diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..19c1af2 --- /dev/null +++ b/.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: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/R/mc3_mthds.R b/R/mc3_mthds.R index 983776b..6469856 100644 --- a/R/mc3_mthds.R +++ b/R/mc3_mthds.R @@ -185,6 +185,8 @@ #' \eqn{resp=cval/bval-1}{resp = cval/bval - 1}. Typically used for increasing responses.} #' \item{resp.mult100}{Multiply the normalized response value (resp) by 100; #' \eqn{100*resp}{100*resp}.} +#' `\item{resp.censormed.neg25}{Censor (remove) response values from +#' concentrations which median falls below -25.} #' } #' } #' @@ -692,7 +694,15 @@ mc3_mthds <- function() { e1 <- bquote(dat[J(.(aeids)), pval := -100, by=list(aeid)]) list(e1) - } + }, + + resp.censormed.neg25 = function(aeids) { + + e1 <- bquote(dat[J(.(aeids)), med := median(resp), by=list(aeid,spid,conc)]) + e2 <- bquote(dat <- dat[med >= -25]) + e3 <- bquote(dat[ , med := NULL]) + list(e1,e2,e3) + } diff --git a/R/tcplSubsetChid.R b/R/tcplSubsetChid.R index d71365d..f360dd5 100644 --- a/R/tcplSubsetChid.R +++ b/R/tcplSubsetChid.R @@ -92,9 +92,9 @@ tcplSubsetChid <- function(dat, flag = TRUE, type = "mc", export_ready = FALSE) } if (!"casn" %in% names(dat)) dat <- tcplPrepOtpt(dat) # for now we treat all >=.9 hitcall equally - dat[, hitc := hitc >= .9] - dat[, chit := mean(hitc[hitc %in% 0:1]) >= 0.5, by = list(aeid, chid)] - dat <- dat[hitc == chit | (is.na(chit) & (hitc == -1 | is.na(m4id)))] + dat[, actc := hitc >= .9] + dat[, chit := mean(actc[actc %in% 0:1]) >= 0.5, by = list(aeid, chid)] + dat <- dat[actc == chit | (is.na(chit) & (actc == -1 | is.na(m4id)))] dat[, fitc.ordr := NA_integer_] diff --git a/README.Rmd b/README.Rmd index 774259f..11ae8ba 100644 --- a/README.Rmd +++ b/README.Rmd @@ -21,7 +21,7 @@ knitr::opts_chunk$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) ## Welcome to the GitHub repository for the tcpl package. diff --git a/README.md b/README.md index 40cf4fb..1e81c83 100644 --- a/README.md +++ b/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) ## Welcome to the GitHub repository for the tcpl package. diff --git a/man/MC3_Methods.Rd b/man/MC3_Methods.Rd index edb2986..40d9c18 100644 --- a/man/MC3_Methods.Rd +++ b/man/MC3_Methods.Rd @@ -189,6 +189,8 @@ available in the package vignette, "Data_processing." \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.} } } }