Merge pull request #300 from USEPA/dev

Update main branch for tcpl v3.2 CRAN release

.Rbuildignore

@@ -6,7 +6,7 @@
 ^inst/sql/create_sql_files\.R$
 man-roxygen
 tcpl.Rcheck
-README.md
+^README\.Rmd$
 CONTRIBUTING.md
 cran-comments.md
 ^CRAN-RELEASE$

.github/workflows/test-on-PR.yaml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   pull_request:
-    branches: [main]
+    branches: [main, dev]
 
 name: test-coverage
 

DESCRIPTION

@@ -1,31 +1,29 @@
 Package: tcpl
 Title: ToxCast Data Analysis Pipeline
-Version: 3.1.0
+Version: 3.2.0
 Authors@R: c(
-    person("Richard S", "Judson",role = c("ctb","ths"), email = "[email protected]"),
-    person("Dayne L", "Filer", role = "aut",email = "[email protected]"),
-    person("Jason","Brown",role = "cre", email = "[email protected]"),
-    person("Sarah E","Davidson-Fritz",role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-2891-9380")),
+    person("Richard S", "Judson",role = c("ctb","ths"), comment = c(ORCID = "0000-0002-2348-9633")),
+    person("Dayne L", "Filer", role = "aut"),
+    person("Jason","Brown", role = "cre", email = "[email protected]", comment = c(ORCID = "0009-0000-2294-641X")),
+    person("Sarah E","Davidson-Fritz", role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-2891-9380")),
     person("Madison","Feshuk",role = "ctb",email = "[email protected]", comment = c(ORCID = "0000-0002-1390-6405")),
-    person("Lori","Kolaczkowski",role = "ctb",email = "[email protected]"),
-    person("Kurt", "Dunham", role = "ctb", email = "[email protected]"),
     person("Carter", "Thunes", role = "ctb", email = "[email protected]"),
     person("Ashley", "Ko", role = "ctb", email = "[email protected]"),
-    person("Todd", "Zurlinden", role="ctb"),
+    person("Kelly", "Carstens", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0002-1746-5379")),
+    person("Todd", "Zurlinden", role="ctb", comment = c(ORCID = "0000-0003-1372-3913")),
+    person("Lori","Kolaczkowski",role = "ctb"),
+    person("Kurt", "Dunham", role = "ctb"),
     person("Parth", "Kothiya", role = "ctb"),
     person("Woodrow R", "Setzer", role = "ctb"),
     person("Matthew T", "Martin", role = c("ctb", "ths")),
     person("Katie", "Paul Friedman", role=c("ctb"), email = "[email protected]", comment = c(ORCID = "0000-0002-2710-1691"))
     )
-Description: A set of tools for processing and modeling high-throughput and
-    high-content chemical screening data. The package was developed for the
-    the chemical screening data generated by the US EPA ToxCast program, but
-    can be used for diverse chemical screening efforts.
-URL: https://github.com/USEPA/CompTox-ToxCast-tcpl
+Description: The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.
+URL: https://github.com/USEPA/CompTox-ToxCast-tcpl, https://www.epa.gov/comptox-tools/toxicity-forecasting-toxcast
 Depends:
     R (>= 3.5.0)
 Imports:
-    data.table (>= 1.9.4),
+    data.table (>= 1.15.0),
     DBI,
     RMariaDB,
     numDeriv,
@@ -42,7 +40,9 @@ Imports:
     tcplfit2,
     ggplot2,
     gridExtra,
-    stringr
+    stringr,
+    rlang,
+    ctxR
 Suggests:
     roxygen2,
     knitr,
@@ -55,10 +55,13 @@ Suggests:
     kableExtra,
     colorspace,
     magrittr,
-    vdiffr
+    vdiffr,
+    httptest,
+    rmdformats
 License: MIT + file LICENSE
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Encoding: UTF-8
 Config/testthat/edition: 3
+BugReports: https://github.com/USEPA/CompTox-ToxCast-tcpl/issues

NAMESPACE

@@ -8,7 +8,6 @@ export(tcplAddModel)
 export(tcplCode2CASN)
 export(tcplConf)
 export(tcplConfDefault)
-export(tcplConfExample)
 export(tcplConfList)
 export(tcplConfLoad)
 export(tcplConfReset)
@@ -26,8 +25,10 @@ export(tcplLoadAeid)
 export(tcplLoadAid)
 export(tcplLoadAsid)
 export(tcplLoadChem)
-export(tcplLoadClib)
+export(tcplLoadChemList)
+export(tcplLoadConcUnit)
 export(tcplLoadData)
+export(tcplLoadUnit)
 export(tcplLvlCount)
 export(tcplMakeAeidMultiPlts)
 export(tcplMakeAeidPlts)
@@ -43,10 +44,12 @@ export(tcplObjHill)
 export(tcplPlot)
 export(tcplPlotFitc)
 export(tcplPlotFits)
+export(tcplPlotLoadData)
 export(tcplPlotM4ID)
 export(tcplPlotPlate)
 export(tcplPrepOtpt)
 export(tcplQuery)
+export(tcplQueryAPI)
 export(tcplRegister)
 export(tcplRun)
 export(tcplSendQuery)
@@ -61,8 +64,12 @@ import(gridExtra)
 import(stringr)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(RMariaDB,MariaDB)
+importFrom(ctxR,get_all_assays)
+importFrom(ctxR,get_bioactivity_details_batch)
+importFrom(ctxR,register_ctx_api_key)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,.data)
+importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,as_tibble)
@@ -71,9 +78,11 @@ importFrom(dplyr,contains)
 importFrom(dplyr,ends_with)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
+importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
+importFrom(dplyr,matches)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_if)
 importFrom(dplyr,pull)
@@ -96,9 +105,11 @@ importFrom(ggplot2,ggsave)
 importFrom(ggplot2,guide_legend)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,margin)
+importFrom(ggplot2,scale_color_manual)
 importFrom(ggplot2,scale_color_viridis_d)
 importFrom(ggplot2,scale_linetype_manual)
 importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,unit)
 importFrom(ggplot2,xlab)
@@ -107,6 +118,7 @@ importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,graphics.off)
 importFrom(grDevices,pdf)
+importFrom(grDevices,pdf.options)
 importFrom(grDevices,rgb)
 importFrom(graphics,abline)
 importFrom(graphics,arrows)
@@ -133,6 +145,8 @@ importFrom(parallel,mclapply)
 importFrom(plotly,add_annotations)
 importFrom(plotly,add_trace)
 importFrom(plotly,plot_ly)
+importFrom(rlang,exec)
+importFrom(rlang,sym)
 importFrom(sqldf,sqldf)
 importFrom(stats,constrOptim)
 importFrom(stats,dist)
@@ -142,15 +156,16 @@ importFrom(stats,mad)
 importFrom(stats,median)
 importFrom(stats,optim)
 importFrom(stats,quantile)
-importFrom(stats,reformulate)
 importFrom(stats,setNames)
 importFrom(tcplfit2,tcplfit2_core)
 importFrom(tcplfit2,tcplhit2_core)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate_wider_delim)
+importFrom(tidyr,unnest)
+importFrom(tidyr,unnest_longer)
 importFrom(utils,data)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)
 importFrom(utils,tail)
-importFrom(utils,write.csv)
 importFrom(utils,write.table)

NEWS → NEWS.md

@@ -1,36 +1,50 @@
-tcpl v3.1.0
-==============
-*updated vignettes for tcplfit2 fitting
-*bidirectional fitting by default
-*this is the version used to create invitrodb v4.1
-
-tcpl v3.0.1
-==============
-*fixes error from ggplot2
-*minor bug fixes
-
-tcpl v3.0.0
-==============
-*add functionality for additional model fitting with tcplfit2
-*updated vignettes for new fitting
-*created updated plotting function
-
-tcpl v2.1.0
-==============
-*updated for release with toxcast invitrodb data
-*added option to allow change in single conc bmad calculation
-
-tcpl v2.0.3
-==============
-*Created tcplPlot a generic plotting function with call similar to tcplLoadData
-*added option for concentration units to be different during plotting.
-*fixed tcpllite bug for schema change
-*filtered gnls from tcplCytopt
-*updated to Rmariadb
-*various bugfixes
-
-tcpl v2.0.2
-==============
+# tcpl 3.2.0
+
+* Added a `NEWS.md` file to track changes to the package.
+* updated vignettes
+* Updated plotting including standalone and comparisons
+* Added bidirectional summary stats and updated functions to work with newest version of invitrodb
+* Added level 6 flags
+* Implemented API functionality
+* Removed tcplLite
+
+# tcpl 3.1.0
+
+* updated vignettes for tcplfit2 fitting
+* bidirectional fitting by default
+* this is the version used to create invitrodb v4.1
+
+# tcpl 3.0.1
+
+* fixes error from ggplot2
+
+* minor bug fixes
+
+# tcpl 3.0.0
+
+* add functionality for additional model fitting with tcplfit2
+
+* updated vignettes for new fitting
+
+* created updated plotting function
+
+# tcpl 2.1.0
+
+* updated for release with toxcast invitrodb data
+
+* added option to allow change in single conc bmad calculation
+
+# tcpl 2.0.3
+
+* Created tcplPlot a generic plotting function with call similar to tcplLoadData
+* added option for concentration units to be different during plotting.
+* fixed tcpllite bug for schema change
+* filtered gnls from tcplCytopt
+* updated to Rmariadb
+* various bugfixes
+
+# tcpl 2.0.2
+
 * Updated tcplLoadChem to return dsstox substance ids
 * Moved data.table to imports instead of depends
 * Added new level 6 method for flagging viability gnls winners
@@ -39,21 +53,24 @@ tcpl v2.0.2
 * Added ability to determine lowest effective concentration (loec) as level 5 method
 * Added new AEID plot functionality to visualize 2 aeids on same plot through tcplMakeAeidPlts
 
-tcpl v2.0.1
-==============
-Updated vignettes to use tempdir and thus not write to install folder.
+# tcpl 2.0.1
 
+* Updated vignettes to use tempdir and thus not write to install folder.
+
+
+# tcpl 2.0
 
-tcpl v2.0
-==============
 
 Major change for tcpl v2.0:
+
 * Incorporation of tcplLite into the package, a functionality that allows the user to work from local files formatted like invitrodb tables, rather than a MySQL database.
-	* Using tcplLite is ideal for handling smaller datasets. 
-	* The SQLite driver was removed from the package.
-	* tcplConf() default is now for tcplLite, which uses .csv files rather than tables in a MySQL database. 
-	* The MySQL driver is available and recommended for interacting with the entire dataset as a database. 
-	* The package vignettes run using tcplLite.
+
+* Using tcplLite is ideal for handling smaller datasets. 
+
+* The SQLite driver was removed from the package.
+* tcplConf() default is now for tcplLite, which uses .csv files rather than tables in a MySQL database. 
+* The MySQL driver is available and recommended for interacting with the entire dataset as a database. 
+* The package vignettes run using tcplLite.
 Additional updates for tcpl v2.0
 * tcplLvlCount: function added to count the samples at each level of processing for each aeid.
 * Addition of mc4 methods: the baseline median absolute deviation can now be calculated based on the lowest two concentrations or on the neutral control wells. An mc4 method must now be assigned for analysis.
@@ -63,8 +80,8 @@ Additional updates for tcpl v2.0
 * Vignettes are now posted as html from RMarkdown files for Introduction and appendices, data retrieval, and data processing.
 * Various bug fixes and additions to the methods tables.
 
-tcpl v1.4.0
-==============
+# tcpl 1.4.0
+
 
 Changes from v1.2.2
 
@@ -93,8 +110,8 @@ Changes from v1.2.2
 
 
 
-tcpl v1.2.3
-==============
+# tcpl 1.2.3
+
 
 Changes from v1.2.2
 
@@ -120,8 +137,8 @@ Changes from v1.2.2
   imports were removed to simplify the package, as they were found unnecessary.
   (PR#29)
 
-tcpl v1.2.2
-==============
+# tcpl 1.2.2
+
 
 Changes from v1.2
 
@@ -130,8 +147,8 @@ Changes from v1.2
   running the checks for the package. 
 
 
-tcpl v1.2 
-==============
+# tcpl 1.2 
+
 
 Changes from beta versions:
 

R/assay_funcs.R

@@ -19,12 +19,7 @@
 #' return the assay source ID (asid) and assay source name (asnm). 
 #' 
 #' @examples
-#' ## Store the current config settings, so they can be reloaded at the end 
-#' ## of the examples
-#' conf_store <- tcplConfList()
-#' TCPLlite <- file.path(system.file(package = "tcpl"), "example")
-#' tcplConf(db = TCPLlite, user = NA, host = NA, drvr = "tcplLite")
-#' 
+#' \dontrun{
 #' ## The load assay functions can be used without any parameters to list the 
 #' ## full list of registered assay elements:
 #' tcplLoadAsid()
@@ -43,9 +38,7 @@
 #' a1 <- tcplLoadAeid(fld = "anm", val = "Steroidogenesis")
 #' a2 <- tcplLoadAeid(fld = "assay_name", val = "Steroidogenesis")
 #' identical(a1, a2)
-#' 
-#' ## Reset configuration
-#' options(conf_store)
+#' }
 #' 
 #' @return A data.table containing the ID, name, and any additional fields.
 NULL