151 cran 310 release (#152)

* updated docs * added github to buildignore * added documentation for invitrodb_dd data file * updated version number * fixes variable binding note * moved vdiffr from imports to suggests since it is only used in tests and not required to use the package normally * added default multi for old style plots * accepted and resolved minor snapshot test difference based on testing environment * updated news and cran-comments * added additional rhub to cran comments
USEPA · Oct 6, 2023 · 8f8a646 · 8f8a646
1 parent fcd4354
commit 8f8a646
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,4 @@ cran-comments.md
 ^CRAN-SUBMISSION$
 ^data-raw$
 ^LICENSE\.md$
+^\.github$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: tcpl
 Title: ToxCast Data Analysis Pipeline
-Version: 3.0.1
+Version: 3.1.0
 Authors@R: c(
     person("Richard S", "Judson",role = c("ctb","ths"), email = "Judson.Richard@epa.gov"),
     person("Dayne L", "Filer", role = "aut",email = "dayne.filer@gmail.com"),
@@ -42,8 +42,7 @@ Imports:
     tcplfit2,
     ggplot2,
     gridExtra,
-    stringr,
-    vdiffr
+    stringr
 Suggests:
     roxygen2,
     knitr,
@@ -55,7 +54,8 @@ Suggests:
     viridis,
     kableExtra,
     colorspace,
-    magrittr
+    magrittr,
+    vdiffr
 License: MIT + file LICENSE
 LazyData: true
 RoxygenNote: 7.2.3

diff --git a/NAMESPACE b/NAMESPACE
@@ -81,6 +81,7 @@ importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tibble)
+importFrom(dplyr,ungroup)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)
@@ -147,6 +148,7 @@ importFrom(tcplfit2,tcplfit2_core)
 importFrom(tcplfit2,tcplhit2_core)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
+importFrom(utils,data)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)
 importFrom(utils,tail)

diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+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

diff --git a/R/data.R b/R/data.R
@@ -459,3 +459,14 @@
 #'   }
 #' }
 "sc_vignette"
+
+
+#' Short descriptions of fields for different tables are stored in a data dictionary.
+#' @format A data frame with 44 rows and 3 variables:
+#' \describe{
+#'  \item{invitrodb_table}{Table of the data dictionary}
+#'   \item{invitrodb_field}{Field of the data dictionary}
+#'    \item{description}{Description}
+#' }
+#' @source ToxCast database
+"invitrodb_dd"
diff --git a/R/mc6.R b/R/mc6.R
@@ -20,7 +20,7 @@
 mc6 <- function(ae, wr = FALSE) {
 
   ## Variable-binding to pass R CMD Check
-  mthd_id <- m4id <- m5id <- lval <- rval <- J <- mthd <- bmad <- cell_viability_assay <- NULL
+  modl <- aeid <- mthd_id <- m4id <- m5id <- lval <- rval <- J <- mthd <- bmad <- cell_viability_assay <- NULL
 
   #owarn <- getOption("warn")
   #options(warn = 1)

diff --git a/R/sc2.R b/R/sc2.R
@@ -23,7 +23,7 @@
 sc2 <- function(ae, wr = FALSE) {
 
   ## Variable-binding to pass R CMD Check
-  bmad <- resp <- wllt <- tmp <- spid <- logc <- hitc <- max_med <- NULL
+  max_tmp <- bmad <- resp <- wllt <- tmp <- spid <- logc <- hitc <- max_med <- NULL
 
   owarn <- getOption("warn")
   options(warn = 1)

diff --git a/R/tcplCytoPt.R b/R/tcplCytoPt.R
@@ -114,7 +114,7 @@ tcplCytoPt <- function(chid = NULL, aeid = NULL, flag = TRUE,
 
   ## Variable-binding to pass R CMD Check
   ac50var <- hitc <- code <- chnm <- casn <- used_in_global_mad_calc <- nhit <- modl <- NULL
-  ntst <- global_mad <- cyto_pt <- med <- cyto_pt_um <- lower_bnd_um <- burstpct <- NULL
+  top <- ntst <- global_mad <- cyto_pt <- med <- cyto_pt_um <- lower_bnd_um <- burstpct <- NULL
 
   cat("1: Checking if aeid or chid is specified\n")
   if (!is.null(aeid) & !is.vector(aeid)) {

diff --git a/R/tcplDefine.R b/R/tcplDefine.R
@@ -47,14 +47,18 @@
 #' parameters.
 #' 
 #' @import data.table
+#' @importFrom utils data
+#' 
 #' @export
 
 tcplDefine <- function(val = NULL) {
 
   drvr <- getOption("TCPL_DRVR")
+  invitrodb_dd <- NULL
 
   # example driver
   if (drvr == "example"){
+    data("invitrodb_dd", envir=environment())
 
     dd <- invitrodb_dd[]
 

diff --git a/R/tcplFit2.R b/R/tcplFit2.R
@@ -51,12 +51,13 @@ tcplFit2 <- function(dat,
 #' 
 #'
 #' @return Data.table with key value pairs of hitcalling parameters
-#' @importFrom dplyr %>% filter group_by summarise left_join inner_join select rowwise mutate pull
+#' @importFrom dplyr %>% filter group_by summarise left_join inner_join select rowwise mutate pull ungroup
 #' @importFrom tidyr pivot_longer
 #' @importFrom tcplfit2 tcplhit2_core
 tcplHit2 <- function(mc4, coff) {
 
   #variable binding
+  top <- a <- b <- ga <- la <- p <- tp <- logc_min <- logc_max <- fitc <- NULL
   model <- m4id  <-model_param  <-model_val  <-resp  <- NULL
   params  <-conc  <-bmed  <-onesd  <-df  <-aeid  <- NULL
   fit_method  <-hitcall  <-cutoff  <-top_over_cutoff  <-bmd  <-hit_val <- NULL
@@ -103,7 +104,7 @@ tcplHit2 <- function(mc4, coff) {
   res <- res %>%
     rowwise() %>%
     mutate(ac95 = tcplfit2::acy(.95 * top, list(a = a, b = b, ga = ga, la = la, p = p, q = q, tp = tp)[!is.na(list(a = a, b = b, ga = ga, la = la, p = p, q = q, tp = tp))], fit_method)) %>%
-    ungroup()
+    dplyr::ungroup()
   res <- res %>% mutate(coff_upper = 1.2 * cutoff, coff_lower = .8 * cutoff)
   res <- res %>%
     left_join(mc4 %>% select(m4id, logc_min, logc_max) %>% unique(), by = "m4id") %>%

diff --git a/R/tcplLoadData.R b/R/tcplLoadData.R
@@ -75,12 +75,13 @@
 #'
 #' @import data.table
 #' @importFrom tidyr pivot_wider
+#' @importFrom utils data
 #' @export
 
 tcplLoadData <- function(lvl, fld = NULL, val = NULL, type = "mc", add.fld = TRUE) {
   #variable binding
   model <- model_param <- model_val <- NULL
-  hit_param <- hit_val <- NULL
+  hit_param <- hit_val <- sc_vignette <- mc_vignette <- NULL
 
   if (length(lvl) > 1 | length(type) > 1) {
     stop("'lvl' & 'type' must be of length 1.")
@@ -91,6 +92,7 @@ tcplLoadData <- function(lvl, fld = NULL, val = NULL, type = "mc", add.fld = TRU
   drvr <- getOption("TCPL_DRVR")
   if (drvr == "example"){
     if (type == "sc"){
+      data("sc_vignette", envir = environment())
       if (lvl == 0L) {
         sc0 <- sc_vignette[["sc0"]]
         sc0 <- sc0[,c("s0id","spid","acid","apid","rowi","coli","wllt","wllq","conc","rval","srcf")]
@@ -118,6 +120,7 @@ tcplLoadData <- function(lvl, fld = NULL, val = NULL, type = "mc", add.fld = TRU
     }
 
     if (type == "mc" ) {
+      data("mc_vignette", envir = environment())
       if (lvl == 0L) {
         mc0 <- mc_vignette[["mc0"]]
         mc0 <- mc0[,c("m0id","spid","acid","apid","rowi","coli","wllt","wllq","conc","rval","srcf")]

diff --git a/R/tcplPlot.R b/R/tcplPlot.R
@@ -55,7 +55,7 @@
 #' options(conf_store)
 tcplPlot <- function(lvl = 5, fld = "m4id", val = NULL, type = "mc", by = NULL, output = c("console", "pdf", "png", "jpg", "svg", "tiff"), fileprefix = paste0("tcplPlot_", Sys.Date()), multi = NULL, verbose = FALSE, nrow = NULL, ncol = NULL, dpi = 600) {
   #variable binding
-  resp <- NULL
+  conc_unit <- bmd <- resp <- NULL
   # check_tcpl_db_schema is a user-defined function found in v3_schema_functions.R file
   if (check_tcpl_db_schema()) {
     # check that input combination is unique
@@ -148,6 +148,9 @@ tcplPlot <- function(lvl = 5, fld = "m4id", val = NULL, type = "mc", by = NULL,
     }
 
   } else {
+    if(is.null(multi)){
+      multi <- FALSE
+    }
     if (length(lvl) > 1 | !lvl %in% 4:7) stop("invalid lvl input.")
     if (length(output) > 1) output <- output[1]
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,20 +1,38 @@
-Minor release for fixing errors on CRAN
-Some small bug fixes included
+3.1.0 Release integrates package tcplfit2 bidirectional fitting a major update that impacts resulting invitrodb database
 
 ## Test environments
 
-* local Windows 10 install, R 4.2.1
-* R Under development (unstable) (2022-10-11 r83083 ucrt)
+* local Windows 10 install, R 4.2.2
+* R Under development (unstable) (2023-10-04 r85267 ucrt)
+* Rhub Windows Server 2022, R-devel, 64 bit
 * Rhub Fedora Linux, R-devel, clang, gfortran
 * Rhub Ubuntu Linux 20.04.1 LTS, R-release, GCC
-* Rhub Windows Server 2022, R-devel, 64 bit
 
 ## rhub CMD check results
-- Note appears to be related to testing environment
+- All notes appear to be related to testing (rhub) environment
+Found the following (possibly) invalid URLs:
+  URL: https://www.epa.gov/chemical-research/exploring-toxcast-data-downloadable-data
+    From: inst/doc/Data_retrieval.html
+          inst/doc/Introduction_Appendices.html
+    Status: 403
+    Message: Forbidden
+  URL: https://www.epa.gov/chemical-research/toxicity-forecasting
+    From: inst/doc/Introduction_Appendices.html
+    Status: 403
+    Message: Forbidden
+* checking HTML version of manual ... [13s] NOTE
+Skipping checking math rendering: package 'V8' unavailable
+* checking for non-standard things in the check directory ... NOTE
+Found the following files/directories:
+  ''NULL''
 * checking for detritus in the temp directory ... NOTE
 Found the following files/directories:
   'lastMiKTeXException'
 
+## win devel check results
+1 NOTE - Found the following (possibly) invalid URLs...
+All links appear to work correctly when hyperlinked from the vignette, similar note to the rhub testing
+
 ## local R CMD check results
 
 0 ERRORs | 0 WARNINGs | 0 NOTES.

diff --git a/man/MC2_Methods.Rd b/man/MC2_Methods.Rd
diff --git a/man/MC4_Methods.Rd b/man/MC4_Methods.Rd
diff --git a/man/invitrodb_dd.Rd b/man/invitrodb_dd.Rd