add level 3 method resp.censormed.neg25

.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")'

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)
+    }
 
 
 

R/tcplSubsetChid.R

@@ -92,9 +92,9 @@ tcplSubsetChid <- function(dat, flag = TRUE, type = "mc", export_ready = FALSE)
     }
     if (!"casn" %in% names(dat)) dat <- tcplPrepOtpt(dat)
     # for now we treat all >=.9 hitcall equally
-    dat[, hitc := hitc >= .9]
-    dat[, chit := mean(hitc[hitc %in% 0:1]) >= 0.5, by = list(aeid, chid)]
-    dat <- dat[hitc == chit | (is.na(chit) & (hitc == -1 | is.na(m4id)))]
+    dat[, actc := hitc >= .9]
+    dat[, chit := mean(actc[actc %in% 0:1]) >= 0.5, by = list(aeid, chid)]
+    dat <- dat[actc == chit | (is.na(chit) & (actc == -1 | is.na(m4id)))]
 
 
     dat[, fitc.ordr := NA_integer_]

README.Rmd

@@ -21,7 +21,7 @@ knitr::opts_chunk$set(
 [![Active](http://img.shields.io/badge/Status-Active-green.svg)](https://cran.r-project.org/package=tcpl) 
 [![Monthly Downloads](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)
 [![DOI](https://zenodo.org/badge/doi/	10.32614/CRAN.package.tcpl.svg)](http://dx.doi.org/10.32614/CRAN.package.tcpl)
-
+[![R-CMD-check](https://github.com/USEPA/CompTox-ToxCast-tcpl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/USEPA/CompTox-ToxCast-tcpl/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ## Welcome to the GitHub repository for the tcpl package.

README.md

@@ -10,7 +10,7 @@
 [![Monthly
 Downloads](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)](https://cranlogs.r-pkg.org/badges/last-month/tcpl?color=7BAFD4)
 [![DOI](https://zenodo.org/badge/doi/%2010.32614/CRAN.package.tcpl.svg)](http://dx.doi.org/10.32614/CRAN.package.tcpl)
-
+[![R-CMD-check](https://github.com/USEPA/CompTox-ToxCast-tcpl/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/USEPA/CompTox-ToxCast-tcpl/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ## Welcome to the GitHub repository for the tcpl package.