Merge branch 'dev' into 215-add-ggplot-output-option-to-tcplPlot

.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

@@ -2,30 +2,28 @@ Package: tcpl
 Title: ToxCast Data Analysis Pipeline
 Version: 3.1.0
 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,
@@ -44,7 +42,7 @@ Imports:
     gridExtra,
     stringr,
     rlang,
-    ccdR
+    ctxR
 Suggests:
     roxygen2,
     knitr,
@@ -58,7 +56,8 @@ Suggests:
     colorspace,
     magrittr,
     vdiffr,
-    httptest
+    httptest,
+    rmdformats
 License: MIT + file LICENSE
 LazyData: true
 RoxygenNote: 7.3.1

NAMESPACE

@@ -8,7 +8,6 @@ export(tcplAddModel)
 export(tcplCode2CASN)
 export(tcplConf)
 export(tcplConfDefault)
-export(tcplConfExample)
 export(tcplConfList)
 export(tcplConfLoad)
 export(tcplConfReset)
@@ -26,7 +25,7 @@ export(tcplLoadAeid)
 export(tcplLoadAid)
 export(tcplLoadAsid)
 export(tcplLoadChem)
-export(tcplLoadClib)
+export(tcplLoadChemList)
 export(tcplLoadData)
 export(tcplLvlCount)
 export(tcplMakeAeidMultiPlts)
@@ -43,6 +42,7 @@ export(tcplObjHill)
 export(tcplPlot)
 export(tcplPlotFitc)
 export(tcplPlotFits)
+export(tcplPlotLoadData)
 export(tcplPlotM4ID)
 export(tcplPlotPlate)
 export(tcplPrepOtpt)
@@ -62,9 +62,9 @@ import(gridExtra)
 import(stringr)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(RMariaDB,MariaDB)
-importFrom(ccdR,get_all_assays)
-importFrom(ccdR,get_bioactivity_details_batch)
-importFrom(ccdR,register_ccdr)
+importFrom(ctxR,get_all_assays)
+importFrom(ctxR,get_bioactivity_details_batch)
+importFrom(ctxR,register_ctx_api_key)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,.data)
 importFrom(dplyr,all_of)

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

R/chemQueries.R

@@ -61,18 +61,19 @@
 #-------------------------------------------------------------------------------
 
 #-------------------------------------------------------------------------------
-# .ClibQ: Create tcplLoadClib query string 
+# .ChemListQ: Create tcplLoadChemList query string 
 #-------------------------------------------------------------------------------
 
-.ClibQ <- function(field, val) {
+.ChemListQ <- function(field, val) {
 
-  qformat <- "SELECT chid, clib FROM chemical_library"
+  qformat <- "SELECT * FROM chemical_lists"
 
   if (!is.null(field)) {
 
     nfld <- switch(field,
                    chid = "chid",
-                   clib = "clib")
+                   dsstox_substance_id = "dsstox_substance_id",
+                   list_acronym = "list_acronym")
 
     qformat <- paste(qformat, "WHERE %s IN (%s);")
     qstring <- sprintf(qformat, nfld, paste0("\"", val, "\"", collapse = ","))
@@ -88,6 +89,6 @@
 }
 
 #-------------------------------------------------------------------------------
-# END .ClibQ
+# END .ChemListQ
 #-------------------------------------------------------------------------------
 

R/config_funcs.R

@@ -14,8 +14,8 @@
 #' @param ... Additional arguments that should be passed to dbConnect function
 #' 
 #' @details
-#' Currently, the tcpl package only supports the "MySQL" and "tcplLite" database
-#' drivers.
+#' Currently, the tcpl package supports the "MySQL", "example", and "API" 
+#' database drivers.
 #' 
 #' The settings can be stored in a configuration file to make the using the 
 #' package more user-friendly. To create the configuration file, the user must
@@ -48,8 +48,7 @@
 #' configuration file.
 #' 
 #' \code{tcplConfDefault} changes the \code{options} to reflect the default
-#' settings for the example tcplLite database, i.e. local directory, but does  
-#' not alter the configuration file.
+#' settings for the API connection, but does not alter the configuration file.
 #' 
 #' \code{tcplConfReset} is used to generate the initial configuration script,
 #' and can be used to reset or regenerate the configuration script by the user.