r-tcpl - v3.3.0

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 generated by the US EPA’s Toxicity Forecaster (ToxCast) program. tcpl can be used to support diverse chemical screening efforts.

tcpl v3.3.0, along with the dependency package tcplfit2 v0.1.8, was used to process data in invitrodb v4.3. ToxCast’s invitrodb v4.3 (anticipated Fall 2025) as well as past versions are available for download here: https://www.epa.gov/chemical-research/exploring-toxcast-data.

Updates

• 🚀 Plotting updates #325
  • tcplPlot() gains a compare parameter, which replaces the compare.val parameter, for selecting a plot-data field by which samples are grouped into comparison plots. tcplPlot() also gains group.fld, group.threshold, and hide_losing_models parameters, providing more customizability to comparison and individual concentration-response plots alike.
• 🚀Data retrieval updates: tcplLoadData(), and by extension tcplPlot() and tcplPlotLoadData(), now support chemical queries via the fld parameter #162
• 🚀 Data processing improvements:
  • Level 4 fields nmed_gtbl_neg (number of median responses greater than baseline in the negative direction) and nmed_gtbl_pos (same in the positive direction) are now correctly calculated #340
  • tcplRun() gains a ready_only parameter to only process endpoints annotated with export_ready = 1 #333. Note: This update supports internal workflows.
• 🚀 Methods updates:
  • New Level 5 LOEC (lowest observed effective concentration) methods, ow_loec.coff and include_loec.coff #312 #348
  • New single-concentration method Level 2 pc40 #310
  • New Level 3 method resp.censormed.neg25 #301
• 🚀 Add z-score calculation as output in tcplVarMat() variable matrices #334
• 🐞Refine representative sample logic under tcplSubsetChid to prevent overwriting hitcalls. The continuous hitcall is now preserved as a binary actc value #302
• 🐞Level 3 multi- and level 1 single-concentration processing now retains un-rounded concentrations #332
• 🐞Improve Level 6 model directionality flag is improved #341
• 🛠️ Developer tools, such as DEV branch versioning, CRAN checks, and unit testing #303 #307 #318 #328 #329 #353
• 📄 Vignette updates #320 #321 #349 #354 #357
  • Vignette now uses flag descriptions in place of flag names to be more clear, includes an image detailing visual examples of flags, and contains examples showcasing new tcplPlot() functionality, among many other small, general improvements.
• 📄 General package documentation updates #331 #351

Full Changelog: https://github.com/USEPA/CompTox-ToxCast-tcpl/compare/v3.2.0...v3.3.0

Contributors

@cthunes @brown-jason @madison-feshuk @sedavid01 @ElizabethGilson @knuppla @Kelly-Carstens-EPA @kpaulfriedman

New Contributors

• @ElizabethGilson made their first contribution in https://github.com/USEPA/CompTox-ToxCast-tcpl/pull/318
• @knuppla made their first contribution in https://github.com/USEPA/CompTox-ToxCast-tcpl/pull/349

Emoji Legend

🚀 Feature - this is a new feature or improvement to the existing application 🧪 In Progress - a feature actively under development; may not yet be available in production 🐞 Bug - fixed an error in the current software 📄 Documentation - updated user/developer documentation 🔒 Security Updates - security related updates 🛠️ Developer Tools - updated internal tooling for a better developer experience

- R
Published by madison-feshuk 10 months ago

r-tcpl - v3.2.0

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 generated by the US EPA’s Toxicity Forecaster (ToxCast) program. tcpl can be used to support diverse chemical screening efforts.

tcpl v3.2.0, along with the dependency package tcplfit2 v0.1.7, was used to process data in invitrodb v4.2. ToxCast’s invitrodb v4.2 (September 2024) is available for download here: https://www.epa.gov/chemical-research/exploring-toxcast-data.

Updates

• 🚀 Integration with the Computational Toxicology and Exposure (CTX) Bioactivity API via the ctxR package #221 #233 #257 #273 #283
• 🚀 Plotting updates #146 #153 #160 #167 #168 #171 #174 #204 #229 #242 #274
• 🚀 Data processing logic improvements #126 #129 #158 #170 #181 #199 #205 #209 #222
• 🚀 Updates related to schema changes and backwards compatibility #135 #139 #173 #205 #209 #214 #222 #225 #262 #277
  • Logged conc (logc) --> conc #188 #177 #179 #183
  • Chemical Lists #270
• 🚀 Methods updates #123 #129 #130 #136 #138 #143 #194 #195 #220 #239 #243 #261
• 🚀 Cytotoxicity Burst #141 #269 #279
• 🚀 Variable Matrices #186 #264
• 🛠️ Unit tests #282
• 📄 Vignette updates #201 #240 #260 #271 #287 #289 #292
• 📄 General package documentation updates #159 #157 #295 #298 #299

Full Changelog: https://github.com/USEPA/CompTox-ToxCast-tcpl/compare/v3.1.0...v3.2.0

Contributors

@brown-jason @cthunes @madison-feshuk @Ashley-Ko @sedavid01 @gracezhihuizhao @Kelly-Carstens-EPA @kpaulfriedman

New Contributors

• @Kelly-Carstens-EPA made their first contribution in https://github.com/USEPA/CompTox-ToxCast-tcpl/pull/261
• @gracezhihuizhao made their first contribution in https://github.com/USEPA/CompTox-ToxCast-tcpl/pull/240

Emoji Legend

🚀 Feature - this is a new feature or improvement to the existing application 🧪 In Progress - a feature actively under development; may not yet be available in production 🐞 Bug - fixed an error in the current software 📄 Documentation - updated user/developer documentation 🔒 Security Updates - security related updates 🛠️ Developer Tools - updated internal tooling for a better developer experience

- R
Published by madison-feshuk over 1 year ago

r-tcpl - v3.1.0

fy23 final release with updated docs

- R
Published by brown-jason over 2 years ago