (! is.na(SEX)) & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #> 3     is.na(SEX) & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #> 4     SEX == 'F' & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #> 5     SEX == 'M' & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #>                                             Xanomeline High Dose #> 1           TRUE & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #> 2 (! is.na(SEX)) & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #> 3     is.na(SEX) & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #> 4     SEX == 'F' & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #> 5     SEX == 'M' & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #>  #> $listing #> NULL #>  #> $histogram #> NULL #>"},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect observation record index from observation dataset — collect_observation_index","title":"Collect observation record index from observation dataset — collect_observation_index","text":"Collect observation record index observation dataset","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect observation record index from observation dataset — collect_observation_index","text":"","code":"collect_observation_index(meta, population, observation, parameter)"},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect observation record index from observation dataset — collect_observation_index","text":"meta meta_adam object. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect observation record index from observation dataset — collect_observation_index","text":"vector patient index within observation group.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect observation record index from observation dataset — collect_observation_index","text":"","code":"meta <- meta_example() collect_observation_index(meta, \"apat\", \"wk12\", \"ser\") #> [1]  689 1131 1173"},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect observation record from observation dataset — collect_observation_record","title":"Collect observation record from observation dataset — collect_observation_record","text":"key variables used id, group, subset displayed default.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect observation record from observation dataset — collect_observation_record","text":"","code":"collect_observation_record(   meta,   population,   observation,   parameter,   var = NULL )"},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect observation record from observation dataset — collect_observation_record","text":"meta meta_adam object. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. var character vector additional variables displayed output.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect observation record from observation dataset — collect_observation_record","text":"data frame observation dataset.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect observation record from observation dataset — collect_observation_record","text":"","code":"meta <- meta_example() collect_observation_record(meta, \"apat\", \"wk12\", \"ser\") #>          USUBJID                 TRTA #> 689  01-709-1424 Xanomeline High Dose #> 1131 01-718-1170  Xanomeline Low Dose #> 1173 01-718-1371 Xanomeline High Dose #>                                             AEDECOD SAFFL AESER #> 689                                         SYNCOPE     Y     Y #> 1131                                        SYNCOPE     Y     Y #> 1173 PARTIAL SEIZURES WITH SECONDARY GENERALISATION     Y     Y collect_observation_record(meta, \"apat\", \"wk12\", \"ser\", var = \"AEDECOD\") #>          USUBJID                 TRTA #> 689  01-709-1424 Xanomeline High Dose #> 1131 01-718-1170  Xanomeline Low Dose #> 1173 01-718-1371 Xanomeline High Dose #>                                             AEDECOD SAFFL AESER #> 689                                         SYNCOPE     Y     Y #> 1131                                        SYNCOPE     Y     Y #> 1173 PARTIAL SEIZURES WITH SECONDARY GENERALISATION     Y     Y"},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect specification for population definition — collect_population","title":"Collect specification for population definition — collect_population","text":"Collect specification population definition","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect specification for population definition — collect_population","text":"","code":"collect_population(meta, population, observation = NULL, parameter = NULL)"},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect specification for population definition — collect_population","text":"meta meta_adam object. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect specification for population definition — collect_population","text":"list covering filter population, observation (given) parameter (given).","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect specification for population definition — collect_population","text":"","code":"meta <- meta_example() collect_population(meta, \"apat\") #> $population #> [1] \"SAFFL == 'Y'\" #>  collect_population(meta, \"apat\", \"wk12\") #> $population #> [1] \"SAFFL == 'Y'\" #>  #> $observation #> [1] \"SAFFL == 'Y'\" #>  collect_population(meta, \"apat\", \"wk12\", \"ser\") #> $population #> [1] \"SAFFL == 'Y'\" #>  #> $observation #> [1] \"SAFFL == 'Y'\" #>  #> $parameter #> [1] \"AESER == 'Y'\" #>"},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect subject identifier information from population dataset — collect_population_id","title":"Collect subject identifier information from population dataset — collect_population_id","text":"Collect subject identifier information population dataset","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect subject identifier information from population dataset — collect_population_id","text":"","code":"collect_population_id(meta, population)"},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect subject identifier information from population dataset — collect_population_id","text":"meta meta_adam object. population character value population term name. term name used key link information.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect subject identifier information from population dataset — collect_population_id","text":"vector patient ID within population group.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect subject identifier information from population dataset — collect_population_id","text":"","code":"meta <- meta_example() head(collect_population_id(meta, \"apat\")) #> [1] \"01-701-1015\" \"01-701-1023\" \"01-701-1028\" \"01-701-1033\" \"01-701-1034\" #> [6] \"01-701-1047\""},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect population record index from population dataset — collect_population_index","title":"Collect population record index from population dataset — collect_population_index","text":"Collect population record index population dataset","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect population record index from population dataset — collect_population_index","text":"","code":"collect_population_index(meta, population)"},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect population record index from population dataset — collect_population_index","text":"meta meta_adam object. population character value population term name. term name used key link information.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect population record index from population dataset — collect_population_index","text":"vector patient index within population group.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect population record index from population dataset — collect_population_index","text":"","code":"meta <- meta_example() head(collect_population_index(meta, \"apat\")) #> [1] 1 2 3 4 5 6"},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect population record from population dataset — collect_population_record","title":"Collect population record from population dataset — collect_population_record","text":"key variables used id, group, subset displayed default.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect population record from population dataset — collect_population_record","text":"","code":"collect_population_record(meta, population, var = NULL)"},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect population record from population dataset — collect_population_record","text":"meta meta_adam object. population character value population term name. term name used key link information. var character vector additional variables displayed output.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect population record from population dataset — collect_population_record","text":"data frame containing variables population dataset.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect population record from population dataset — collect_population_record","text":"","code":"meta <- meta_example() head(collect_population_record(meta, \"apat\")) #>       USUBJID                 TRTA SAFFL #> 1 01-701-1015              Placebo     Y #> 2 01-701-1023              Placebo     Y #> 3 01-701-1028 Xanomeline High Dose     Y #> 4 01-701-1033  Xanomeline Low Dose     Y #> 5 01-701-1034 Xanomeline High Dose     Y #> 6 01-701-1047              Placebo     Y head(collect_population_record(meta, \"apat\", var = \"AGE\")) #>       USUBJID                 TRTA SAFFL AGE #> 1 01-701-1015              Placebo     Y  63 #> 2 01-701-1023              Placebo     Y  64 #> 3 01-701-1028 Xanomeline High Dose     Y  71 #> 4 01-701-1033  Xanomeline Low Dose     Y  74 #> 5 01-701-1034 Xanomeline High Dose     Y  77 #> 6 01-701-1047              Placebo     Y  85"},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect specification for title — collect_title","title":"Collect specification for title — collect_title","text":"Collect specification title","code":""},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect specification for title — collect_title","text":"","code":"collect_title(   meta,   population,   observation,   parameter,   analysis,   title_order = c(\"analysis\", \"observation\", \"population\") )"},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect specification for title — collect_title","text":"meta meta_adam object. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. analysis character value analysis term name. term name used key link information. title_order character vector define order title component.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect specification for title — collect_title","text":"vector strings compose table captions.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect specification for title — collect_title","text":"","code":"meta <- meta_example() collect_title(meta, \"apat\", \"wk12\", \"ser\", \"ae_summary\") #> [1] \"Summary of Adverse Events\"   \"Weeks 0 to 12\"               #> [3] \"All Participants as Treated\" collect_title(meta, \"apat\", \"wk12\", \"ser\", \"ae_specific\") #> [1] \"Participants With Serious Adverse Events\" #> [2] \"Weeks 0 to 12\"                            #> [3] \"All Participants as Treated\""},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply default values to ADaM mappings — default_apply","title":"Apply default values to ADaM mappings — default_apply","text":"Apply default values ADaM mappings","code":""},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply default values to ADaM mappings — default_apply","text":"","code":"default_apply(x)"},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply default values to ADaM mappings — default_apply","text":"x adam_mapping object.","code":""},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply default values to ADaM mappings — default_apply","text":"Similar input, missing values updated default values.","code":""},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply default values to ADaM mappings — default_apply","text":"","code":"default_apply(adam_mapping(name = \"apat\")) #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> NULL #> * `var`    -> NULL #> * `subset` -> NULL #> * `label`  -> \"All Participants as Treated\""},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis function meta information for ADaM dataset — define_analysis","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"Define analysis function meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"","code":"define_analysis(meta, name, ...)"},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"meta meta_adam object. name character value term name. term name used key link information. ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"metadata object analysis details defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan = plan) |>   define_analysis(     name = \"ae_summary\",     title = \"Summary of Adverse Events\"   ) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>  #>   Analysis function: #>           name                          label #> 1 'ae_summary' 'Table: adverse event summary' #>"},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis observation meta information for ADaM dataset — define_observation","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"Define analysis observation meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"","code":"define_observation(   meta,   name,   id = \"USUBJID\",   group = NULL,   var = NULL,   subset = NULL,   label = NULL,   ... )"},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"meta meta_adam object. name character value term name. term name used key link information. id character value subject identifier variable name ADaM dataset. group character vector group variable names ADaM dataset. var character vector useful variable names ADaM dataset. subset expression identify analysis records. See base::subset(). label character value analysis label. ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"metadata object observation defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan = plan) |>   define_observation(     name = \"wk12\",     group = \"TRTA\",     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>  #>   Analysis observation type: #>     name        id  group var       subset           label #> 1 'wk12' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'Weeks 0 to 12' #>  #>"},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis parameter meta information for ADaM dataset — define_parameter","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"Define analysis parameter meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"","code":"define_parameter(meta, name, subset = NULL, ...)"},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"meta meta_adam object. name character value term name. term name used key link information. subset expression identify analysis records. See base::subset(). ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"metadata object parameters defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan = plan) |>   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>  #>   Analysis parameter type: #>    name                         label                               subset #> 1 'rel' 'drug-related adverse events' AEREL %in% c('POSSIBLE', 'PROBABLE') #>  #>"},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis plan meta information for ADaM dataset — define_plan","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"Define analysis plan meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"","code":"define_plan(meta, plan)"},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"meta meta_adam object. plan data frame analysis plan.","code":""},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"metadata object plans defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>"},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis population meta information for ADaM dataset — define_population","title":"Define analysis population meta information for ADaM dataset — define_population","text":"Define analysis population meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis population meta information for ADaM dataset — define_population","text":"","code":"define_population(   meta,   name,   id = \"USUBJID\",   group = NULL,   var = NULL,   subset = NULL,   label = NULL,   ... )"},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis population meta information for ADaM dataset — define_population","text":"meta meta_adam object. name character value term name. term name used key link information. id character value subject identifier variable name ADaM dataset. group character vector group variable names ADaM dataset. var character vector useful variable names ADaM dataset. subset expression identify analysis records. See base::subset(). label character value analysis label. ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis population meta information for ADaM dataset — define_population","text":"metadata object population defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis population meta information for ADaM dataset — define_population","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan) |>   define_population(name = \"apat\") #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>  #>   Analysis population type: #>     name        id group var subset                         label #> 1 'apat' 'USUBJID'                  'All Participants as Treated' #>  #>"},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to get the labels of data frame columns — get_label","title":"A function to get the labels of data frame columns — get_label","text":"function get labels data frame columns","code":""},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to get the labels of data frame columns — get_label","text":"","code":"get_label(data)"},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to get the labels of data frame columns — get_label","text":"data data frame.","code":""},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to get the labels of data frame columns — get_label","text":"Labels input data frame.","code":""},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A function to get the labels of data frame columns — get_label","text":"","code":"get_label(r2rtf::r2rtf_adae) #>                                   STUDYID  #>                        \"Study Identifier\"  #>                                    SITEID  #>                   \"Study Site Identifier\"  #>                                   USUBJID  #>               \"Unique Subject Identifier\"  #>                                      TRTA  #>                        \"Actual Treatment\"  #>                                     TRTAN  #>                    \"Actual Treatment (N)\"  #>                                       AGE  #>                                     \"Age\"  #>                                    AGEGR1  #>                      \"Pooled Age Group 1\"  #>                                   AGEGR1N  #>                  \"Pooled Age Group 1 (N)\"  #>                                      RACE  #>                                    \"Race\"  #>                                     RACEN  #>                                \"Race (N)\"  #>                                       SEX  #>                                     \"Sex\"  #>                                     SAFFL  #>                  \"Safety Population Flag\"  #>                                    TRTSDT  #>     \"Date of First Exposure to Treatment\"  #>                                    TRTEDT  #>      \"Date of Last Exposure to Treatment\"  #>                                     ASTDT  #>                     \"Analysis Start Date\"  #>                                    ASTDTF  #>     \"Analysis Start Date Imputation Flag\"  #>                                     ASTDY  #>             \"Analysis Start Relative Day\"  #>                                     AENDT  #>                       \"Analysis End Date\"  #>                                     AENDY  #>               \"Analysis End Relative Day\"  #>                                     ADURN  #>                         \"AE Duration (N)\"  #>                                     ADURU  #>                       \"AE Duration Units\"  #>                                    AETERM  #>     \"Reported Term for the Adverse Event\"  #>                                     AELLT  #>                       \"Lowest Level Term\"  #>                                   AELLTCD  #>                  \"Lowest Level Term Code\"  #>                                   AEDECOD  #>                 \"Dictionary-Derived Term\"  #>                                    AEPTCD  #>                     \"Preferred Term Code\"  #>                                     AEHLT  #>                         \"High Level Term\"  #>                                   AEHLTCD  #>                    \"High Level Term Code\"  #>                                    AEHLGT  #>                   \"High Level Group Term\"  #>                                  AEHLGTCD  #>              \"High Level Group Term Code\"  #>                                  AEBODSYS  #>              \"Body System or Organ Class\"  #>                                     AESOC  #>              \"Primary System Organ Class\"  #>                                   AESOCCD  #>         \"Primary System Organ Class Code\"  #>                                     AESEV  #>                      \"Severity/Intensity\"  #>                                     AESER  #>                           \"Serious Event\"  #>                                    AESCAN  #>                         \"Involves Cancer\"  #>                                   AESCONG  #>      \"Congenital Anomaly or Birth Defect\"  #>                                  AESDISAB  #> \"Persist or Signif Disability/Incapacity\"  #>                                    AESDTH  #>                        \"Results in Death\"  #>                                   AESHOSP  #>    \"Requires or Prolongs Hospitalization\"  #>                                   AESLIFE  #>                     \"Is Life Threatening\"  #>                                     AESOD  #>                  \"Occurred with Overdose\"  #>                                     AEREL  #>                               \"Causality\"  #>                                     AEACN  #>       \"Action Taken with Study Treatment\"  #>                                     AEOUT  #>                \"Outcome of Adverse Event\"  #>                                     AESEQ  #>                         \"Sequence Number\"  #>                                   TRTEMFL  #>        \"Treatment Emergent Analysis Flag\"  #>                                    AOCCFL  #>           \"1st Occurrence of Any AE Flag\"  #>                                   AOCCSFL  #>              \"1st Occurrence of SOC Flag\"  #>                                   AOCCPFL  #>   \"1st Occurrence of Preferred Term Flag\"  #>                                  AOCC02FL  #>      \"1st Occurrence 02 Flag for Serious\"  #>                                  AOCC03FL  #>  \"1st Occurrence 03 Flag for Serious SOC\"  #>                                  AOCC04FL  #>   \"1st Occurrence 04 Flag for Serious PT\"  #>                                   CQ01NAM  #>                \"Customized Query 01 Name\"  #>                                  AOCC01FL  #>         \"1st Occurrence 01 Flag for CQ01\""},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a metadata representation for ADaM data analysis — meta_adam","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"Create metadata representation ADaM data analysis","code":""},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"","code":"meta_adam(observation, population = observation)"},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"observation data frame observation level data. population data frame population level data. Default observation.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"initialized metadata object observation population defined.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"","code":"meta_adam(observation = r2rtf::r2rtf_adae, population = r2rtf::r2rtf_adae) #> ADaM metadata:  #>    .$data_population \tPopulation data with 1191 subjects  #>    .$data_observation \tObservation data with 1191 records  #>  #>"},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":null,"dir":"Reference","previous_headings":"","what":"Add duplicate data to enable a total group — meta_add_total","title":"Add duplicate data to enable a total group — meta_add_total","text":"Add duplicate data enable total group","code":""},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add duplicate data to enable a total group — meta_add_total","text":"","code":"meta_add_total(meta, total = \"Total\")"},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add duplicate data to enable a total group — meta_add_total","text":"meta metalite object. total character value total group name.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add duplicate data to enable a total group — meta_add_total","text":"metadata object total group added.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add duplicate data to enable a total group — meta_add_total","text":"","code":"x <- meta_add_total(meta_example()) # A `Total` group is added table(x$data_population$TRTA) #>  #>              Placebo  Xanomeline Low Dose Xanomeline High Dose  #>                   86                   84                   84  #>                Total  #>                  254"},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":null,"dir":"Reference","previous_headings":"","what":"Build complete meta information — meta_build","title":"Build complete meta information — meta_build","text":"Build complete meta information","code":""},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build complete meta information — meta_build","text":"","code":"meta_build(meta)"},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build complete meta information — meta_build","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build complete meta information — meta_build","text":"composed metadata object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Build complete meta information — meta_build","text":"","code":"meta_adam(   observation = r2rtf::r2rtf_adae,   population = r2rtf::r2rtf_adsl ) |>   # define analysis plan   define_plan(     plan(       analysis = \"ae_summary\",       population = \"apat\",       observation = c(\"wk12\"),       parameter = \"any;rel\"     )   ) |>   # define population   define_population(     name = \"apat\",     group = \"TRT01A\",     subset = SAFFL == \"Y\"   ) |>   # define observation   define_observation(     name = \"wk12\",     group = \"TRTA\",     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) |>   # define parameter - rel   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) |>   # define analysis   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) |>   meta_build() #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 1 plans  #>  #>  #>   Analysis population type: #>     name        id    group var       subset                         label #> 1 'apat' 'USUBJID' 'TRT01A'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var       subset           label #> 1 'wk12' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'Weeks 0 to 12' #>  #>  #>   Analysis parameter type: #>    name                         label                               subset #> 1 'rel' 'drug-related adverse events' AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2 'any'          'any adverse events'                                      #>  #>  #>   Analysis function: #>           name                          label #> 1 'ae_summary' 'Table: adverse event summary' #>"},{"path":"https://merck.github.io/metalite/reference/meta_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an example meta_adam object — meta_example","title":"Create an example meta_adam object — meta_example","text":"function illustration purposes. r2rtf package required.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an example meta_adam object — meta_example","text":"","code":"meta_example()"},{"path":"https://merck.github.io/metalite/reference/meta_example.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an example meta_adam object — meta_example","text":"metadata object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an example meta_adam object — meta_example","text":"","code":"meta_example() #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' #>"},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a data exploration meta_adam object — meta_example_exploration","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"Create data exploration meta_adam object","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"","code":"meta_example_exploration(   data,   group,   name = \"ase\",   subset = NULL,   label = \"All Subjects Enrolled\" )"},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"data data frame. group character vector group variable names ADaM dataset. name character value term name. term name used key link information. subset expression identify analysis records. See base::subset(). label character value analysis label.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"metadata object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"","code":"meta <- meta_example_exploration(r2rtf::r2rtf_adsl, group = \"TRT01A\") collect_n_subject(meta, \"ase\", \"AGE\") #> $table #>                 name           Placebo             Total Xanomeline High Dose #> 1 Number of Subjects                86               254                   84 #> 2                Age                                              #> 3 Subjects with Data                86               254                   84 #> 4          Mean (SD)        75.2 (8.6)        75.1 (8.2)           74.4 (7.9) #> 5  Median [Min, Max] 76.0 [52.0, 89.0] 77.0 [51.0, 89.0]    76.0 [56.0, 88.0] #>   Xanomeline Low Dose #> 1                  84 #> 2                 #> 3                  84 #> 4          75.7 (8.3) #> 5   77.5 [51.0, 88.0] #>  #> $n #>                 name Placebo Total Xanomeline High Dose Xanomeline Low Dose #> 1 Number of Subjects      86   254                   84                  84 #>  #> $subset #>                 name                                     Placebo #> 1 Number of Subjects           TRUE & TRT01A == 'Placebo' & NULL #> 2 Subjects with Data (! is.na(AGE)) & TRT01A == 'Placebo' & NULL #> 3                    is.na(AGE) & TRT01A == 'Placebo' & NULL #>                                       Xanomeline High Dose #> 1           TRUE & TRT01A == 'Xanomeline High Dose' & NULL #> 2 (! is.na(AGE)) & TRT01A == 'Xanomeline High Dose' & NULL #> 3     is.na(AGE) & TRT01A == 'Xanomeline High Dose' & NULL #>                                       Xanomeline Low Dose #> 1           TRUE & TRT01A == 'Xanomeline Low Dose' & NULL #> 2 (! is.na(AGE)) & TRT01A == 'Xanomeline Low Dose' & NULL #> 3     is.na(AGE) & TRT01A == 'Xanomeline Low Dose' & NULL #>  #> $listing #> NULL #>  #> $histogram #> NULL #>  collect_n_subject(meta, \"ase\", \"SEX\") #> $table #>                 name     Placebo        Total Xanomeline High Dose #> 1 Number of Subjects          86          254                   84 #> 2                Sex                                   #> 3 Subjects with Data          86          254                   84 #> 4                  F 53 ( 61.6%) 143 ( 56.3%)          40 ( 47.6%) #> 5                  M 33 ( 38.4%) 111 ( 43.7%)          44 ( 52.4%) #>   Xanomeline Low Dose #> 1                  84 #> 2                 #> 3                  84 #> 4         50 ( 59.5%) #> 5         34 ( 40.5%) #>  #> $n #>                 name Placebo Total Xanomeline High Dose Xanomeline Low Dose #> 1 Number of Subjects      86   254                   84                  84 #>  #> $subset #>                 name                                     Placebo #> 1 Number of Subjects           TRUE & TRT01A == 'Placebo' & NULL #> 2 Subjects with Data (! is.na(SEX)) & TRT01A == 'Placebo' & NULL #> 3                    is.na(SEX) & TRT01A == 'Placebo' & NULL #> 4                  F     SEX == 'F' & TRT01A == 'Placebo' & NULL #> 5                  M     SEX == 'M' & TRT01A == 'Placebo' & NULL #>                                       Xanomeline High Dose #> 1           TRUE & TRT01A == 'Xanomeline High Dose' & NULL #> 2 (! is.na(SEX)) & TRT01A == 'Xanomeline High Dose' & NULL #> 3     is.na(SEX) & TRT01A == 'Xanomeline High Dose' & NULL #> 4     SEX == 'F' & TRT01A == 'Xanomeline High Dose' & NULL #> 5     SEX == 'M' & TRT01A == 'Xanomeline High Dose' & NULL #>                                       Xanomeline Low Dose #> 1           TRUE & TRT01A == 'Xanomeline Low Dose' & NULL #> 2 (! is.na(SEX)) & TRT01A == 'Xanomeline Low Dose' & NULL #> 3     is.na(SEX) & TRT01A == 'Xanomeline Low Dose' & NULL #> 4     SEX == 'F' & TRT01A == 'Xanomeline Low Dose' & NULL #> 5     SEX == 'M' & TRT01A == 'Xanomeline Low Dose' & NULL #>  #> $listing #> NULL #>  #> $histogram #> NULL #>"},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":null,"dir":"Reference","previous_headings":"","what":"Inherit meta information by keywords — meta_inherit","title":"Inherit meta information by keywords — meta_inherit","text":"Inherit meta information keywords","code":""},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Inherit meta information by keywords — meta_inherit","text":"","code":"meta_inherit(meta, inherit, name, overwrite = FALSE)"},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Inherit meta information by keywords — meta_inherit","text":"meta meta_adam object. inherit meta_adam object inherit. name vector keywords meta_inherit meta_adam. overwrite logical value force mapping update.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Inherit meta information by keywords — meta_inherit","text":"metadata object population defined.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Inherit meta information by keywords — meta_inherit","text":"","code":"meta_adam(population = r2rtf::r2rtf_adsl,           observation = r2rtf::r2rtf_adae) |>   meta_inherit(meta_example(), c(\"apat\", \"wk12\", \"ae_summary\")) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>      .location #> 1 'population' #>  #>  #>   Analysis observation type: #>     name        id  group var       subset           label     .location #> 1 'wk12' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'Weeks 0 to 12' 'observation' #>  #>  #>   Analysis function: #>           name                          label #> 1 'ae_summary' 'Table: adverse event summary' #>"},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":null,"dir":"Reference","previous_headings":"","what":"Execute analysis based on the analysis plan — meta_run","title":"Execute analysis based on the analysis plan — meta_run","text":"Execute analysis based analysis plan","code":""},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Execute analysis based on the analysis plan — meta_run","text":"","code":"meta_run(meta, i = NULL, ...)"},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Execute analysis based on the analysis plan — meta_run","text":"meta meta_adam object. vector integers indicate -th analysis meta$plan. ... Additional arguments passed [spec_call_program()].","code":""},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Execute analysis based on the analysis plan — meta_run","text":"Executed analysis based analysis plan.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Execute analysis based on the analysis plan — meta_run","text":"","code":"if (interactive()) {   meta <- meta_example()   ae_summary <- function(...) {     \"results of ae_summary\"   }   ae_specific <- function(...) {     \"results of ae_specific\"   }   meta_run(meta)   meta_run(meta, i = 2) }"},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split metadata into groups — meta_split","title":"Split metadata into groups — meta_split","text":"Split metadata groups","code":""},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split metadata into groups — meta_split","text":"","code":"meta_split(meta, by)"},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split metadata into groups — meta_split","text":"meta meta_adam object. character variable name population level observation level data metadata object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split metadata into groups — meta_split","text":"metadata object split input variable.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split metadata into groups — meta_split","text":"","code":"meta_example() |> meta_split(\"RACE\") #> $`AMERICAN INDIAN OR ALASKA NATIVE` #> ADaM metadata:  #>    .$data_population \tPopulation data with 1 subjects  #>    .$data_observation \tObservation data with 15 records  #>    .$plan \tAnalysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' #>  #>  #> $`BLACK OR AFRICAN AMERICAN` #> ADaM metadata:  #>    .$data_population \tPopulation data with 23 subjects  #>    .$data_observation \tObservation data with 90 records  #>    .$plan \tAnalysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' #>  #>  #> $WHITE #> ADaM metadata:  #>    .$data_population \tPopulation data with 230 subjects  #>    .$data_observation \tObservation data with 1086 records  #>    .$plan \tAnalysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' #>  #>"},{"path":"https://merck.github.io/metalite/reference/metalite-package.html","id":null,"dir":"Reference","previous_headings":"","what":"metalite: ADaM Metadata Structure — metalite-package","title":"metalite: ADaM Metadata Structure — metalite-package","text":"metadata structure clinical data analysis reporting based Analysis Data Model (ADaM) datasets. package simplifies clinical analysis reporting tool development defining standardized inputs, outputs, workflow. package can used create analysis reporting planning grid, mock table, validated analysis reporting results based consistent inputs.","code":""},{"path":[]},{"path":"https://merck.github.io/metalite/reference/metalite-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"metalite: ADaM Metadata Structure — metalite-package","text":"Maintainer: Yujie Zhao yujie.zhao@merck.com Authors: Yilong Zhang Nan Xiao contributors: Benjamin Wang [contributor] Brian Lang [contributor] Howard Baek [contributor] Ruchitbhai Patel [contributor] Madhusudhan Ginnaram [contributor] Sarad Nepal [contributor] Venkatesh Burla [contributor] Merck Sharp & Dohme Corp [copyright holder]","code":""},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of unique subjects — n_subject","title":"Count number of unique subjects — n_subject","text":"Count number unique subjects","code":""},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of unique subjects — n_subject","text":"","code":"n_subject(   id,   group,   par = NULL,   na = \"Missing\",   use_na = c(\"ifany\", \"no\", \"always\") )"},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of unique subjects — n_subject","text":"id character vector subject identifier. group factor vector group name. par character vector parameter name. na character string used label missing values. Defaults \"Missing\". use_na character value whether include NA values table. See useNA argument base::table() details.","code":""},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of unique subjects — n_subject","text":"data frame summarizing number unique subjects different arms.","code":""},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of unique subjects — n_subject","text":"","code":"library(r2rtf)  r2rtf_adae$TRTA <- factor(r2rtf_adae$TRTA) r2rtf_adae$SEX[1:5] <- NA  n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA) #>   Placebo Xanomeline High Dose Xanomeline Low Dose #> 1      69                   79                  77 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX) #>      name Placebo Xanomeline High Dose Xanomeline Low Dose #> 1       F      39                   37                  44 #> 2       M      29                   42                  33 #> 3 Missing       2                    0                   0 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, use_na = \"always\") #>      name Placebo Xanomeline High Dose Xanomeline Low Dose Missing #> 1       F      39                   37                  44       0 #> 2       M      29                   42                  33       0 #> 3 Missing       2                    0                   0       0 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, na = \"Null\") #>   name Placebo Xanomeline High Dose Xanomeline Low Dose #> 1    F      39                   37                  44 #> 2    M      29                   42                  33 #> 3 Null       2                    0                   0"},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":null,"dir":"Reference","previous_headings":"","what":"Construct outdata class — outdata","title":"Construct outdata class — outdata","text":"outdata class defines standard output format analysis reporting.","code":""},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Construct outdata class — outdata","text":"","code":"outdata(   meta,   population,   observation,   parameter,   n,   order,   group,   reference_group,   ... )"},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Construct outdata class — outdata","text":"meta metadata object created metalite. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. n data frame number subjects criteria. order numeric vector row display order. group character vector group variable names ADaM dataset. reference_group numeric value indicate reference group levels group. ... Additional variables save outdata.","code":""},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Construct outdata class — outdata","text":"list class outdata. Components list either quosures constants.","code":""},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Construct outdata class — outdata","text":"design inspired ggplot2::aes().","code":""},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Construct outdata class — outdata","text":"","code":"outdata(   meta = meta_example(),   population = \"apat\",   observation = \"wk12\",   parameter = \"rel\",   n = data.frame(     TRTA = c(\"Placebo\", \"Xanomeline Low Dose\", \"Xanomeline High Dose\"),     n = c(86, 84, 84)   ),   group = \"TRTA\",   reference_group = 1,   order = 1:3 ) #> List of 8 #>  $ meta           :List of 7 #>  $ population     : chr \"apat\" #>  $ observation    : chr \"wk12\" #>  $ parameter      : chr \"rel\" #>  $ n              :'data.frame':\t3 obs. of  2 variables: #>  $ order          : int [1:3] 1 2 3 #>  $ group          : chr \"TRTA\" #>  $ reference_group: num 1"},{"path":"https://merck.github.io/metalite/reference/plan.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a analysis plan from all combination of variables — plan","title":"Create a analysis plan from all combination of variables — plan","text":"function wrapper base::expand.grid().","code":""},{"path":"https://merck.github.io/metalite/reference/plan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a analysis plan from all combination of variables — plan","text":"","code":"plan(analysis, population, observation, parameter, mock = 1, ...)"},{"path":"https://merck.github.io/metalite/reference/plan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a analysis plan from all combination of variables — plan","text":"analysis character value analysis term name. term name used key link information. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. mock numeric value mock table number. ... Additional arguments.","code":""},{"path":"https://merck.github.io/metalite/reference/plan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a analysis plan from all combination of variables — plan","text":"data frame containing analysis plan.","code":""},{"path":"https://merck.github.io/metalite/reference/plan.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a analysis plan from all combination of variables — plan","text":"","code":"# Example 1 # Create an analysis plan of AE summary # with any AE, drug-related AE, and serious AE plan(   analysis = \"ae_summary\",   population = \"apat\",   observation = c(\"wk12\", \"wk24\"),   parameter = \"any;rel;ser\" ) #>   mock   analysis population observation   parameter #> 1    1 ae_summary       apat        wk12 any;rel;ser #> 2    1 ae_summary       apat        wk24 any;rel;ser  # Example 2 # Create an analysis plan of AE specific # with any AE, drug-related AE, and serious AE plan(   analysis = \"ae_specific\",   population = \"apat\",   observation = c(\"wk12\", \"wk24\"),   parameter = c(\"any\", \"rel\", \"ser\") ) #>   mock    analysis population observation parameter #> 1    1 ae_specific       apat        wk12       any #> 2    1 ae_specific       apat        wk24       any #> 3    1 ae_specific       apat        wk12       rel #> 4    1 ae_specific       apat        wk24       rel #> 5    1 ae_specific       apat        wk12       ser #> 6    1 ae_specific       apat        wk24       ser"},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":null,"dir":"Reference","previous_headings":"","what":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"Print metadata object population, observation, analysis plans","code":""},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"","code":"# S3 method for meta_adam print(x, ...)"},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"x object returned meta_adam(). ... Additional parameters print() (used).","code":""},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"printed summary metadata.","code":""},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"","code":"meta_adam(observation = r2rtf::r2rtf_adae, population = r2rtf::r2rtf_adae) |> print() #> ADaM metadata:  #>    .$data_population \tPopulation data with 1191 subjects  #>    .$data_observation \tObservation data with 1191 records  #>  #>"},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Specification for population definition — spec_analysis_population","title":"Specification for population definition — spec_analysis_population","text":"Specification population definition","code":""},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specification for population definition — spec_analysis_population","text":"","code":"spec_analysis_population(meta)"},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specification for population definition — spec_analysis_population","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specification for population definition — spec_analysis_population","text":"vector character strings containing populations used order analysis plans.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specification for population definition — spec_analysis_population","text":"","code":"meta <- meta_example() spec_analysis_population(meta) #>  [1] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y'\"                                         #>  [2] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y'\"                                      #>  [3] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y'\"                                         #>  [4] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y'\"                                      #>  [5] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y' AEOSI == 'Y'\"                            #>  [6] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y' AEOSI == 'Y'\"                         #>  [7] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y' AEREL %in% c('POSSIBLE', 'PROBABLE')\"    #>  [8] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y' AEREL %in% c('POSSIBLE', 'PROBABLE')\" #>  [9] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y' AESER == 'Y'\"                            #> [10] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y' AESER == 'Y'\""},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":null,"dir":"Reference","previous_headings":"","what":"Specification for analysis call program — spec_call_program","title":"Specification for analysis call program — spec_call_program","text":"Specification analysis call program","code":""},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specification for analysis call program — spec_call_program","text":"","code":"spec_call_program(meta, ...)"},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specification for analysis call program — spec_call_program","text":"meta meta_adam object. ... Additional arguments used call programs.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specification for analysis call program — spec_call_program","text":"vector character strings containing call program order analysis plans.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specification for analysis call program — spec_call_program","text":"","code":"meta <- meta_example() spec_call_program(meta) #>  [1] \"ae_summary(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any;rel;ser')\" #>  [2] \"ae_summary(meta = meta, population = 'apat', observation = 'wk24', parameter = 'any;rel;ser')\" #>  [3] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any')\"        #>  [4] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'any')\"        #>  [5] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'aeosi')\"      #>  [6] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'aeosi')\"      #>  [7] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'rel')\"        #>  [8] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'rel')\"        #>  [9] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'ser')\"        #> [10] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'ser')\"        spec_call_program(meta, data_source = \"[Study CDISCpilot: adam-adsl; adae]\") #>  [1] \"ae_summary(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any;rel;ser', data_source = '[Study CDISCpilot: adam-adsl; adae]')\" #>  [2] \"ae_summary(meta = meta, population = 'apat', observation = 'wk24', parameter = 'any;rel;ser', data_source = '[Study CDISCpilot: adam-adsl; adae]')\" #>  [3] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #>  [4] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'any', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #>  [5] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'aeosi', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"      #>  [6] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'aeosi', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"      #>  [7] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'rel', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #>  [8] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'rel', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #>  [9] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'ser', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #> [10] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'ser', data_source = '[Study CDISCpilot: adam-adsl; adae]')\""},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":null,"dir":"Reference","previous_headings":"","what":"Specification for analysis output filename — spec_filename","title":"Specification for analysis output filename — spec_filename","text":"Specification analysis output filename","code":""},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specification for analysis output filename — spec_filename","text":"","code":"spec_filename(meta)"},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specification for analysis output filename — spec_filename","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specification for analysis output filename — spec_filename","text":"vector character strings containing RTF file names.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specification for analysis output filename — spec_filename","text":"","code":"meta <- meta_example() spec_filename(meta) #>  [1] \"ae0summary0wk12.rtf\"        \"ae0summary0wk24.rtf\"        #>  [3] \"ae0specific0wk120any.rtf\"   \"ae0specific0wk240any.rtf\"   #>  [5] \"ae0specific0wk120aeosi.rtf\" \"ae0specific0wk240aeosi.rtf\" #>  [7] \"ae0specific0wk120rel.rtf\"   \"ae0specific0wk240rel.rtf\"   #>  [9] \"ae0specific0wk120ser.rtf\"   \"ae0specific0wk240ser.rtf\""},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":null,"dir":"Reference","previous_headings":"","what":"Specification for analysis title — spec_title","title":"Specification for analysis title — spec_title","text":"Specification analysis title","code":""},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specification for analysis title — spec_title","text":"","code":"spec_title(meta)"},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specification for analysis title — spec_title","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specification for analysis title — spec_title","text":"vector character strings containing table captions order analysis plans.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specification for analysis title — spec_title","text":"","code":"meta <- meta_example() spec_title(meta) #>  [1] \"Summary of Adverse Events\\nWeeks 0 to 12\\nAll Participants as Treated\"                            #>  [2] \"Summary of Adverse Events\\nWeeks 0 to 24\\nAll Participants as Treated\"                            #>  [3] \"Participants With Adverse Events\\nWeeks 0 to 12\\nAll Participants as Treated\"                     #>  [4] \"Participants With Adverse Events\\nWeeks 0 to 24\\nAll Participants as Treated\"                     #>  [5] \"Participants With Adverse Events of special interest\\nWeeks 0 to 12\\nAll Participants as Treated\" #>  [6] \"Participants With Adverse Events of special interest\\nWeeks 0 to 24\\nAll Participants as Treated\" #>  [7] \"Participants With Drug-Related Adverse Events\\nWeeks 0 to 12\\nAll Participants as Treated\"        #>  [8] \"Participants With Drug-Related Adverse Events\\nWeeks 0 to 24\\nAll Participants as Treated\"        #>  [9] \"Participants With Serious Adverse Events\\nWeeks 0 to 12\\nAll Participants as Treated\"             #> [10] \"Participants With Serious Adverse Events\\nWeeks 0 to 24\\nAll Participants as Treated\""},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Update mapping rule in adam_mapping — update_adam_mapping","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"Update mapping rule adam_mapping","code":""},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"","code":"update_adam_mapping(meta, name, ...)"},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"meta meta_adam object. name vector keywords. ... Additional variables added mapping rule among keywords.","code":""},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"metadata object input updated.","code":""},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"","code":"meta <- meta_example() meta <- update_adam_mapping(meta, names(meta$parameter), start_date = \"ASTDT\") collect_adam_mapping(meta, \"ser\") #> ADaM mapping:  #> * `name`       -> \"ser\" #> * `id`         -> NULL #> * `group`      -> NULL #> * `var`        -> \"AEDECOD\" #> * `subset`     -> AESER == \"Y\" #> * `label`      -> \"serious adverse events\" #> * `soc`        -> \"AEBODSYS\" #> * `seq`        -> 401 #> * `term1`      -> \"Serious\" #> * `term2`      -> \"\" #> * `summ_row`   -> \"with serious adverse events\" #> * `.location`  -> \"parameter\" #> * `start_date` -> \"ASTDT\""},{"path":"https://merck.github.io/metalite/news/index.html","id":"metalite-013","dir":"Changelog","previous_headings":"","what":"metalite 0.1.3","title":"metalite 0.1.3","text":"CRAN release: 2023-08-10 n_subject() now new argument na labeling missing values. Update GitHub Actions workflows.","code":""},{"path":"https://merck.github.io/metalite/news/index.html","id":"metalite-012","dir":"Changelog","previous_headings":"","what":"metalite 0.1.2","title":"metalite 0.1.2","text":"CRAN release: 2023-05-19 Add styler workflow. Fix bug count unique mock number properly plan(). Fix bug display NA values properly collect_n_subject(). Export n_subject(). Add test cases functions within collect_n_subject.R.","code":""},{"path":"https://merck.github.io/metalite/news/index.html","id":"metalite-011","dir":"Changelog","previous_headings":"","what":"metalite 0.1.1","title":"metalite 0.1.1","text":"CRAN release: 2023-02-08 Updated DESCRIPTION file add details Description field. Removed usage ::: documentation.","code":""},{"path":"https://merck.github.io/metalite/news/index.html","id":"metalite-010","dir":"Changelog","previous_headings":"","what":"metalite 0.1.0","title":"metalite 0.1.0","text":"Initial version submitted CRAN Added NEWS.md file track changes package.","code":""}]
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Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://merck.github.io/metalite/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C)     This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see .   Copyright (C)    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to Variable Mapping","text":"design abstraction variable mapping enhance robustness metadata information. goal follow dependency inversion principle software design. design inspired ggplot2::aes(). typical analysis, require developer provide variable names : name: reference name key link components. Subject identifier (id): typically using USUBJID ADaM data. Treatment group (group): typically using TRTXX ADaM data. variables (var): additional variables required analysis. subset: subset expression define analysis. Typically using analysis flag XXFL ADaM data. label: natural language describe purpose adam_mapping object.","code":""},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"example-1-all-participants-as-treated-apat","dir":"Articles","previous_headings":"","what":"Example 1: All Participants as Treated (apat)","title":"Introduction to Variable Mapping","text":"example, define adam_mapping APaT population. example illustrate use case decouple variable name ADSL based data_mapping abstract layer. defined variable mapping, development standard function can rely abstraction. long study team provide proper data associate adam_mapping, standard function can used. R, abstraction named list can accessed .$subset assigned <-. goal summarize var group within population defined subset. can write R scripts abstract layer using base R tidy evaluation .","code":"x <- adam_mapping(   name = \"apat\",   id = \"USUBJID\",   group = \"TRT01A\",   subset = TRTFL == \"Y\",   label = \"All Participants as Treated\" )  x #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> \"TRT01A\" #> * `var`    -> NULL #> * `subset` -> TRTFL == \"Y\" #> * `label`  -> \"All Participants as Treated\" x$subset #> TRTFL == \"Y\" x$var <- \"AGE\" x$subset <- quote(SAFFL == \"Y\") # using quote for an expression x #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> \"TRT01A\" #> * `var`    -> \"AGE\" #> * `subset` -> SAFFL == \"Y\" #> * `label`  -> \"All Participants as Treated\""},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"base-r","dir":"Articles","previous_headings":"Example 1: All Participants as Treated (apat)","what":"Base R","title":"Introduction to Variable Mapping","text":"Reference: eval expression.","code":"df <- r2rtf::r2rtf_adsl ana <- df[eval(x$subset, df), ]  split(ana, ana[[x$group]]) |>   sapply(function(y) mean(y[[x$var]])) #>              Placebo Xanomeline High Dose  Xanomeline Low Dose  #>             75.20930             74.38095             75.66667"},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"tidy-evaluation","dir":"Articles","previous_headings":"Example 1: All Participants as Treated (apat)","what":"Tidy evaluation","title":"Introduction to Variable Mapping","text":"Reference: Programming dplyr. using adam_mapping abstract layer, creates additional challenges develop R program, yet can reduce maintenance future.","code":"library(dplyr) df |>   dplyr::filter(!!x$subset) |>   dplyr::group_by(.data[[x$group]]) |>   dplyr::summarise(mean = mean(.data[[x$var]]))"},{"path":"https://merck.github.io/metalite/articles/adam-mapping.html","id":"example-2-serious-adverse-events-ser","dir":"Articles","previous_headings":"","what":"Example 2: Serious adverse events (ser)","title":"Introduction to Variable Mapping","text":"example, define adam_mapping serious adverse events (AE). example illustrate use case inherit default values defined metalite. organization conventions define different analysis terms. can define default values commonly used analysis terms. example, define default adam_mapping object . real example can found metalite:::default_parameter_ae. default values, user can reduce input still allow override default values required. Assuming user define adam_mapping study, study require footnote explain meaning serious adverse events. merge user defined default adam_mapping objects. (always left join) can keep user defined variables. add default subset variable, defined user. Note: adam_mapping object also allow user define variables. example, added footnote variable.","code":"ser_default <- adam_mapping(   name = \"ser\",   label = \"serious adverse events\",   subset = quote(AESER == \"Y\") )  ser_default #> ADaM mapping:  #> * `name`   -> \"ser\" #> * `id`     -> NULL #> * `group`  -> NULL #> * `var`    -> NULL #> * `subset` -> AESER == \"Y\" #> * `label`  -> \"serious adverse events\" ser_user <- adam_mapping(   name = \"ser\",   id = \"USUBJID\",   group = \"TRT01A\",   label = \"serious{^a} adverse events\",   footnote = \"{^a} this is a footnote\" ) ser_user #> ADaM mapping:  #> * `name`     -> \"ser\" #> * `id`       -> \"USUBJID\" #> * `group`    -> \"TRT01A\" #> * `var`      -> NULL #> * `subset`   -> NULL #> * `label`    -> \"serious{^a} adverse events\" #> * `footnote` -> \"{^a} this is a footnote\" merge(ser_user, ser_default) #> ADaM mapping:  #> * `name`     -> \"ser\" #> * `id`       -> \"USUBJID\" #> * `group`    -> \"TRT01A\" #> * `var`      -> NULL #> * `subset`   -> AESER == \"Y\" #> * `label`    -> \"serious{^a} adverse events\" #> * `footnote` -> \"{^a} this is a footnote\""},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Create AR Grid","text":"document, illustrate create &R grid metalite.","code":""},{"path":[]},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-1-input-the-population-and-observation-datasets","dir":"Articles","previous_headings":"Build metadata","what":"Step 1: input the population and observation datasets","title":"Create AR Grid","text":"","code":"metadata <- meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae )"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-2-create-statistical-analysis-plans","dir":"Articles","previous_headings":"Build metadata","what":"Step 2: create statistical analysis plans","title":"Create AR Grid","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" ) |>   add_plan(     analysis = \"ae_specific\", population = \"apat\",     observation = c(\"wk12\", \"wk24\"),     parameter = c(\"any\", \"aeosi\", \"rel\", \"ser\")   )"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-3-feed-in-the-analysis-plan-to-the-existing-metadata","dir":"Articles","previous_headings":"Build metadata","what":"Step 3: feed in the analysis plan to the existing metadata","title":"Create AR Grid","text":"","code":"metadata <- metadata |> define_plan(plan)"},{"path":[]},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-4-1-define-the-key-words-in-population-observation","dir":"Articles","previous_headings":"Build metadata","what":"Step 4.1: define the key words in population & observation","title":"Create AR Grid","text":"","code":"metadata <- metadata |>   define_population(     name = \"apat\",     group = \"TRT01A\",     subset = SAFFL == \"Y\"   ) |>   define_observation(     name = \"wk12\",     group = \"TRTA\",     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) |>   define_observation(     name = \"wk24\",     group = \"TRTA\",     subset = AOCC01FL == \"Y\", # just for demo, another flag shall be used.     label = \"Weeks 0 to 24\"   )"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-4-2-define-the-key-words-in-the-analysis-plans","dir":"Articles","previous_headings":"Build metadata","what":"Step 4.2 define the key words in the analysis plans","title":"Create AR Grid","text":"","code":"metadata <- metadata |>   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) |>   define_parameter(     name = \"aeosi\",     subset = AEOSI == \"Y\",     label = \"adverse events of special interest\"   ) |>   define_analysis(     name = \"ae_summary\",     title = \"Summary of Adverse Events\"   ) |>   define_analysis(     name = \"ae_specific\",     title = \"Summary of Specific Adverse Events\"   )"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"step-5-build-the-metadata","dir":"Articles","previous_headings":"Build metadata","what":"Step 5: build the metadata","title":"Create AR Grid","text":"","code":"metadata <- metadata |> meta_build()"},{"path":"https://merck.github.io/metalite/articles/ar-grid.html","id":"create-ar-grid","dir":"Articles","previous_headings":"","what":"Create A&R grid","title":"Create AR Grid","text":"Summary Adverse EventsWeeks 0 12All Participants Treated ae0summary0wk12.rtf ae_summary Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ Summary Adverse EventsWeeks 0 24All Participants Treated ae0summary0wk24.rtf ae_summary Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ Summary Specific Adverse EventsWeeks 0 12All Participants Treated ae0specific0wk120any.rtf ae_specific Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ Summary Specific Adverse EventsWeeks 0 24All Participants Treated ae0specific0wk240any.rtf ae_specific Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ Summary Specific Adverse EventsWeeks 0 12All Participants Treated ae0specific0wk120aeosi.rtf ae_specific Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ AEOSI == ‘Y’ Summary Specific Adverse EventsWeeks 0 24All Participants Treated ae0specific0wk240aeosi.rtf ae_specific Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ AEOSI == ‘Y’ Summary Specific Adverse EventsWeeks 0 12All Participants Treated ae0specific0wk120rel.rtf ae_specific Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ AEREL %% c(‘POSSIBLE’, ‘PROBABLE’) Summary Specific Adverse EventsWeeks 0 24All Participants Treated ae0specific0wk240rel.rtf ae_specific Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ AEREL %% c(‘POSSIBLE’, ‘PROBABLE’) Summary Specific Adverse EventsWeeks 0 12All Participants Treated ae0specific0wk120ser.rtf ae_specific Population: SAFFL == ‘Y’Observation: SAFFL == ‘Y’ AESER == ‘Y’ Summary Specific Adverse EventsWeeks 0 24All Participants Treated ae0specific0wk240ser.rtf ae_specific Population: SAFFL == ‘Y’Observation: AOCC01FL == ‘Y’ AESER == ‘Y’","code":"ar_grid <- data.frame(   title = spec_title(metadata),   filename = spec_filename(metadata),   function_name = metadata$plan$analysis,   population = spec_analysis_population(metadata) ) ar_grid |>   mutate(across(everything(), ~ gsub(\"\\n\", \"
\", .x))) |>   gt::gt() |>   gt::fmt_markdown(columns = gt::everything()) |>   gt::tab_options(table.font.size = 15)"},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-adam-mapping","dir":"Articles","previous_headings":"","what":"Collect ADaM mapping","title":"Collect Components","text":"object meta organized list ADaM mapping objects. example, can directly access ADaM mapping object list. created helper function help access components component name. example, can collect apat component meta name using collect_adam_mapping(). Collect ADaM mapping participants treated. can collect ADaM mapping serious adverse events parameter meta$parameter$ser. can collect ADaM mapping AE summary analysis method meta$analysis$ae_summary.","code":"meta$population$apat #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> \"TRTA\" #> * `var`    -> NULL #> * `subset` -> SAFFL == \"Y\" #> * `label`  -> \"All Participants as Treated\" collect_adam_mapping(meta, name = \"apat\") #> ADaM mapping:  #> * `name`      -> \"apat\" #> * `id`        -> \"USUBJID\" #> * `group`     -> \"TRTA\" #> * `var`       -> NULL #> * `subset`    -> SAFFL == \"Y\" #> * `label`     -> \"All Participants as Treated\" #> * `.location` -> \"population\" collect_adam_mapping(meta, name = \"ser\") #> ADaM mapping:  #> * `name`      -> \"ser\" #> * `id`        -> NULL #> * `group`     -> NULL #> * `var`       -> \"AEDECOD\" #> * `subset`    -> AESER == \"Y\" #> * `label`     -> \"serious adverse events\" #> * `soc`       -> \"AEBODSYS\" #> * `seq`       -> 401 #> * `term1`     -> \"Serious\" #> * `term2`     -> \"\" #> * `summ_row`  -> \"with serious adverse events\" #> * `.location` -> \"parameter\" collect_adam_mapping(meta, name = \"ae_summary\") #> ADaM mapping:  #> * `name`      -> \"ae_summary\" #> * `id`        -> NULL #> * `group`     -> NULL #> * `var`       -> NULL #> * `subset`    -> NULL #> * `label`     -> \"Table: adverse event summary\" #> * `title`     -> \"Summary of Adverse Events\" #> * `.location` -> \"analysis\""},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-population","dir":"Articles","previous_headings":"","what":"Collect population","title":"Collect Components","text":"developing tools, developer also need access subset condition population. can access information list Equivalently, can also use collect_population() collect definition population. example, can collect subset condition apat using collect_population(), can find subset condition multiple levels. example, can collect analysis population definition apat population, wk12 observation ser parameters.","code":"meta$population$apat$subset #> SAFFL == \"Y\" collect_population(meta, population = \"apat\") #> $population #> [1] \"SAFFL == 'Y'\" collect_population(meta,   population = \"apat\",   observation = \"wk12\",   parameter = \"ser\" ) #> $population #> [1] \"SAFFL == 'Y'\" #>  #> $observation #> [1] \"SAFFL == 'Y'\" #>  #> $parameter #> [1] \"AESER == 'Y'\""},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-population-records","dir":"Articles","previous_headings":"","what":"Collect population records","title":"Collect Components","text":"User may want identify records belong analysis population. can use collect_population_index() show population record index. example, user get index population data set apat participants treated. Alternatively, people may want know ID subjects population. case, collect_population_id() can used collect ID - > USUBJID apat population. can directly collect observations using collect_population_record(). default, key variables used id, group, subset displayed. example shows collect population record population data set participants treated display default variables. example show add variables population data set display. can also add add multiple additional variable display","code":"population_index <- collect_population_index(meta, \"apat\") head(collect_population_index(meta, \"apat\")) #> [1] 1 2 3 4 5 6 population_id <- collect_population_id(meta, \"apat\") head(collect_population_id(meta, \"apat\")) #> [1] \"01-701-1015\" \"01-701-1023\" \"01-701-1028\" \"01-701-1033\" \"01-701-1034\" #> [6] \"01-701-1047\" head(collect_population_record(meta, \"apat\")) #>       USUBJID                 TRTA SAFFL #> 1 01-701-1015              Placebo     Y #> 2 01-701-1023              Placebo     Y #> 3 01-701-1028 Xanomeline High Dose     Y #> 4 01-701-1033  Xanomeline Low Dose     Y #> 5 01-701-1034 Xanomeline High Dose     Y #> 6 01-701-1047              Placebo     Y head(collect_population_record(meta, \"apat\", var = \"AGE\")) #>       USUBJID                 TRTA SAFFL AGE #> 1 01-701-1015              Placebo     Y  63 #> 2 01-701-1023              Placebo     Y  64 #> 3 01-701-1028 Xanomeline High Dose     Y  71 #> 4 01-701-1033  Xanomeline Low Dose     Y  74 #> 5 01-701-1034 Xanomeline High Dose     Y  77 #> 6 01-701-1047              Placebo     Y  85 head(collect_population_record(meta, \"apat\", var = c(\"AGE\", \"TRT01P\"))) #>       USUBJID                 TRTA SAFFL AGE               TRT01P #> 1 01-701-1015              Placebo     Y  63              Placebo #> 2 01-701-1023              Placebo     Y  64              Placebo #> 3 01-701-1028 Xanomeline High Dose     Y  71 Xanomeline High Dose #> 4 01-701-1033  Xanomeline Low Dose     Y  74  Xanomeline Low Dose #> 5 01-701-1034 Xanomeline High Dose     Y  77 Xanomeline High Dose #> 6 01-701-1047              Placebo     Y  85              Placebo"},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-observation-record","dir":"Articles","previous_headings":"","what":"Collect observation record","title":"Collect Components","text":"Similarly can collect observation records examples . example shows collect observation record index observation data set serious AE weeks 0 12 using collect_observation_index() can also directly collect records using collect_observation_record(). default, key variables used id, group, subset displayed. example shows collect observation record observation data set participants treated 0 12 week serious AE display default variables. example show add variables observation data set display.","code":"collect_observation_index(meta, \"apat\", \"wk12\", \"ser\") #> [1]  689 1131 1173 collect_observation_record(meta, \"apat\", \"wk12\", \"ser\") #>          USUBJID                 TRTA #> 689  01-709-1424 Xanomeline High Dose #> 1131 01-718-1170  Xanomeline Low Dose #> 1173 01-718-1371 Xanomeline High Dose #>                                             AEDECOD SAFFL AESER #> 689                                         SYNCOPE     Y     Y #> 1131                                        SYNCOPE     Y     Y #> 1173 PARTIAL SEIZURES WITH SECONDARY GENERALISATION     Y     Y collect_observation_record(meta, \"apat\", \"wk12\", \"ser\", var = \"AEDECOD\") #>          USUBJID                 TRTA #> 689  01-709-1424 Xanomeline High Dose #> 1131 01-718-1170  Xanomeline Low Dose #> 1173 01-718-1371 Xanomeline High Dose #>                                             AEDECOD SAFFL AESER #> 689                                         SYNCOPE     Y     Y #> 1131                                        SYNCOPE     Y     Y #> 1173 PARTIAL SEIZURES WITH SECONDARY GENERALISATION     Y     Y"},{"path":"https://merck.github.io/metalite/articles/component.html","id":"collect-specifications","dir":"Articles","previous_headings":"","what":"Collect specifications","title":"Collect Components","text":"also provided helper functions collect commonly used items Developer can collect table title analysis function meta information using collect_title(). Developer can collect specification data set name using collect_dataname(). show data set name population observation.","code":"collect_title(meta, \"apat\", \"wk12\", \"ser\", \"ae_summary\") #> [1] \"Summary of Adverse Events\"   \"Weeks 0 to 12\"               #> [3] \"All Participants as Treated\" collect_dataname(meta) #>  population observation  #>      \"adsl\"      \"adae\""},{"path":"https://merck.github.io/metalite/articles/metalite.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to metalite","text":"purpose metalite unify data structure saving metadata information clinical analysis & reporting (&R), leveraging Analysis Data Model (ADaM) datasets consistent accurate metadata representation. metalite framework designed : Standardize function input analysis reporting. Enable use pipes (|>). Reduce manual steps maintain SDLC documentation. Ensure consistency analysis specification, mock, results. built metalite following principles: Automation: prefer function call checklist. example, enter data source one time AE analysis. End--end: cover steps software development lifecycle (SDLC) define delivery.","code":""},{"path":"https://merck.github.io/metalite/articles/metalite.html","id":"use-cases","dir":"Articles","previous_headings":"","what":"Use cases","title":"Introduction to metalite","text":"metalite package offers foundation simplify tool development create standard engineering workflows. example, metalite can used : Standardize input output &R functions. Create analysis reporting planning grid. Create mock table. Create validate &R results. Trace analysis records. metalite needs work R packages complete work. idea illustrated diagram .","code":""},{"path":"https://merck.github.io/metalite/articles/metalite.html","id":"mental-model","dir":"Articles","previous_headings":"","what":"Mental model","title":"Introduction to metalite","text":"typical analysis reporting based ADaM data contain three layers. Data Analysis plan Analysis metadata design metalite align layers using meta_adam define_xxx functions.","code":""},{"path":"https://merck.github.io/metalite/articles/metalite.html","id":"example-adverse-events-analysis","dir":"Articles","previous_headings":"Mental model","what":"Example: adverse events analysis","title":"Introduction to metalite","text":"use simplified adverse events analysis example illustrate mental model. Observation level: ADAE Population level: ADSL typical adverse events analysis, AE records saved ADAE (observation level) population information saved ADSL (population level). demo ADaM datasets r2rtf package, can construct object using meta_adam(). &R grid validation tracker mock table also need understand analysis plan adverse events analysis. Specifically, details table, listing figure (TLF) use two helper functions (plan() add_plan()) create analysis plan. analysis plan data frame indicate specification TLF. code , construct 10 TLFs based different combination analysis function, population, observation parameter. , can define analysis plan using define_plan(). population (define_population()): e.g.: name = \"apat\", group = \"TRT01A\", subset = SAFFL == \"Y\" observation (define_observation()): e.g.: name = \"wk12\", group = \"TRTA\", subset = SAFFL == \"Y\", label = \"Weeks 0 12\" parameter (define_parameter()): e.g.: name = \"ser\", subset = AESER == \"Y\", label = \"serious adverse events\" analysis (define_analysis()): AE summary, Specific AE table, Rainfall plot (static interactive), Volcano plot, etc. details needs defined metadata information. example, select APaT population ADSL dataset. achieved defining population. defined built-information follows &R conventions. , programs know meaning apat . project specific information still needs provided study team group variable name subset flag condition. Similarly, can define meta information analysis observation, parameter function. also use meta_build() add default values name specified. metalite, saved demo meta_example() illustrate different use cases. developer, can reuse meta information development. also allow developers standardize input functions. plan$analysis analysis name. meta columns plan() function arguments","code":"meta_adam(   observation = r2rtf_adae,   population = r2rtf_adsl ) #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" ) |>   add_plan(     analysis = \"ae_specific\", population = \"apat\",     observation = c(\"wk12\", \"wk24\"),     parameter = c(\"any\", \"aeosi\", \"rel\", \"ser\")   )  plan #>    mock    analysis population observation   parameter #> 1     1  ae_summary       apat        wk12 any;rel;ser #> 2     1  ae_summary       apat        wk24 any;rel;ser #> 3     2 ae_specific       apat        wk12         any #> 4     2 ae_specific       apat        wk24         any #> 5     2 ae_specific       apat        wk12       aeosi #> 6     2 ae_specific       apat        wk24       aeosi #> 7     2 ae_specific       apat        wk12         rel #> 8     2 ae_specific       apat        wk24         rel #> 9     2 ae_specific       apat        wk12         ser #> 10    2 ae_specific       apat        wk24         ser meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae ) |>   define_plan(plan) #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 10 plans meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae ) |>   define_plan(plan) |>   define_population(name = \"apat\") #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id group var subset                         label #> 1 'apat' 'USUBJID'                  'All Participants as Treated' meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae ) |>   define_plan(plan) |>   define_population(     name = \"apat\",     group = \"TRT01A\",     subset = SAFFL == \"Y\"   ) #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id    group var       subset                         label #> 1 'apat' 'USUBJID' 'TRT01A'     SAFFL == 'Y' 'All Participants as Treated' meta_adam(   population = r2rtf_adsl,   observation = r2rtf_adae ) |>   define_plan(plan = plan) |>   define_population(     name = \"apat\",     group = \"TRT01A\",     subset = SAFFL == \"Y\"   ) |>   define_observation(     name = \"wk12\",     group = \"TRTA\",     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) |>   define_observation(     name = \"wk24\",     group = \"TRTA\",     subset = AOCC01FL == \"Y\", # just for demo, another flag shall be used.     label = \"Weeks 0 to 24\"   ) |>   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) |>   define_parameter(     name = \"aeosi\",     subset = AEOSI == \"Y\",     label = \"adverse events of special interest\"   ) |>   define_analysis(     name = \"ae_summary\",     title = \"Summary of Adverse Events\"   ) |>   meta_build() #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id    group var       subset                         label #> 1 'apat' 'USUBJID' 'TRT01A'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' ae_summary(   meta,   population,   observation,   parameter, ... )"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"overview-of-the-example-we-used","dir":"Articles","previous_headings":"","what":"Overview of the example we used","title":"Create Mockup Table Based on Metadata","text":"example, available datasets adae adsl, available r2rtf package, .e., r2rtf::r2rtf_adae r2rtf::r2rtf_adsl. two datasets, objective conduct two adverse event (AE) analysis: (1) AE summary analysis (3) specific AE analysis. population two analysis participants treated (APaT). Besides, one observations two analysis: weeks 0-12. analysis, interested three types AEs: (1) AEs, (2) series AEs, (3) drug-related AEs. Please note example servers illustration purpose, instead comprehensive production ready work. users interested AE analysis AE categories, get types populations/observations, modification code vignette needed.","code":""},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"prepare-the-metadata","dir":"Articles","previous_headings":"","what":"Prepare the metadata","title":"Create Mockup Table Based on Metadata","text":"section, introduce steps prepare metadata used aforementioned two AE analysis.","code":""},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"step-1-define-the-metadata","dir":"Articles","previous_headings":"Prepare the metadata","what":"Step 1: Define the metadata","title":"Create Mockup Table Based on Metadata","text":"define metadata, users need specify population observations datasets. example, observation dataset comes r2rtf::r2rtf_adae population dataset comes r2rtf::r2rtf_adsl. define metadata meta_adam() follows, users can specify observation dataset name population dataset name.","code":"adae <- r2rtf::r2rtf_adae adsl <- r2rtf::r2rtf_adsl |> rename(TRTA = TRT01A) meta <- meta_adam(   observation = adae,   population = adsl )"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"step-2-define-the-analysis-plan","dir":"Articles","previous_headings":"Prepare the metadata","what":"Step 2: Define the analysis plan","title":"Create Mockup Table Based on Metadata","text":"start mockup tables, begin defining mockup analysis plan. define analysis plan, use plan() add_plan() add details per one mockup analysis. Recall example, 2 analysis plans: AE summary; Specific AE analysis. AE summary analysis, define analysis = \"ae_summary\". Similarly define proper population, observation parameter key words population = \"apat\": Participants Treated (APaT). observation = \"wk12\": Weeks 0-12 analyses. parameter = \";rel;ser\": table cover “”, “drug related” “serious” adverse events. AE specific analysis, users can follow similar logic AE summary. , can define analysis plan total 2 mockup generate 4 TLFs. , use incorporate defined plan metadata using define_plan(), .e.,","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = \"wk12\", parameter = \"any;rel;ser\" ) |>   add_plan(     analysis = \"ae_specific\", population = \"apat\",     observation = \"wk12\",     parameter = c(\"any\", \"rel\", \"ser\")   ) plan #>   mock    analysis population observation   parameter #> 1    1  ae_summary       apat        wk12 any;rel;ser #> 2    2 ae_specific       apat        wk12         any #> 3    2 ae_specific       apat        wk12         rel #> 4    2 ae_specific       apat        wk12         ser meta <- meta |> define_plan(plan)"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"step-3-define-the-keywords","dir":"Articles","previous_headings":"Prepare the metadata","what":"Step 3: Define the keywords","title":"Create Mockup Table Based on Metadata","text":"defining overview analysis plan, begin define meaning key words. Define keywords population: following code define keywords \"apat\", population keywords APaT population. also cover key information group variable, group order, etc… Define keywords observation: following code define keywords \"wk12\", observation keywords Weeks 0-12 observations. Define keywords analysis plans: Note analysis plan, 5 keywords: \"\": parameter keywords adverse events. \"rel\": parameter keywords drug-related adverse events. \"ser\": parameter keywords serious adverse events. \"ae_summary\": analysis keywords AE summary analysis. \"ae_specific\": analysis keywords specific AE analysis. first three keywords, can define define_parameter() follows. can add (1) endnotes, (2) labels, (3) criterion filter, etc. last two keywords, can define define_analysis(). vignette, present mockup table AE summary. users interested specific AE analysis, please define keywords \"ae_specific\" define_analysis(name = \"ae_specific\", title = ...).","code":"meta <- meta |>   define_population(     name = \"apat\",     group = \"TRTA\",     group_order = c(       \"High Dose\" = \"Xanomeline High Dose\",       \"Placebo\" = \"Placebo\"     ),     subset = SAFFL == \"Y\"   ) meta <- meta |>   define_observation(     name = \"wk12\",     group = \"TRTA\",     ae_var = \"AEDECOD\",     var = c(\"AEREL\", \"AESER\"),     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) meta <- meta |>   define_parameter(     name = \"any\",     end_notes = c()   ) |>   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\"),     label = \"drug-realted adverse events\"   ) |>   define_parameter(     name = \"ser\",     subset = AESER == \"Y\",     label = \"serious adverse events\",     end_notes = c(\"Serious adverse events up to 90 days of last dose are included.\")   ) meta <- meta |>   define_analysis(     name = \"ae_summary\",     title = \"Summary of Adverse Events\"   )"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"step-4-build-and-review-the-metadata","dir":"Articles","previous_headings":"Prepare the metadata","what":"Step 4: Build and review the metadata","title":"Create Mockup Table Based on Metadata","text":"keywords, datasets, analysis plan defined, users can build metadata compose information. entire metadata built, users can review analysis plan entire meta ","code":"meta <- meta |> meta_build() meta$plan #>   mock    analysis population observation   parameter #> 1    1  ae_summary       apat        wk12 any;rel;ser #> 2    2 ae_specific       apat        wk12         any #> 3    2 ae_specific       apat        wk12         rel #> 4    2 ae_specific       apat        wk12         ser meta #> ADaM metadata:  #>    .$data_population     Population data with 254 subjects  #>    .$data_observation    Observation data with 1191 records  #>    .$plan    Analysis plan with 4 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>                     group_order #> 1 Xanomeline High Dose, Placebo #>  #>  #>   Analysis observation type: #>     name        id  group          var       subset           label    ae_var #> 1 'wk12' 'USUBJID' 'TRTA' AEREL, AESER SAFFL == 'Y' 'Weeks 0 to 12' 'AEDECOD' #>  #>  #>   Analysis parameter type: #>    name                         label                               subset #> 1 'any'          'any adverse events'                                      #> 2 'rel' 'drug-realted adverse events' AEREL %in% c('POSSIBLE', 'PROBABLE') #> 3 'ser'      'serious adverse events'                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event'"},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"add-components-of-mockup-table","dir":"Articles","previous_headings":"","what":"Add components of mockup table","title":"Create Mockup Table Based on Metadata","text":"Based mockup table, specify additional parameters required function define next section. mockup = TRUE create mockup analysis. output_report define output path based analysis keywords. plan updated, can construct call program. also provide global argument data source. pending effort define ae_summary() ae_specific() function can generate mock tables based inputs.","code":"meta$plan <- meta$plan |>   mutate(     mockup = TRUE,     output_report = paste0(\"./tlf/mock-\", analysis, \".rtf\")   ) meta$plan #>   mock    analysis population observation   parameter mockup #> 1    1  ae_summary       apat        wk12 any;rel;ser   TRUE #> 2    2 ae_specific       apat        wk12         any   TRUE #> 3    2 ae_specific       apat        wk12         rel   TRUE #> 4    2 ae_specific       apat        wk12         ser   TRUE #>                output_report #> 1  ./tlf/mock-ae_summary.rtf #> 2 ./tlf/mock-ae_specific.rtf #> 3 ./tlf/mock-ae_specific.rtf #> 4 ./tlf/mock-ae_specific.rtf spec_call_program(meta,   data_source = \"[adam-adsl; adae]\" ) #> [1] \"ae_summary(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any;rel;ser', mockup = TRUE, output_report = './tlf/mock-ae_summary.rtf', data_source = '[adam-adsl; adae]')\" #> [2] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any', mockup = TRUE, output_report = './tlf/mock-ae_specific.rtf', data_source = '[adam-adsl; adae]')\"       #> [3] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'rel', mockup = TRUE, output_report = './tlf/mock-ae_specific.rtf', data_source = '[adam-adsl; adae]')\"       #> [4] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'ser', mockup = TRUE, output_report = './tlf/mock-ae_specific.rtf', data_source = '[adam-adsl; adae]')\""},{"path":"https://merck.github.io/metalite/articles/mockup-table.html","id":"create-functions","dir":"Articles","previous_headings":"","what":"Create functions","title":"Create Mockup Table Based on Metadata","text":"Let’s create simplified version ae_summary() illustrate idea. illustration purposes, create mock table first row.","code":"ae_summary <- function(meta,                        population,                        observation,                        parameter,                        mockup,                        output_report,                        data_source,                        ...) {   # Identify parameter keywords   para_list <- unlist(strsplit(parameter, \";\"))    # Row label   ae_label <- vapply(para_list,     FUN = function(x) {       collect_adam_mapping(meta, x)$label     },     FUN.VALUE = character(1)   )    # Get treatment grouping order   trt_order <- eval(collect_adam_mapping(meta, population)$group_order)    # Get the title/endnotes of TLF   title_text <- collect_title(     meta = meta,     population = population,     observation = observation,     parameter = parameter, analysis = \"ae_summary\"   )   title_text[2] <- \"{Week}\"    # Logic to create mockup table   if (mockup) {     # Generate RTF     x <- tibble::tibble(       ae_label = ae_label,       n_1 = rep(\"x\", length(ae_label)),       n_2 = rep(\"x\", length(ae_label)), # no display_total/CI       pct_1 = rep(\"x.xx\", length(ae_label)),       pct_2 = rep(\"x.xx\", length(ae_label))     ) |>       dplyr::select(ae_label, n_1, pct_1, n_2, pct_2, everything()) |>       # r2rtf::rtf_title(rtf_mock_color(title_text)) |>       r2rtf::rtf_title(title_text) |>       r2rtf::rtf_colheader(paste0(\" | \", paste(names(trt_order), collapse = \" | \"), \" \"),         col_rel_width = c(3, rep(2, length(trt_order)))       ) |>       r2rtf::rtf_colheader(\" | n | (%) | n | (%) \",         border_top = c(\"\", rep(\"single\", 2 * length(trt_order))),         border_bottom = \"single\",         border_left = c(\"single\", rep(c(\"single\", \"\"), length(trt_order))),         col_rel_width = c(3, rep(1, 2 * length(trt_order)))       ) |>       r2rtf::rtf_body(         col_rel_width = c(3, rep(1, 2 * length(trt_order))),         border_left = c(\"single\", rep(c(\"single\", \"\"), length(trt_order))),         text_justification = c(\"l\", rep(\"c\", 2 * length(trt_order)))       ) |>       r2rtf::rtf_source(data_source)      # Require r2rtf to use color     attr(x, \"page\")$use_color <- TRUE      # Save RTF to a path     if (!is.null(output_report)) {       x |>         r2rtf::rtf_encode() |>         r2rtf::write_rtf(output_report)     }   }    if (!mockup) {     # Logic to perform actual AE summary table.     # Omit here   }    output_report } meta_run(meta,   i = 1,   data_source = \"[adam-adsl; adae]\" ) #> $`ae_summary(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any;rel;ser', mockup = TRUE, output_report = './tlf/mock-ae_summary.rtf', data_source = '[adam-adsl; adae]')` #> [1] \"./tlf/mock-ae_summary.rtf\""},{"path":[]},{"path":"https://merck.github.io/metalite/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yilong Zhang. Author. Yujie Zhao. Author, maintainer. Nan Xiao. Author. Benjamin Wang. Contributor. Brian Lang. Contributor. Howard Baek. Contributor. Ruchitbhai Patel. Contributor. Madhusudhan Ginnaram. Contributor. Sarad Nepal. Contributor. Venkatesh Burla. Contributor. Merck Sharp & Dohme Corp. Copyright holder.","code":""},{"path":"https://merck.github.io/metalite/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhang Y, Zhao Y, Xiao N (2024). metalite: ADaM Metadata Structure. R package version 0.1.3, https://github.com/Merck/metalite, https://merck.github.io/metalite/.","code":"@Manual{,   title = {metalite: ADaM Metadata Structure},   author = {Yilong Zhang and Yujie Zhao and Nan Xiao},   year = {2024},   note = {R package version 0.1.3, https://github.com/Merck/metalite},   url = {https://merck.github.io/metalite/}, }"},{"path":"https://merck.github.io/metalite/index.html","id":"metalite-","dir":"","previous_headings":"","what":"ADaM Metadata Structure","title":"ADaM Metadata Structure","text":"Unified representation metadata structure clinical analysis & reporting (&R) leveraging Analysis Data Model (ADaM) datasets.","code":""},{"path":"https://merck.github.io/metalite/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"ADaM Metadata Structure","text":"easiest way get metalite install CRAN: Alternatively, use new feature get bug fix, can install development version metalite GitHub:","code":"install.packages(\"metalite\") # install.packages(\"remotes\") remotes::install_github(\"Merck/metalite\")"},{"path":"https://merck.github.io/metalite/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"ADaM Metadata Structure","text":"metalite framework designed : Standardize function input analysis reporting. Separate analysis logic data source. Enable use pipes (|>). Reduce manual steps develop maintain documentation clinical trial development. Ensure consistency analysis specification, mock, results.","code":""},{"path":"https://merck.github.io/metalite/index.html","id":"use-cases","dir":"","previous_headings":"","what":"Use cases","title":"ADaM Metadata Structure","text":"metalite package offers foundation simplify tool development create standard engineering workflows. example, metalite can used : Standardize input output &R functions. Create analysis reporting planning grid. Create mock table. Create validate &R results. Trace analysis records. Note: metalite low-level R package needs work R packages complete work. idea illustrated diagram .","code":""},{"path":"https://merck.github.io/metalite/index.html","id":"design-principles","dir":"","previous_headings":"","what":"Design principles","title":"ADaM Metadata Structure","text":"built metalite following principles: Automation: prefer function call checklist. example, enter data source one time AE analysis. End--end: cover steps software development lifecycle (SDLC) define delivery.","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Construct ADaM mappings — adam_mapping","title":"Construct ADaM mappings — adam_mapping","text":"ADaM mappings describe variables meta information ADaM data mapped standardized term.","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Construct ADaM mappings — adam_mapping","text":"","code":"adam_mapping(   name,   id = NULL,   group = NULL,   var = NULL,   subset = NULL,   label = NULL,   ... )"},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Construct ADaM mappings — adam_mapping","text":"name character value term name. term name used key link information. id character value subject identifier variable name ADaM dataset. group character vector group variable names ADaM dataset. var character vector useful variable names ADaM dataset. subset expression identify analysis records. See base::subset(). label character value analysis label. ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Construct ADaM mappings — adam_mapping","text":"list class adam_mapping. Components list either quosures constants.","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Construct ADaM mappings — adam_mapping","text":"design inspired ggplot2::aes().","code":""},{"path":"https://merck.github.io/metalite/reference/adam_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Construct ADaM mappings — adam_mapping","text":"","code":"adam_mapping(   name = \"apat\",   id = \"USUBJID\",   group = \"TRT01A\",   subset = TRTFL == \"Y\",   label = \"All Participants as Treated\" ) #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> \"TRT01A\" #> * `var`    -> NULL #> * `subset` -> TRTFL == \"Y\" #> * `label`  -> \"All Participants as Treated\""},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":null,"dir":"Reference","previous_headings":"","what":"Add additional analysis plan — add_plan","title":"Add additional analysis plan — add_plan","text":"Add additional analysis plan","code":""},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add additional analysis plan — add_plan","text":"","code":"add_plan(plan, analysis, population, observation, parameter, ...)"},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add additional analysis plan — add_plan","text":"plan meta_plan object. analysis character value analysis term name. term name used key link information. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. ... Additional arguments.","code":""},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add additional analysis plan — add_plan","text":"data frame containing analysis plans new plans added.","code":""},{"path":"https://merck.github.io/metalite/reference/add_plan.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add additional analysis plan — add_plan","text":"","code":"plan(\"ae_summary\",   population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel\" ) |>   add_plan(\"ae_specific\",     population = \"apat\",     observation = c(\"wk12\", \"wk24\"), parameter = c(\"any\", \"rel\")   ) #>   mock    analysis population observation parameter #> 1    1  ae_summary       apat        wk12   any;rel #> 2    1  ae_summary       apat        wk24   any;rel #> 3    2 ae_specific       apat        wk12       any #> 4    2 ae_specific       apat        wk24       any #> 5    2 ae_specific       apat        wk12       rel #> 6    2 ae_specific       apat        wk24       rel"},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to assign labels to a data frame — assign_label","title":"A function to assign labels to a data frame — assign_label","text":"function assign labels data frame","code":""},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to assign labels to a data frame — assign_label","text":"","code":"assign_label(data, var = names(data), label = names(data))"},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to assign labels to a data frame — assign_label","text":"data data frame. var variables assign labels. label labels assigned.","code":""},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to assign labels to a data frame — assign_label","text":"data frame labels updated.","code":""},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A function to assign labels to a data frame — assign_label","text":"Case 1: variable's label already define original data frame redefined assign_label(...), original labels kept. Case 2: variable's label already define original data frame re-defined assign_label(...), labels re-defined. Case 3: variable's label define original data frame defined assign_label(...), labels added. Case 4: variable's label define original data frame, neither defined assign_label(...), labels variable name .","code":""},{"path":"https://merck.github.io/metalite/reference/assign_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A function to assign labels to a data frame — assign_label","text":"","code":"assign_label(r2rtf::r2rtf_adae) |> head() #>        STUDYID SITEID     USUBJID    TRTA TRTAN AGE AGEGR1 AGEGR1N  RACE RACEN #> 1 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 2 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 3 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 4 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #> 5 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #> 6 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #>   SEX SAFFL     TRTSDT     TRTEDT      ASTDT ASTDTF ASTDY      AENDT AENDY #> 1   F     Y 2014-01-02 2014-07-02 2014-01-03            2           NA #> 2   F     Y 2014-01-02 2014-07-02 2014-01-03            2           NA #> 3   F     Y 2014-01-02 2014-07-02 2014-01-09            8 2014-01-11    10 #> 4   M     Y 2012-08-05 2012-09-01 2012-08-07            3 2012-08-30    26 #> 5   M     Y 2012-08-05 2012-09-01 2012-08-07            3           NA #> 6   M     Y 2012-08-05 2012-09-01 2012-08-26           22           NA #>   ADURN ADURU                               AETERM                    AELLT #> 1    NA                  APPLICATION SITE ERYTHEMA APPLICATION SITE REDNESS #> 2    NA                  APPLICATION SITE PRURITUS APPLICATION SITE ITCHING #> 3     3   DAY                            DIARRHOEA                 DIARRHEA #> 4    24   DAY                             ERYTHEMA                 ERYTHEMA #> 5    NA                                   ERYTHEMA       LOCALIZED ERYTHEMA #> 6    NA       ATRIOVENTRICULAR BLOCK SECOND DEGREE   AV BLOCK SECOND DEGREE #>   AELLTCD                              AEDECOD AEPTCD    AEHLT AEHLTCD #> 1      NA            APPLICATION SITE ERYTHEMA     NA HLT_0617      NA #> 2      NA            APPLICATION SITE PRURITUS     NA HLT_0317      NA #> 3      NA                            DIARRHOEA     NA HLT_0148      NA #> 4      NA                             ERYTHEMA     NA HLT_0284      NA #> 5      NA                             ERYTHEMA     NA HLT_0284      NA #> 6      NA ATRIOVENTRICULAR BLOCK SECOND DEGREE     NA HLT_0415      NA #>      AEHLGT AEHLGTCD                                             AEBODSYS #> 1 HLGT_0152       NA GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS #> 2 HLGT_0338       NA GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS #> 3 HLGT_0588       NA                           GASTROINTESTINAL DISORDERS #> 4 HLGT_0192       NA               SKIN AND SUBCUTANEOUS TISSUE DISORDERS #> 5 HLGT_0192       NA               SKIN AND SUBCUTANEOUS TISSUE DISORDERS #> 6 HLGT_0086       NA                                    CARDIAC DISORDERS #>                                                  AESOC AESOCCD    AESEV AESER #> 1 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS      NA     MILD     N #> 2 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS      NA     MILD     N #> 3                           GASTROINTESTINAL DISORDERS      NA     MILD     N #> 4               SKIN AND SUBCUTANEOUS TISSUE DISORDERS      NA     MILD     N #> 5               SKIN AND SUBCUTANEOUS TISSUE DISORDERS      NA MODERATE     N #> 6                                    CARDIAC DISORDERS      NA     MILD     N #>   AESCAN AESCONG AESDISAB AESDTH AESHOSP AESLIFE AESOD    AEREL AEACN #> 1      N       N        N      N       N       N     N PROBABLE       #> 2      N       N        N      N       N       N     N PROBABLE       #> 3      N       N        N      N       N       N     N   REMOTE       #> 4      N       N        N      N       N       N     N POSSIBLE       #> 5      N       N        N      N       N       N     N PROBABLE       #> 6      N       N        N      N       N       N     N POSSIBLE       #>                        AEOUT AESEQ TRTEMFL AOCCFL AOCCSFL AOCCPFL AOCC02FL #> 1 NOT RECOVERED/NOT RESOLVED     1       Y      Y       Y       Y          #> 2 NOT RECOVERED/NOT RESOLVED     2       Y                      Y          #> 3         RECOVERED/RESOLVED     3       Y              Y       Y          #> 4 NOT RECOVERED/NOT RESOLVED     1       Y      Y       Y       Y          #> 5 NOT RECOVERED/NOT RESOLVED     2       Y                                 #> 6 NOT RECOVERED/NOT RESOLVED     3       Y              Y       Y          #>   AOCC03FL AOCC04FL             CQ01NAM AOCC01FL #> 1                   DERMATOLOGIC EVENTS        Y #> 2                   DERMATOLOGIC EVENTS          #> 3                                                #> 4                   DERMATOLOGIC EVENTS        Y #> 5                   DERMATOLOGIC EVENTS          #> 6                                                assign_label(   r2rtf::r2rtf_adae,   var = \"USUBJID\",   label = \"Unique subject identifier\" ) |> head() #>        STUDYID SITEID     USUBJID    TRTA TRTAN AGE AGEGR1 AGEGR1N  RACE RACEN #> 1 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 2 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 3 CDISCPILOT01    701 01-701-1015 Placebo     0  63    <65       1 WHITE     1 #> 4 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #> 5 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #> 6 CDISCPILOT01    701 01-701-1023 Placebo     0  64    <65       1 WHITE     1 #>   SEX SAFFL     TRTSDT     TRTEDT      ASTDT ASTDTF ASTDY      AENDT AENDY #> 1   F     Y 2014-01-02 2014-07-02 2014-01-03            2           NA #> 2   F     Y 2014-01-02 2014-07-02 2014-01-03            2           NA #> 3   F     Y 2014-01-02 2014-07-02 2014-01-09            8 2014-01-11    10 #> 4   M     Y 2012-08-05 2012-09-01 2012-08-07            3 2012-08-30    26 #> 5   M     Y 2012-08-05 2012-09-01 2012-08-07            3           NA #> 6   M     Y 2012-08-05 2012-09-01 2012-08-26           22           NA #>   ADURN ADURU                               AETERM                    AELLT #> 1    NA                  APPLICATION SITE ERYTHEMA APPLICATION SITE REDNESS #> 2    NA                  APPLICATION SITE PRURITUS APPLICATION SITE ITCHING #> 3     3   DAY                            DIARRHOEA                 DIARRHEA #> 4    24   DAY                             ERYTHEMA                 ERYTHEMA #> 5    NA                                   ERYTHEMA       LOCALIZED ERYTHEMA #> 6    NA       ATRIOVENTRICULAR BLOCK SECOND DEGREE   AV BLOCK SECOND DEGREE #>   AELLTCD                              AEDECOD AEPTCD    AEHLT AEHLTCD #> 1      NA            APPLICATION SITE ERYTHEMA     NA HLT_0617      NA #> 2      NA            APPLICATION SITE PRURITUS     NA HLT_0317      NA #> 3      NA                            DIARRHOEA     NA HLT_0148      NA #> 4      NA                             ERYTHEMA     NA HLT_0284      NA #> 5      NA                             ERYTHEMA     NA HLT_0284      NA #> 6      NA ATRIOVENTRICULAR BLOCK SECOND DEGREE     NA HLT_0415      NA #>      AEHLGT AEHLGTCD                                             AEBODSYS #> 1 HLGT_0152       NA GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS #> 2 HLGT_0338       NA GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS #> 3 HLGT_0588       NA                           GASTROINTESTINAL DISORDERS #> 4 HLGT_0192       NA               SKIN AND SUBCUTANEOUS TISSUE DISORDERS #> 5 HLGT_0192       NA               SKIN AND SUBCUTANEOUS TISSUE DISORDERS #> 6 HLGT_0086       NA                                    CARDIAC DISORDERS #>                                                  AESOC AESOCCD    AESEV AESER #> 1 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS      NA     MILD     N #> 2 GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS      NA     MILD     N #> 3                           GASTROINTESTINAL DISORDERS      NA     MILD     N #> 4               SKIN AND SUBCUTANEOUS TISSUE DISORDERS      NA     MILD     N #> 5               SKIN AND SUBCUTANEOUS TISSUE DISORDERS      NA MODERATE     N #> 6                                    CARDIAC DISORDERS      NA     MILD     N #>   AESCAN AESCONG AESDISAB AESDTH AESHOSP AESLIFE AESOD    AEREL AEACN #> 1      N       N        N      N       N       N     N PROBABLE       #> 2      N       N        N      N       N       N     N PROBABLE       #> 3      N       N        N      N       N       N     N   REMOTE       #> 4      N       N        N      N       N       N     N POSSIBLE       #> 5      N       N        N      N       N       N     N PROBABLE       #> 6      N       N        N      N       N       N     N POSSIBLE       #>                        AEOUT AESEQ TRTEMFL AOCCFL AOCCSFL AOCCPFL AOCC02FL #> 1 NOT RECOVERED/NOT RESOLVED     1       Y      Y       Y       Y          #> 2 NOT RECOVERED/NOT RESOLVED     2       Y                      Y          #> 3         RECOVERED/RESOLVED     3       Y              Y       Y          #> 4 NOT RECOVERED/NOT RESOLVED     1       Y      Y       Y       Y          #> 5 NOT RECOVERED/NOT RESOLVED     2       Y                                 #> 6 NOT RECOVERED/NOT RESOLVED     3       Y              Y       Y          #>   AOCC03FL AOCC04FL             CQ01NAM AOCC01FL #> 1                   DERMATOLOGIC EVENTS        Y #> 2                   DERMATOLOGIC EVENTS          #> 3                                                #> 4                   DERMATOLOGIC EVENTS        Y #> 5                   DERMATOLOGIC EVENTS          #> 6"},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"Collect adam_mapping meta_adam name","code":""},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"","code":"collect_adam_mapping(meta, name)"},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"meta meta_adam object. name keyword value.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"adam_mapping class object containing definition search variable name.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_adam_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect adam_mapping from meta_adam by name — collect_adam_mapping","text":"","code":"meta <- meta_example() collect_adam_mapping(meta, \"apat\") #> ADaM mapping:  #> * `name`      -> \"apat\" #> * `id`        -> \"USUBJID\" #> * `group`     -> \"TRTA\" #> * `var`       -> NULL #> * `subset`    -> SAFFL == \"Y\" #> * `label`     -> \"All Participants as Treated\" #> * `.location` -> \"population\""},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect specification for dataset name — collect_dataname","title":"Collect specification for dataset name — collect_dataname","text":"Collect specification dataset name","code":""},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect specification for dataset name — collect_dataname","text":"","code":"collect_dataname(meta)"},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect specification for dataset name — collect_dataname","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect specification for dataset name — collect_dataname","text":"vector character strings containing name population/observation.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_dataname.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect specification for dataset name — collect_dataname","text":"","code":"meta <- meta_example() collect_dataname(meta) #>  population observation  #>      \"adsl\"      \"adae\""},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect number of subjects and its subset condition — collect_n_subject","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"Collect number subjects subset condition","code":""},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"","code":"collect_n_subject(   meta,   population,   parameter,   listing = FALSE,   histogram = FALSE,   var_listing = NULL,   remove_blank_group = FALSE,   type = \"Subjects\",   use_na = c(\"ifany\", \"no\", \"always\"),   display_total = TRUE )"},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"meta meta_adam object. population character value population term name. term name used key link information. parameter character value parameter term name. term name used key link information. listing logical value display drill listing per row. histogram logical value display histogram group. var_listing character vector additional variables included listing. remove_blank_group logical value remove group missing value parameter. type character value control title name, e.g., Subjects Records. use_na character value whether include NA values table. See useNA argument base::table() details. display_total logical value display total column.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"list containing number subjects subset condition.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_n_subject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect number of subjects and its subset condition — collect_n_subject","text":"","code":"suppressWarnings(   meta <- meta_example() |>     define_parameter(name = \"sex\", var = \"SEX\", label = \"Sex\") ) collect_n_subject(meta, \"apat\", \"sex\") #> $table #>                 name     Placebo Xanomeline Low Dose Xanomeline High Dose #> 1 Number of Subjects          86                  84                   84 #> 2                Sex                                          #> 3 Subjects with Data          86                  84                   84 #> 4                  F 53 ( 61.6%)         50 ( 59.5%)          40 ( 47.6%) #> 5                  M 33 ( 38.4%)         34 ( 40.5%)          44 ( 52.4%) #>          Total #> 1          254 #> 2          #> 3          254 #> 4 143 ( 56.3%) #> 5 111 ( 43.7%) #>  #> $n #>                 name Placebo Xanomeline Low Dose Xanomeline High Dose Total #> 1 Number of Subjects      86                  84                   84   254 #>  #> $subset #>                 name                                           Placebo #> 1 Number of Subjects           TRUE & TRTA == 'Placebo' & SAFFL == 'Y' #> 2 Subjects with Data (! is.na(SEX)) & TRTA == 'Placebo' & SAFFL == 'Y' #> 3                    is.na(SEX) & TRTA == 'Placebo' & SAFFL == 'Y' #> 4                  F     SEX == 'F' & TRTA == 'Placebo' & SAFFL == 'Y' #> 5                  M     SEX == 'M' & TRTA == 'Placebo' & SAFFL == 'Y' #>                                             Xanomeline Low Dose #> 1           TRUE & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #> 2 (! is.na(SEX)) & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #> 3     is.na(SEX) & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #> 4     SEX == 'F' & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #> 5     SEX == 'M' & TRTA == 'Xanomeline Low Dose' & SAFFL == 'Y' #>                                             Xanomeline High Dose #> 1           TRUE & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #> 2 (! is.na(SEX)) & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #> 3     is.na(SEX) & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #> 4     SEX == 'F' & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #> 5     SEX == 'M' & TRTA == 'Xanomeline High Dose' & SAFFL == 'Y' #>  #> $listing #> NULL #>  #> $histogram #> NULL #>"},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect observation record index from observation dataset — collect_observation_index","title":"Collect observation record index from observation dataset — collect_observation_index","text":"Collect observation record index observation dataset","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect observation record index from observation dataset — collect_observation_index","text":"","code":"collect_observation_index(meta, population, observation, parameter)"},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect observation record index from observation dataset — collect_observation_index","text":"meta meta_adam object. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect observation record index from observation dataset — collect_observation_index","text":"vector patient index within observation group.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_index.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect observation record index from observation dataset — collect_observation_index","text":"","code":"meta <- meta_example() collect_observation_index(meta, \"apat\", \"wk12\", \"ser\") #> [1]  689 1131 1173"},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect observation record from observation dataset — collect_observation_record","title":"Collect observation record from observation dataset — collect_observation_record","text":"key variables used id, group, subset displayed default.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect observation record from observation dataset — collect_observation_record","text":"","code":"collect_observation_record(   meta,   population,   observation,   parameter,   var = NULL )"},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect observation record from observation dataset — collect_observation_record","text":"meta meta_adam object. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. var character vector additional variables displayed output.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect observation record from observation dataset — collect_observation_record","text":"data frame observation dataset.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_observation_record.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect observation record from observation dataset — collect_observation_record","text":"","code":"meta <- meta_example() collect_observation_record(meta, \"apat\", \"wk12\", \"ser\") #>          USUBJID                 TRTA #> 689  01-709-1424 Xanomeline High Dose #> 1131 01-718-1170  Xanomeline Low Dose #> 1173 01-718-1371 Xanomeline High Dose #>                                             AEDECOD SAFFL AESER #> 689                                         SYNCOPE     Y     Y #> 1131                                        SYNCOPE     Y     Y #> 1173 PARTIAL SEIZURES WITH SECONDARY GENERALISATION     Y     Y collect_observation_record(meta, \"apat\", \"wk12\", \"ser\", var = \"AEDECOD\") #>          USUBJID                 TRTA #> 689  01-709-1424 Xanomeline High Dose #> 1131 01-718-1170  Xanomeline Low Dose #> 1173 01-718-1371 Xanomeline High Dose #>                                             AEDECOD SAFFL AESER #> 689                                         SYNCOPE     Y     Y #> 1131                                        SYNCOPE     Y     Y #> 1173 PARTIAL SEIZURES WITH SECONDARY GENERALISATION     Y     Y"},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect specification for population definition — collect_population","title":"Collect specification for population definition — collect_population","text":"Collect specification population definition","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect specification for population definition — collect_population","text":"","code":"collect_population(meta, population, observation = NULL, parameter = NULL)"},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect specification for population definition — collect_population","text":"meta meta_adam object. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect specification for population definition — collect_population","text":"list covering filter population, observation (given) parameter (given).","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect specification for population definition — collect_population","text":"","code":"meta <- meta_example() collect_population(meta, \"apat\") #> $population #> [1] \"SAFFL == 'Y'\" #>  collect_population(meta, \"apat\", \"wk12\") #> $population #> [1] \"SAFFL == 'Y'\" #>  #> $observation #> [1] \"SAFFL == 'Y'\" #>  collect_population(meta, \"apat\", \"wk12\", \"ser\") #> $population #> [1] \"SAFFL == 'Y'\" #>  #> $observation #> [1] \"SAFFL == 'Y'\" #>  #> $parameter #> [1] \"AESER == 'Y'\" #>"},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect subject identifier information from population dataset — collect_population_id","title":"Collect subject identifier information from population dataset — collect_population_id","text":"Collect subject identifier information population dataset","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect subject identifier information from population dataset — collect_population_id","text":"","code":"collect_population_id(meta, population)"},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect subject identifier information from population dataset — collect_population_id","text":"meta meta_adam object. population character value population term name. term name used key link information.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect subject identifier information from population dataset — collect_population_id","text":"vector patient ID within population group.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_id.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect subject identifier information from population dataset — collect_population_id","text":"","code":"meta <- meta_example() head(collect_population_id(meta, \"apat\")) #> [1] \"01-701-1015\" \"01-701-1023\" \"01-701-1028\" \"01-701-1033\" \"01-701-1034\" #> [6] \"01-701-1047\""},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect population record index from population dataset — collect_population_index","title":"Collect population record index from population dataset — collect_population_index","text":"Collect population record index population dataset","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect population record index from population dataset — collect_population_index","text":"","code":"collect_population_index(meta, population)"},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect population record index from population dataset — collect_population_index","text":"meta meta_adam object. population character value population term name. term name used key link information.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect population record index from population dataset — collect_population_index","text":"vector patient index within population group.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_index.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect population record index from population dataset — collect_population_index","text":"","code":"meta <- meta_example() head(collect_population_index(meta, \"apat\")) #> [1] 1 2 3 4 5 6"},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect population record from population dataset — collect_population_record","title":"Collect population record from population dataset — collect_population_record","text":"key variables used id, group, subset displayed default.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect population record from population dataset — collect_population_record","text":"","code":"collect_population_record(meta, population, var = NULL)"},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect population record from population dataset — collect_population_record","text":"meta meta_adam object. population character value population term name. term name used key link information. var character vector additional variables displayed output.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect population record from population dataset — collect_population_record","text":"data frame containing variables population dataset.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_population_record.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect population record from population dataset — collect_population_record","text":"","code":"meta <- meta_example() head(collect_population_record(meta, \"apat\")) #>       USUBJID                 TRTA SAFFL #> 1 01-701-1015              Placebo     Y #> 2 01-701-1023              Placebo     Y #> 3 01-701-1028 Xanomeline High Dose     Y #> 4 01-701-1033  Xanomeline Low Dose     Y #> 5 01-701-1034 Xanomeline High Dose     Y #> 6 01-701-1047              Placebo     Y head(collect_population_record(meta, \"apat\", var = \"AGE\")) #>       USUBJID                 TRTA SAFFL AGE #> 1 01-701-1015              Placebo     Y  63 #> 2 01-701-1023              Placebo     Y  64 #> 3 01-701-1028 Xanomeline High Dose     Y  71 #> 4 01-701-1033  Xanomeline Low Dose     Y  74 #> 5 01-701-1034 Xanomeline High Dose     Y  77 #> 6 01-701-1047              Placebo     Y  85"},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":null,"dir":"Reference","previous_headings":"","what":"Collect specification for title — collect_title","title":"Collect specification for title — collect_title","text":"Collect specification title","code":""},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collect specification for title — collect_title","text":"","code":"collect_title(   meta,   population,   observation,   parameter,   analysis,   title_order = c(\"analysis\", \"observation\", \"population\") )"},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collect specification for title — collect_title","text":"meta meta_adam object. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. analysis character value analysis term name. term name used key link information. title_order character vector define order title component.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collect specification for title — collect_title","text":"vector strings compose table captions.","code":""},{"path":"https://merck.github.io/metalite/reference/collect_title.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collect specification for title — collect_title","text":"","code":"meta <- meta_example() collect_title(meta, \"apat\", \"wk12\", \"ser\", \"ae_summary\") #> [1] \"Summary of Adverse Events\"   \"Weeks 0 to 12\"               #> [3] \"All Participants as Treated\" collect_title(meta, \"apat\", \"wk12\", \"ser\", \"ae_specific\") #> [1] \"Participants With Serious Adverse Events\" #> [2] \"Weeks 0 to 12\"                            #> [3] \"All Participants as Treated\""},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply default values to ADaM mappings — default_apply","title":"Apply default values to ADaM mappings — default_apply","text":"Apply default values ADaM mappings","code":""},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply default values to ADaM mappings — default_apply","text":"","code":"default_apply(x)"},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply default values to ADaM mappings — default_apply","text":"x adam_mapping object.","code":""},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply default values to ADaM mappings — default_apply","text":"Similar input, missing values updated default values.","code":""},{"path":"https://merck.github.io/metalite/reference/default_apply.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply default values to ADaM mappings — default_apply","text":"","code":"default_apply(adam_mapping(name = \"apat\")) #> ADaM mapping:  #> * `name`   -> \"apat\" #> * `id`     -> \"USUBJID\" #> * `group`  -> NULL #> * `var`    -> NULL #> * `subset` -> NULL #> * `label`  -> \"All Participants as Treated\""},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis function meta information for ADaM dataset — define_analysis","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"Define analysis function meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"","code":"define_analysis(meta, name, ...)"},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"meta meta_adam object. name character value term name. term name used key link information. ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"metadata object analysis details defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_analysis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis function meta information for ADaM dataset — define_analysis","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan = plan) |>   define_analysis(     name = \"ae_summary\",     title = \"Summary of Adverse Events\"   ) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>  #>   Analysis function: #>           name                          label #> 1 'ae_summary' 'Table: adverse event summary' #>"},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis observation meta information for ADaM dataset — define_observation","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"Define analysis observation meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"","code":"define_observation(   meta,   name,   id = \"USUBJID\",   group = NULL,   var = NULL,   subset = NULL,   label = NULL,   ... )"},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"meta meta_adam object. name character value term name. term name used key link information. id character value subject identifier variable name ADaM dataset. group character vector group variable names ADaM dataset. var character vector useful variable names ADaM dataset. subset expression identify analysis records. See base::subset(). label character value analysis label. ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"metadata object observation defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_observation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis observation meta information for ADaM dataset — define_observation","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan = plan) |>   define_observation(     name = \"wk12\",     group = \"TRTA\",     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>  #>   Analysis observation type: #>     name        id  group var       subset           label #> 1 'wk12' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'Weeks 0 to 12' #>  #>"},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis parameter meta information for ADaM dataset — define_parameter","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"Define analysis parameter meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"","code":"define_parameter(meta, name, subset = NULL, ...)"},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"meta meta_adam object. name character value term name. term name used key link information. subset expression identify analysis records. See base::subset(). ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"metadata object parameters defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_parameter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis parameter meta information for ADaM dataset — define_parameter","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan = plan) |>   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>  #>   Analysis parameter type: #>    name                         label                               subset #> 1 'rel' 'drug-related adverse events' AEREL %in% c('POSSIBLE', 'PROBABLE') #>  #>"},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis plan meta information for ADaM dataset — define_plan","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"Define analysis plan meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"","code":"define_plan(meta, plan)"},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"meta meta_adam object. plan data frame analysis plan.","code":""},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"metadata object plans defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_plan.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis plan meta information for ADaM dataset — define_plan","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>"},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Define analysis population meta information for ADaM dataset — define_population","title":"Define analysis population meta information for ADaM dataset — define_population","text":"Define analysis population meta information ADaM dataset","code":""},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define analysis population meta information for ADaM dataset — define_population","text":"","code":"define_population(   meta,   name,   id = \"USUBJID\",   group = NULL,   var = NULL,   subset = NULL,   label = NULL,   ... )"},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define analysis population meta information for ADaM dataset — define_population","text":"meta meta_adam object. name character value term name. term name used key link information. id character value subject identifier variable name ADaM dataset. group character vector group variable names ADaM dataset. var character vector useful variable names ADaM dataset. subset expression identify analysis records. See base::subset(). label character value analysis label. ... Additional variables.","code":""},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define analysis population meta information for ADaM dataset — define_population","text":"metadata object population defined.","code":""},{"path":"https://merck.github.io/metalite/reference/define_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define analysis population meta information for ADaM dataset — define_population","text":"","code":"plan <- plan(   analysis = \"ae_summary\", population = \"apat\",   observation = c(\"wk12\", \"wk24\"), parameter = \"any;rel;ser\" )  meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   define_plan(plan) |>   define_population(name = \"apat\") #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 2 plans  #>  #>  #>   Analysis population type: #>     name        id group var subset                         label #> 1 'apat' 'USUBJID'                  'All Participants as Treated' #>  #>"},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to get the labels of data frame columns — get_label","title":"A function to get the labels of data frame columns — get_label","text":"function get labels data frame columns","code":""},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to get the labels of data frame columns — get_label","text":"","code":"get_label(data)"},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to get the labels of data frame columns — get_label","text":"data data frame.","code":""},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to get the labels of data frame columns — get_label","text":"Labels input data frame.","code":""},{"path":"https://merck.github.io/metalite/reference/get_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A function to get the labels of data frame columns — get_label","text":"","code":"get_label(r2rtf::r2rtf_adae) #>                                   STUDYID  #>                        \"Study Identifier\"  #>                                    SITEID  #>                   \"Study Site Identifier\"  #>                                   USUBJID  #>               \"Unique Subject Identifier\"  #>                                      TRTA  #>                        \"Actual Treatment\"  #>                                     TRTAN  #>                    \"Actual Treatment (N)\"  #>                                       AGE  #>                                     \"Age\"  #>                                    AGEGR1  #>                      \"Pooled Age Group 1\"  #>                                   AGEGR1N  #>                  \"Pooled Age Group 1 (N)\"  #>                                      RACE  #>                                    \"Race\"  #>                                     RACEN  #>                                \"Race (N)\"  #>                                       SEX  #>                                     \"Sex\"  #>                                     SAFFL  #>                  \"Safety Population Flag\"  #>                                    TRTSDT  #>     \"Date of First Exposure to Treatment\"  #>                                    TRTEDT  #>      \"Date of Last Exposure to Treatment\"  #>                                     ASTDT  #>                     \"Analysis Start Date\"  #>                                    ASTDTF  #>     \"Analysis Start Date Imputation Flag\"  #>                                     ASTDY  #>             \"Analysis Start Relative Day\"  #>                                     AENDT  #>                       \"Analysis End Date\"  #>                                     AENDY  #>               \"Analysis End Relative Day\"  #>                                     ADURN  #>                         \"AE Duration (N)\"  #>                                     ADURU  #>                       \"AE Duration Units\"  #>                                    AETERM  #>     \"Reported Term for the Adverse Event\"  #>                                     AELLT  #>                       \"Lowest Level Term\"  #>                                   AELLTCD  #>                  \"Lowest Level Term Code\"  #>                                   AEDECOD  #>                 \"Dictionary-Derived Term\"  #>                                    AEPTCD  #>                     \"Preferred Term Code\"  #>                                     AEHLT  #>                         \"High Level Term\"  #>                                   AEHLTCD  #>                    \"High Level Term Code\"  #>                                    AEHLGT  #>                   \"High Level Group Term\"  #>                                  AEHLGTCD  #>              \"High Level Group Term Code\"  #>                                  AEBODSYS  #>              \"Body System or Organ Class\"  #>                                     AESOC  #>              \"Primary System Organ Class\"  #>                                   AESOCCD  #>         \"Primary System Organ Class Code\"  #>                                     AESEV  #>                      \"Severity/Intensity\"  #>                                     AESER  #>                           \"Serious Event\"  #>                                    AESCAN  #>                         \"Involves Cancer\"  #>                                   AESCONG  #>      \"Congenital Anomaly or Birth Defect\"  #>                                  AESDISAB  #> \"Persist or Signif Disability/Incapacity\"  #>                                    AESDTH  #>                        \"Results in Death\"  #>                                   AESHOSP  #>    \"Requires or Prolongs Hospitalization\"  #>                                   AESLIFE  #>                     \"Is Life Threatening\"  #>                                     AESOD  #>                  \"Occurred with Overdose\"  #>                                     AEREL  #>                               \"Causality\"  #>                                     AEACN  #>       \"Action Taken with Study Treatment\"  #>                                     AEOUT  #>                \"Outcome of Adverse Event\"  #>                                     AESEQ  #>                         \"Sequence Number\"  #>                                   TRTEMFL  #>        \"Treatment Emergent Analysis Flag\"  #>                                    AOCCFL  #>           \"1st Occurrence of Any AE Flag\"  #>                                   AOCCSFL  #>              \"1st Occurrence of SOC Flag\"  #>                                   AOCCPFL  #>   \"1st Occurrence of Preferred Term Flag\"  #>                                  AOCC02FL  #>      \"1st Occurrence 02 Flag for Serious\"  #>                                  AOCC03FL  #>  \"1st Occurrence 03 Flag for Serious SOC\"  #>                                  AOCC04FL  #>   \"1st Occurrence 04 Flag for Serious PT\"  #>                                   CQ01NAM  #>                \"Customized Query 01 Name\"  #>                                  AOCC01FL  #>         \"1st Occurrence 01 Flag for CQ01\""},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a metadata representation for ADaM data analysis — meta_adam","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"Create metadata representation ADaM data analysis","code":""},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"","code":"meta_adam(observation, population = observation)"},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"observation data frame observation level data. population data frame population level data. Default observation.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"initialized metadata object observation population defined.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_adam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a metadata representation for ADaM data analysis — meta_adam","text":"","code":"meta_adam(observation = r2rtf::r2rtf_adae, population = r2rtf::r2rtf_adae) #> ADaM metadata:  #>    .$data_population \tPopulation data with 1191 subjects  #>    .$data_observation \tObservation data with 1191 records  #>  #>"},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":null,"dir":"Reference","previous_headings":"","what":"Add duplicate data to enable a total group — meta_add_total","title":"Add duplicate data to enable a total group — meta_add_total","text":"Add duplicate data enable total group","code":""},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add duplicate data to enable a total group — meta_add_total","text":"","code":"meta_add_total(meta, total = \"Total\")"},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add duplicate data to enable a total group — meta_add_total","text":"meta metalite object. total character value total group name.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add duplicate data to enable a total group — meta_add_total","text":"metadata object total group added.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_add_total.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add duplicate data to enable a total group — meta_add_total","text":"","code":"x <- meta_add_total(meta_example()) # A `Total` group is added table(x$data_population$TRTA) #>  #>              Placebo  Xanomeline Low Dose Xanomeline High Dose  #>                   86                   84                   84  #>                Total  #>                  254"},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":null,"dir":"Reference","previous_headings":"","what":"Build complete meta information — meta_build","title":"Build complete meta information — meta_build","text":"Build complete meta information","code":""},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build complete meta information — meta_build","text":"","code":"meta_build(meta)"},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build complete meta information — meta_build","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build complete meta information — meta_build","text":"composed metadata object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_build.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Build complete meta information — meta_build","text":"","code":"meta_adam(   observation = r2rtf::r2rtf_adae,   population = r2rtf::r2rtf_adsl ) |>   # define analysis plan   define_plan(     plan(       analysis = \"ae_summary\",       population = \"apat\",       observation = c(\"wk12\"),       parameter = \"any;rel\"     )   ) |>   # define population   define_population(     name = \"apat\",     group = \"TRT01A\",     subset = SAFFL == \"Y\"   ) |>   # define observation   define_observation(     name = \"wk12\",     group = \"TRTA\",     subset = SAFFL == \"Y\",     label = \"Weeks 0 to 12\"   ) |>   # define parameter - rel   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) |>   # define analysis   define_parameter(     name = \"rel\",     subset = AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")   ) |>   meta_build() #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 1 plans  #>  #>  #>   Analysis population type: #>     name        id    group var       subset                         label #> 1 'apat' 'USUBJID' 'TRT01A'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var       subset           label #> 1 'wk12' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'Weeks 0 to 12' #>  #>  #>   Analysis parameter type: #>    name                         label                               subset #> 1 'rel' 'drug-related adverse events' AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2 'any'          'any adverse events'                                      #>  #>  #>   Analysis function: #>           name                          label #> 1 'ae_summary' 'Table: adverse event summary' #>"},{"path":"https://merck.github.io/metalite/reference/meta_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an example meta_adam object — meta_example","title":"Create an example meta_adam object — meta_example","text":"function illustration purposes. r2rtf package required.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an example meta_adam object — meta_example","text":"","code":"meta_example()"},{"path":"https://merck.github.io/metalite/reference/meta_example.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an example meta_adam object — meta_example","text":"metadata object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an example meta_adam object — meta_example","text":"","code":"meta_example() #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>    .$plan \tAnalysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' #>"},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a data exploration meta_adam object — meta_example_exploration","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"Create data exploration meta_adam object","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"","code":"meta_example_exploration(   data,   group,   name = \"ase\",   subset = NULL,   label = \"All Subjects Enrolled\" )"},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"data data frame. group character vector group variable names ADaM dataset. name character value term name. term name used key link information. subset expression identify analysis records. See base::subset(). label character value analysis label.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"metadata object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_example_exploration.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a data exploration meta_adam object — meta_example_exploration","text":"","code":"meta <- meta_example_exploration(r2rtf::r2rtf_adsl, group = \"TRT01A\") collect_n_subject(meta, \"ase\", \"AGE\") #> $table #>                 name           Placebo             Total Xanomeline High Dose #> 1 Number of Subjects                86               254                   84 #> 2                Age                                              #> 3 Subjects with Data                86               254                   84 #> 4          Mean (SD)        75.2 (8.6)        75.1 (8.2)           74.4 (7.9) #> 5  Median [Min, Max] 76.0 [52.0, 89.0] 77.0 [51.0, 89.0]    76.0 [56.0, 88.0] #>   Xanomeline Low Dose #> 1                  84 #> 2                 #> 3                  84 #> 4          75.7 (8.3) #> 5   77.5 [51.0, 88.0] #>  #> $n #>                 name Placebo Total Xanomeline High Dose Xanomeline Low Dose #> 1 Number of Subjects      86   254                   84                  84 #>  #> $subset #>                 name                                     Placebo #> 1 Number of Subjects           TRUE & TRT01A == 'Placebo' & NULL #> 2 Subjects with Data (! is.na(AGE)) & TRT01A == 'Placebo' & NULL #> 3                    is.na(AGE) & TRT01A == 'Placebo' & NULL #>                                       Xanomeline High Dose #> 1           TRUE & TRT01A == 'Xanomeline High Dose' & NULL #> 2 (! is.na(AGE)) & TRT01A == 'Xanomeline High Dose' & NULL #> 3     is.na(AGE) & TRT01A == 'Xanomeline High Dose' & NULL #>                                       Xanomeline Low Dose #> 1           TRUE & TRT01A == 'Xanomeline Low Dose' & NULL #> 2 (! is.na(AGE)) & TRT01A == 'Xanomeline Low Dose' & NULL #> 3     is.na(AGE) & TRT01A == 'Xanomeline Low Dose' & NULL #>  #> $listing #> NULL #>  #> $histogram #> NULL #>  collect_n_subject(meta, \"ase\", \"SEX\") #> $table #>                 name     Placebo        Total Xanomeline High Dose #> 1 Number of Subjects          86          254                   84 #> 2                Sex                                   #> 3 Subjects with Data          86          254                   84 #> 4                  F 53 ( 61.6%) 143 ( 56.3%)          40 ( 47.6%) #> 5                  M 33 ( 38.4%) 111 ( 43.7%)          44 ( 52.4%) #>   Xanomeline Low Dose #> 1                  84 #> 2                 #> 3                  84 #> 4         50 ( 59.5%) #> 5         34 ( 40.5%) #>  #> $n #>                 name Placebo Total Xanomeline High Dose Xanomeline Low Dose #> 1 Number of Subjects      86   254                   84                  84 #>  #> $subset #>                 name                                     Placebo #> 1 Number of Subjects           TRUE & TRT01A == 'Placebo' & NULL #> 2 Subjects with Data (! is.na(SEX)) & TRT01A == 'Placebo' & NULL #> 3                    is.na(SEX) & TRT01A == 'Placebo' & NULL #> 4                  F     SEX == 'F' & TRT01A == 'Placebo' & NULL #> 5                  M     SEX == 'M' & TRT01A == 'Placebo' & NULL #>                                       Xanomeline High Dose #> 1           TRUE & TRT01A == 'Xanomeline High Dose' & NULL #> 2 (! is.na(SEX)) & TRT01A == 'Xanomeline High Dose' & NULL #> 3     is.na(SEX) & TRT01A == 'Xanomeline High Dose' & NULL #> 4     SEX == 'F' & TRT01A == 'Xanomeline High Dose' & NULL #> 5     SEX == 'M' & TRT01A == 'Xanomeline High Dose' & NULL #>                                       Xanomeline Low Dose #> 1           TRUE & TRT01A == 'Xanomeline Low Dose' & NULL #> 2 (! is.na(SEX)) & TRT01A == 'Xanomeline Low Dose' & NULL #> 3     is.na(SEX) & TRT01A == 'Xanomeline Low Dose' & NULL #> 4     SEX == 'F' & TRT01A == 'Xanomeline Low Dose' & NULL #> 5     SEX == 'M' & TRT01A == 'Xanomeline Low Dose' & NULL #>  #> $listing #> NULL #>  #> $histogram #> NULL #>"},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":null,"dir":"Reference","previous_headings":"","what":"Inherit meta information by keywords — meta_inherit","title":"Inherit meta information by keywords — meta_inherit","text":"Inherit meta information keywords","code":""},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Inherit meta information by keywords — meta_inherit","text":"","code":"meta_inherit(meta, inherit, name, overwrite = FALSE)"},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Inherit meta information by keywords — meta_inherit","text":"meta meta_adam object. inherit meta_adam object inherit. name vector keywords meta_inherit meta_adam. overwrite logical value force mapping update.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Inherit meta information by keywords — meta_inherit","text":"metadata object population defined.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_inherit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Inherit meta information by keywords — meta_inherit","text":"","code":"meta_adam(   population = r2rtf::r2rtf_adsl,   observation = r2rtf::r2rtf_adae ) |>   meta_inherit(meta_example(), c(\"apat\", \"wk12\", \"ae_summary\")) #> ADaM metadata:  #>    .$data_population \tPopulation data with 254 subjects  #>    .$data_observation \tObservation data with 1191 records  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>      .location #> 1 'population' #>  #>  #>   Analysis observation type: #>     name        id  group var       subset           label     .location #> 1 'wk12' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'Weeks 0 to 12' 'observation' #>  #>  #>   Analysis function: #>           name                          label #> 1 'ae_summary' 'Table: adverse event summary' #>"},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":null,"dir":"Reference","previous_headings":"","what":"Execute analysis based on the analysis plan — meta_run","title":"Execute analysis based on the analysis plan — meta_run","text":"Execute analysis based analysis plan","code":""},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Execute analysis based on the analysis plan — meta_run","text":"","code":"meta_run(meta, i = NULL, ...)"},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Execute analysis based on the analysis plan — meta_run","text":"meta meta_adam object. vector integers indicate -th analysis meta$plan. ... Additional arguments passed [spec_call_program()].","code":""},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Execute analysis based on the analysis plan — meta_run","text":"Executed analysis based analysis plan.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_run.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Execute analysis based on the analysis plan — meta_run","text":"","code":"if (interactive()) {   meta <- meta_example()   ae_summary <- function(...) {     \"results of ae_summary\"   }   ae_specific <- function(...) {     \"results of ae_specific\"   }   meta_run(meta)   meta_run(meta, i = 2) }"},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split metadata into groups — meta_split","title":"Split metadata into groups — meta_split","text":"Split metadata groups","code":""},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split metadata into groups — meta_split","text":"","code":"meta_split(meta, by)"},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split metadata into groups — meta_split","text":"meta meta_adam object. character variable name population level observation level data metadata object.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split metadata into groups — meta_split","text":"metadata object split input variable.","code":""},{"path":"https://merck.github.io/metalite/reference/meta_split.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split metadata into groups — meta_split","text":"","code":"meta_example() |> meta_split(\"RACE\") #> $`AMERICAN INDIAN OR ALASKA NATIVE` #> ADaM metadata:  #>    .$data_population \tPopulation data with 1 subjects  #>    .$data_observation \tObservation data with 15 records  #>    .$plan \tAnalysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' #>  #>  #> $`BLACK OR AFRICAN AMERICAN` #> ADaM metadata:  #>    .$data_population \tPopulation data with 23 subjects  #>    .$data_observation \tObservation data with 90 records  #>    .$plan \tAnalysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' #>  #>  #> $WHITE #> ADaM metadata:  #>    .$data_population \tPopulation data with 230 subjects  #>    .$data_observation \tObservation data with 1086 records  #>    .$plan \tAnalysis plan with 10 plans  #>  #>  #>   Analysis population type: #>     name        id  group var       subset                         label #> 1 'apat' 'USUBJID' 'TRTA'     SAFFL == 'Y' 'All Participants as Treated' #>  #>  #>   Analysis observation type: #>     name        id  group var          subset           label #> 1 'wk12' 'USUBJID' 'TRTA'        SAFFL == 'Y' 'Weeks 0 to 12' #> 2 'wk24' 'USUBJID' 'TRTA'     AOCC01FL == 'Y' 'Weeks 0 to 24' #>  #>  #>   Analysis parameter type: #>      name                                label #> 1   'rel'        'drug-related adverse events' #> 2 'aeosi' 'adverse events of special interest' #> 3   'any'                 'any adverse events' #> 4   'ser'             'serious adverse events' #>                                 subset #> 1 AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2                         AEOSI == 'Y' #> 3                                      #> 4                         AESER == 'Y' #>  #>  #>   Analysis function: #>            name                           label #> 1  'ae_summary'  'Table: adverse event summary' #> 2 'ae_specific' 'Table: specific adverse event' #>  #>"},{"path":"https://merck.github.io/metalite/reference/metalite-package.html","id":null,"dir":"Reference","previous_headings":"","what":"metalite: ADaM Metadata Structure — metalite-package","title":"metalite: ADaM Metadata Structure — metalite-package","text":"metadata structure clinical data analysis reporting based Analysis Data Model (ADaM) datasets. package simplifies clinical analysis reporting tool development defining standardized inputs, outputs, workflow. package can used create analysis reporting planning grid, mock table, validated analysis reporting results based consistent inputs.","code":""},{"path":[]},{"path":"https://merck.github.io/metalite/reference/metalite-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"metalite: ADaM Metadata Structure — metalite-package","text":"Maintainer: Yujie Zhao yujie.zhao@merck.com Authors: Yilong Zhang Nan Xiao contributors: Benjamin Wang [contributor] Brian Lang [contributor] Howard Baek [contributor] Ruchitbhai Patel [contributor] Madhusudhan Ginnaram [contributor] Sarad Nepal [contributor] Venkatesh Burla [contributor] Merck Sharp & Dohme Corp [copyright holder]","code":""},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of unique subjects — n_subject","title":"Count number of unique subjects — n_subject","text":"Count number unique subjects","code":""},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of unique subjects — n_subject","text":"","code":"n_subject(   id,   group,   par = NULL,   na = \"Missing\",   use_na = c(\"ifany\", \"no\", \"always\") )"},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of unique subjects — n_subject","text":"id character vector subject identifier. group factor vector group name. par character vector parameter name. na character string used label missing values. Defaults \"Missing\". use_na character value whether include NA values table. See useNA argument base::table() details.","code":""},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of unique subjects — n_subject","text":"data frame summarizing number unique subjects different arms.","code":""},{"path":"https://merck.github.io/metalite/reference/n_subject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of unique subjects — n_subject","text":"","code":"library(r2rtf)  r2rtf_adae$TRTA <- factor(r2rtf_adae$TRTA) r2rtf_adae$SEX[1:5] <- NA  n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA) #>   Placebo Xanomeline High Dose Xanomeline Low Dose #> 1      69                   79                  77 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX) #>      name Placebo Xanomeline High Dose Xanomeline Low Dose #> 1       F      39                   37                  44 #> 2       M      29                   42                  33 #> 3 Missing       2                    0                   0 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, use_na = \"always\") #>      name Placebo Xanomeline High Dose Xanomeline Low Dose Missing #> 1       F      39                   37                  44       0 #> 2       M      29                   42                  33       0 #> 3 Missing       2                    0                   0       0 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, na = \"Null\") #>   name Placebo Xanomeline High Dose Xanomeline Low Dose #> 1    F      39                   37                  44 #> 2    M      29                   42                  33 #> 3 Null       2                    0                   0"},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":null,"dir":"Reference","previous_headings":"","what":"Construct outdata class — outdata","title":"Construct outdata class — outdata","text":"outdata class defines standard output format analysis reporting.","code":""},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Construct outdata class — outdata","text":"","code":"outdata(   meta,   population,   observation,   parameter,   n,   order,   group,   reference_group,   ... )"},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Construct outdata class — outdata","text":"meta metadata object created metalite. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. n data frame number subjects criteria. order numeric vector row display order. group character vector group variable names ADaM dataset. reference_group numeric value indicate reference group levels group. ... Additional variables save outdata.","code":""},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Construct outdata class — outdata","text":"list class outdata. Components list either quosures constants.","code":""},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Construct outdata class — outdata","text":"design inspired ggplot2::aes().","code":""},{"path":"https://merck.github.io/metalite/reference/outdata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Construct outdata class — outdata","text":"","code":"outdata(   meta = meta_example(),   population = \"apat\",   observation = \"wk12\",   parameter = \"rel\",   n = data.frame(     TRTA = c(\"Placebo\", \"Xanomeline Low Dose\", \"Xanomeline High Dose\"),     n = c(86, 84, 84)   ),   group = \"TRTA\",   reference_group = 1,   order = 1:3 ) #> List of 8 #>  $ meta           :List of 7 #>  $ population     : chr \"apat\" #>  $ observation    : chr \"wk12\" #>  $ parameter      : chr \"rel\" #>  $ n              :'data.frame':\t3 obs. of  2 variables: #>  $ order          : int [1:3] 1 2 3 #>  $ group          : chr \"TRTA\" #>  $ reference_group: num 1"},{"path":"https://merck.github.io/metalite/reference/plan.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a analysis plan from all combination of variables — plan","title":"Create a analysis plan from all combination of variables — plan","text":"function wrapper base::expand.grid().","code":""},{"path":"https://merck.github.io/metalite/reference/plan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a analysis plan from all combination of variables — plan","text":"","code":"plan(analysis, population, observation, parameter, mock = 1, ...)"},{"path":"https://merck.github.io/metalite/reference/plan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a analysis plan from all combination of variables — plan","text":"analysis character value analysis term name. term name used key link information. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. mock numeric value mock table number. ... Additional arguments.","code":""},{"path":"https://merck.github.io/metalite/reference/plan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a analysis plan from all combination of variables — plan","text":"data frame containing analysis plan.","code":""},{"path":"https://merck.github.io/metalite/reference/plan.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a analysis plan from all combination of variables — plan","text":"","code":"# Example 1 # Create an analysis plan of AE summary # with any AE, drug-related AE, and serious AE plan(   analysis = \"ae_summary\",   population = \"apat\",   observation = c(\"wk12\", \"wk24\"),   parameter = \"any;rel;ser\" ) #>   mock   analysis population observation   parameter #> 1    1 ae_summary       apat        wk12 any;rel;ser #> 2    1 ae_summary       apat        wk24 any;rel;ser  # Example 2 # Create an analysis plan of AE specific # with any AE, drug-related AE, and serious AE plan(   analysis = \"ae_specific\",   population = \"apat\",   observation = c(\"wk12\", \"wk24\"),   parameter = c(\"any\", \"rel\", \"ser\") ) #>   mock    analysis population observation parameter #> 1    1 ae_specific       apat        wk12       any #> 2    1 ae_specific       apat        wk24       any #> 3    1 ae_specific       apat        wk12       rel #> 4    1 ae_specific       apat        wk24       rel #> 5    1 ae_specific       apat        wk12       ser #> 6    1 ae_specific       apat        wk24       ser"},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":null,"dir":"Reference","previous_headings":"","what":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"Print metadata object population, observation, analysis plans","code":""},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"","code":"# S3 method for meta_adam print(x, ...)"},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"x object returned meta_adam(). ... Additional parameters print() (used).","code":""},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"printed summary metadata.","code":""},{"path":"https://merck.github.io/metalite/reference/print.meta_adam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Print a metadata object with its population, observation, and analysis plans — print.meta_adam","text":"","code":"meta_adam(observation = r2rtf::r2rtf_adae, population = r2rtf::r2rtf_adae) |> print() #> ADaM metadata:  #>    .$data_population \tPopulation data with 1191 subjects  #>    .$data_observation \tObservation data with 1191 records  #>  #>"},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":null,"dir":"Reference","previous_headings":"","what":"Specification for population definition — spec_analysis_population","title":"Specification for population definition — spec_analysis_population","text":"Specification population definition","code":""},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specification for population definition — spec_analysis_population","text":"","code":"spec_analysis_population(meta)"},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specification for population definition — spec_analysis_population","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specification for population definition — spec_analysis_population","text":"vector character strings containing populations used order analysis plans.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_analysis_population.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specification for population definition — spec_analysis_population","text":"","code":"meta <- meta_example() spec_analysis_population(meta) #>  [1] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y'\"                                         #>  [2] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y'\"                                      #>  [3] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y'\"                                         #>  [4] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y'\"                                      #>  [5] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y' AEOSI == 'Y'\"                            #>  [6] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y' AEOSI == 'Y'\"                         #>  [7] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y' AEREL %in% c('POSSIBLE', 'PROBABLE')\"    #>  [8] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y' AEREL %in% c('POSSIBLE', 'PROBABLE')\" #>  [9] \"Population: SAFFL == 'Y'\\nObservation: SAFFL == 'Y' AESER == 'Y'\"                            #> [10] \"Population: SAFFL == 'Y'\\nObservation: AOCC01FL == 'Y' AESER == 'Y'\""},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":null,"dir":"Reference","previous_headings":"","what":"Specification for analysis call program — spec_call_program","title":"Specification for analysis call program — spec_call_program","text":"Specification analysis call program","code":""},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specification for analysis call program — spec_call_program","text":"","code":"spec_call_program(meta, ...)"},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specification for analysis call program — spec_call_program","text":"meta meta_adam object. ... Additional arguments used call programs.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specification for analysis call program — spec_call_program","text":"vector character strings containing call program order analysis plans.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_call_program.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specification for analysis call program — spec_call_program","text":"","code":"meta <- meta_example() spec_call_program(meta) #>  [1] \"ae_summary(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any;rel;ser')\" #>  [2] \"ae_summary(meta = meta, population = 'apat', observation = 'wk24', parameter = 'any;rel;ser')\" #>  [3] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any')\"        #>  [4] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'any')\"        #>  [5] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'aeosi')\"      #>  [6] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'aeosi')\"      #>  [7] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'rel')\"        #>  [8] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'rel')\"        #>  [9] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'ser')\"        #> [10] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'ser')\"        spec_call_program(meta, data_source = \"[Study CDISCpilot: adam-adsl; adae]\") #>  [1] \"ae_summary(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any;rel;ser', data_source = '[Study CDISCpilot: adam-adsl; adae]')\" #>  [2] \"ae_summary(meta = meta, population = 'apat', observation = 'wk24', parameter = 'any;rel;ser', data_source = '[Study CDISCpilot: adam-adsl; adae]')\" #>  [3] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'any', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #>  [4] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'any', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #>  [5] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'aeosi', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"      #>  [6] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'aeosi', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"      #>  [7] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'rel', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #>  [8] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'rel', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #>  [9] \"ae_specific(meta = meta, population = 'apat', observation = 'wk12', parameter = 'ser', data_source = '[Study CDISCpilot: adam-adsl; adae]')\"        #> [10] \"ae_specific(meta = meta, population = 'apat', observation = 'wk24', parameter = 'ser', data_source = '[Study CDISCpilot: adam-adsl; adae]')\""},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":null,"dir":"Reference","previous_headings":"","what":"Specification for analysis output filename — spec_filename","title":"Specification for analysis output filename — spec_filename","text":"Specification analysis output filename","code":""},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specification for analysis output filename — spec_filename","text":"","code":"spec_filename(meta)"},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specification for analysis output filename — spec_filename","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specification for analysis output filename — spec_filename","text":"vector character strings containing RTF file names.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_filename.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specification for analysis output filename — spec_filename","text":"","code":"meta <- meta_example() spec_filename(meta) #>  [1] \"ae0summary0wk12.rtf\"        \"ae0summary0wk24.rtf\"        #>  [3] \"ae0specific0wk120any.rtf\"   \"ae0specific0wk240any.rtf\"   #>  [5] \"ae0specific0wk120aeosi.rtf\" \"ae0specific0wk240aeosi.rtf\" #>  [7] \"ae0specific0wk120rel.rtf\"   \"ae0specific0wk240rel.rtf\"   #>  [9] \"ae0specific0wk120ser.rtf\"   \"ae0specific0wk240ser.rtf\""},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":null,"dir":"Reference","previous_headings":"","what":"Specification for analysis title — spec_title","title":"Specification for analysis title — spec_title","text":"Specification analysis title","code":""},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specification for analysis title — spec_title","text":"","code":"spec_title(meta)"},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specification for analysis title — spec_title","text":"meta meta_adam object.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specification for analysis title — spec_title","text":"vector character strings containing table captions order analysis plans.","code":""},{"path":"https://merck.github.io/metalite/reference/spec_title.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Specification for analysis title — spec_title","text":"","code":"meta <- meta_example() spec_title(meta) #>  [1] \"Summary of Adverse Events\\nWeeks 0 to 12\\nAll Participants as Treated\"                            #>  [2] \"Summary of Adverse Events\\nWeeks 0 to 24\\nAll Participants as Treated\"                            #>  [3] \"Participants With Adverse Events\\nWeeks 0 to 12\\nAll Participants as Treated\"                     #>  [4] \"Participants With Adverse Events\\nWeeks 0 to 24\\nAll Participants as Treated\"                     #>  [5] \"Participants With Adverse Events of special interest\\nWeeks 0 to 12\\nAll Participants as Treated\" #>  [6] \"Participants With Adverse Events of special interest\\nWeeks 0 to 24\\nAll Participants as Treated\" #>  [7] \"Participants With Drug-Related Adverse Events\\nWeeks 0 to 12\\nAll Participants as Treated\"        #>  [8] \"Participants With Drug-Related Adverse Events\\nWeeks 0 to 24\\nAll Participants as Treated\"        #>  [9] \"Participants With Serious Adverse Events\\nWeeks 0 to 12\\nAll Participants as Treated\"             #> [10] \"Participants With Serious Adverse Events\\nWeeks 0 to 24\\nAll Participants as Treated\""},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":null,"dir":"Reference","previous_headings":"","what":"Update mapping rule in adam_mapping — update_adam_mapping","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"Update mapping rule adam_mapping","code":""},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"","code":"update_adam_mapping(meta, name, ...)"},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"meta meta_adam object. name vector keywords. ... Additional variables added mapping rule among keywords.","code":""},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"metadata object input updated.","code":""},{"path":"https://merck.github.io/metalite/reference/update_adam_mapping.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update mapping rule in adam_mapping — update_adam_mapping","text":"","code":"meta <- meta_example() meta <- update_adam_mapping(meta, names(meta$parameter), start_date = \"ASTDT\") collect_adam_mapping(meta, \"ser\") #> ADaM mapping:  #> * `name`       -> \"ser\" #> * `id`         -> NULL #> * `group`      -> NULL #> * `var`        -> \"AEDECOD\" #> * `subset`     -> AESER == \"Y\" #> * `label`      -> \"serious adverse events\" #> * `soc`        -> \"AEBODSYS\" #> * `seq`        -> 401 #> * `term1`      -> \"Serious\" #> * `term2`      -> \"\" #> * `summ_row`   -> \"with serious adverse events\" #> * `.location`  -> \"parameter\" #> * `start_date` -> \"ASTDT\""},{"path":"https://merck.github.io/metalite/news/index.html","id":"metalite-013","dir":"Changelog","previous_headings":"","what":"metalite 0.1.3","title":"metalite 0.1.3","text":"CRAN release: 2023-08-10 n_subject() now new argument na labeling missing values. Update GitHub Actions workflows.","code":""},{"path":"https://merck.github.io/metalite/news/index.html","id":"metalite-012","dir":"Changelog","previous_headings":"","what":"metalite 0.1.2","title":"metalite 0.1.2","text":"CRAN release: 2023-05-19 Add styler workflow. Fix bug count unique mock number properly plan(). Fix bug display NA values properly collect_n_subject(). Export n_subject(). Add test cases functions within collect_n_subject.R.","code":""},{"path":"https://merck.github.io/metalite/news/index.html","id":"metalite-011","dir":"Changelog","previous_headings":"","what":"metalite 0.1.1","title":"metalite 0.1.1","text":"CRAN release: 2023-02-08 Updated DESCRIPTION file add details Description field. Removed usage ::: documentation.","code":""},{"path":"https://merck.github.io/metalite/news/index.html","id":"metalite-010","dir":"Changelog","previous_headings":"","what":"metalite 0.1.0","title":"metalite 0.1.0","text":"Initial version submitted CRAN Added NEWS.md file track changes package.","code":""}]