merge conflicts

Author: brown-jason

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

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

@@ -42,7 +42,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

DESCRIPTION

@@ -42,7 +42,7 @@ Imports:
     gridExtra,
     stringr,
     rlang,
-    ctxR
+    ctxR (>= 1.1.0)
 Suggests:
     roxygen2,
     knitr,

R/chemQueries.R

@@ -2,6 +2,18 @@
 # .ChemQ: Create tcplLoadChem query string 
 #-------------------------------------------------------------------------------
 
+#' @title Function to support queries by chemical
+#' @note This function is not exported and not intended to be used by the user.
+#' 
+#' @param field Character, the field to query on
+#' @param val Vector of values to subset on
+#' @param exact Logical, should chemical names be considered exact?
+#' 
+#' @description
+#' \code{.ChemQ} creates tcplLoadChem query string
+#' 
+#' @seealso \code{\link{tcplLoadData}}
+#' @seealso \code{\link{tcplLoadChem}}
 .ChemQ <- function(field, val, exact) {
 
   qformat <- 
@@ -29,11 +41,11 @@
       if (exact) {
         qformat <- paste(qformat, "chnm IN (%s);")
         val <- paste0("\"", val, "\"", collapse = ",")
-        qstring <- sprintf(qformat, val, val)
+        qstring <- sprintf(qformat, val)
       } else {
         qformat <- paste(qformat, "chnm RLIKE %s;")
         val <- paste0("\"", paste(val, collapse = "|"), "\"")
-        qstring <- sprintf(qformat, val, val)
+        qstring <- sprintf(qformat, val)
       }
     } else if (nfld == 'chem.only') {
       qstring <- "
@@ -64,6 +76,16 @@
 # .ChemListQ: Create tcplLoadChemList query string 
 #-------------------------------------------------------------------------------
 
+#' @title Function to support queries by chemical
+#' @note This function is not exported and not intended to be used by the user.
+#' 
+#' @param field Character, the field to query on
+#' @param val Vector of values to subset on
+#' 
+#' @description
+#' \code{.ChemListQ} creates tcplLoadChemList query string
+#' 
+#' @seealso \code{\link{tcplLoadChemList}}
 .ChemListQ <- function(field, val) {
 
   qformat <- "SELECT * FROM chemical_lists"
@@ -90,5 +112,4 @@
 
 #-------------------------------------------------------------------------------
 # END .ChemListQ
-#-------------------------------------------------------------------------------
-
+#-------------------------------------------------------------------------------

R/mc3.R

@@ -55,9 +55,6 @@ mc3 <- function(ac, wr = FALSE) {
 
   stime <- Sys.time()
 
-  ## Force all concentrations to 1 significant figure
-  dat[ , conc := signif(conc, 1)]
-
   ## Load aeid mapping information.
   aeid_info <- tcplLoadAeid("acid", ac)[ , list(acid, aeid)]
   setkey(aeid_info, acid)

R/mc3_mthds.R

@@ -185,6 +185,8 @@
 #'      \eqn{resp=cval/bval-1}{resp = cval/bval - 1}. Typically used for increasing responses.}
 #'     \item{resp.mult100}{Multiply the normalized response value (resp) by 100; 
 #'      \eqn{100*resp}{100*resp}.}
+#'    `\item{resp.censormed.neg25}{Censor (remove) response values from 
+#'      concentrations which median falls below -25.}
 #'   }
 #' }
 #'
@@ -692,7 +694,15 @@ mc3_mthds <- function() {
       e1 <- bquote(dat[J(.(aeids)), pval := -100,
                        by=list(aeid)])
       list(e1)
-      }
+      },
+    
+    resp.censormed.neg25 = function(aeids) {
+      
+      e1 <- bquote(dat[J(.(aeids)), med := median(resp), by=list(aeid,spid,conc)])
+      e2 <- bquote(dat <- dat[med >= -25])
+      e3 <- bquote(dat[ , med := NULL])
+      list(e1,e2,e3)
+    }