Wip features

.Rbuildignore

@@ -12,3 +12,7 @@ BLLFlow.Rproj
 ^images$
 docs$
 vignettes
+^.travis.yml
+^CODE_OF_CONDUCT.md
+^CONTRIBUTING.md
+^config.yml

.gitignore

@@ -8,6 +8,3 @@ man/*
 !man/figures/
 docs
 .RData
-OneDrive_1_8-9-2019
-PoRT MSW - cchsVariableDetails.csv
-PoRT MSW - variablesCCHSFlow.csv

.travis.yml

@@ -13,14 +13,14 @@ before_script:
   - R -e "install.packages('knitr')"
   - R -e "install.packages('roxygen2')"
   - R -e "install.packages('devtools')"
+  - Rscript -e 'devtools::install()'
 
 script:
   - R -e 'devtools::document()'
   - R CMD build .
   - R CMD check *tar.gz
 
 after_success:
-  - Rscript -e 'devtools::install()'
   - R -e "install.packages('pkgdown')"
   - Rscript -e 'pkgdown::build_site(run_dont_run = TRUE)'
 

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Big Life Lab Flow - a Workflow for Predictive Studies
 Description: An implementation of predictive algorithm studies. Predictive 
   Modelling Mark-up Language (PMML) is suported. The workflow has three steps:
-  data prepartation; model development, and; model deployment.
+  data preparation; model development, and; model deployment.
 Version: 0.1.0
 Date: 2018-12-09
 Authors@R: c( 
@@ -24,29 +24,32 @@ Authors@R: c(
 Depends:
   R (>= 3.2),
   tableone,
+  recipes
+Imports: 
   DDIwR,
   xml2,
+  stringr,
   sjlabelled,
-  haven
-Imports:
-  rstudioapi,
-  glue,
-  plotly,
-  Hmisc,
-  tidyr,
-  dplyr
+  haven,
+  magrittr,
+  rms,
+  config,
+  dplyr,
+  labelled,
+  rlang,
+  tibble,
+  tidyr
 Suggests:
-    knitr,
-    rmarkdown,
-    DT,
-    magrittr,
-    survival,
-    testthat
+  knitr,
+  rmarkdown,
+  survival,
+  testthat,
+  cchsflow
 URL: https://github.com/Big-Life-Lab/bllflow
 BugReports: https://github.com/Big-Life-Lab/bllflow/issues
 Maintainer: Rostyslav Vyuha <[email protected]>
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 VignetteBuilder: knitr

NAMESPACE

@@ -1,26 +1,56 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(CheckSmallCells,SummaryData)
-S3method(CheckSmallCells,TableOne)
 S3method(CreateTableOne,BLLFlow)
 S3method(CreateTableOne,default)
-S3method(RecWTable,default)
-S3method(WriteDDIPopulatedMSW,BLLFlow)
-S3method(WriteDDIPopulatedMSW,BLLFlowDDI)
-S3method(clean.Max,BLLFlow)
-S3method(clean.Min,BLLFlow)
-S3method(print,metaDataLog)
-export(BLLFlow)
-export(CheckSmallCells)
+S3method(bake,step_apply_missing_tagged_na)
+S3method(bake,step_tagged_naomit)
+S3method(bake,step_z)
+S3method(get_variables,BLLFlow)
+S3method(get_variables,default)
+S3method(prep,step_apply_missing_tagged_na)
+S3method(prep,step_tagged_naomit)
+S3method(prep,step_z)
+S3method(print,TableOne)
+S3method(run_module,BLLFlow)
+S3method(run_module,default)
+S3method(set_data_labels,BLLFlow)
+S3method(set_data_labels,default)
 export(CreateTableOne)
-export(GetDDIDescription)
-export(GetDDIVariables)
-export(ProcessDDIVariableDetails)
-export(ReadDDI)
-export(RecWTable)
-export(SetDataLabels)
-export(SummaryDataLong)
-export(UpdateMSW)
-export(WriteDDIPopulatedMSW)
-export(clean.Max)
-export(clean.Min)
+export(bllflow_config_combine_data)
+export(bllflow_config_init)
+export(bllflow_config_read_data)
+export(bllflow_config_rec_data)
+export(build_bllflow)
+export(get_variables)
+export(is_equal)
+export(kableone)
+export(read_data)
+export(rec_with_table)
+export(run_module)
+export(scramble_data)
+export(set_data_labels)
+export(step_apply_missing_tagged_na)
+export(step_tagged_naomit)
+export(step_z)
+export(table_one_long)
+importFrom(dplyr,do)
+importFrom(dplyr,rowwise)
+importFrom(dplyr,select)
+importFrom(haven,tagged_na)
+importFrom(labelled,var_label)
+importFrom(magrittr,"%>%")
+importFrom(recipes,bake)
+importFrom(recipes,prep)
+importFrom(recipes,step)
+importFrom(recipes,tidy)
+importFrom(rlang,parse_expr)
+importFrom(sjlabelled,"set_label<-")
+importFrom(sjlabelled,get_labels)
+importFrom(sjlabelled,set_label)
+importFrom(sjlabelled,set_labels)
+importFrom(stats,sd)
+importFrom(stringr,str_match)
+importFrom(tableone,CreateTableOne)
+importFrom(tibble,as.tibble)
+importFrom(tidyr,drop_na)
+importFrom(utils,capture.output)

NEWS.md

@@ -1,4 +1,11 @@
 # bllFlow (development version)
+## Temp dump of changes
+- ReadData function
+- changed table one to use working data
+- changed naming convention to snake case in recode-wit-table.R
+- changed naming convention to snake case in small-cell-check.R
+- changed naming convention to snake case in table-one-long.R
+- changed naming convention to snake case in util-funcs.R
 
 # bllflow 0.1.2 (current build)
 

R/apply_missing_tagged_na.R

@@ -0,0 +1,21 @@
+# ---------- DEPRECATED SEE BLLFLOWRECIPES FOR NEW VERSION ----------
+#' #' Apply missing tagged NA
+#' #'
+#' #' Any non tagged NA has the passed tag applied to them this helps tag NA
+#' #' that were added by other packages
+#' #'
+#' #' @param data
+#' #' @param variables
+#' #' @param tag_type
+#' #'
+#' #' @return passed data with non tagged NA now having the tag_type applied
+#' #' @export
+#' apply_missing_tagged_na <- function(data, variables, tag_type) {
+#'   for (variable in variables) {
+#'     NA_index <- is.na(data[[variable]])
+#'     tagged_NA_index <- haven::is_tagged_na(data[[variable]])
+#'     true_NA_index <- !(NA_index == tagged_NA_index)
+#'     data[true_NA_index, variable] <- haven::tagged_na(tag_type)
+#'   }
+#'   return(data)
+#' }