Refactor R functions, enhance README, and update documentation#47
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hreinwald wants to merge 126 commits intoDoseResponse:masterfrom
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Refactor R functions, enhance README, and update documentation#47hreinwald wants to merge 126 commits intoDoseResponse:masterfrom
hreinwald wants to merge 126 commits intoDoseResponse:masterfrom
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- README.md: Complete rewrite with package overview, installation, quick start examples, available models, key functions, and supported data types - drmEMstandard.R: Remove active print() debug statements in opfct() and remove dead if(FALSE) code block (~170 lines of experimental scratch code) - findbe.r: Remove active print(c(bVal, eVal)) debug statement in findbe2() - llogistic.ssf.R: Remove dead if(FALSE) code block (~200 lines of stale logic) - searchdrc.R: Fix unsafe options(warn=-1) usage with on.exit() for guaranteed warning state restoration - noEffect.R: Fix unscoped variable reference 'resp' in Poisson branch - rdrm.r: Replace eval(parse(text=...)) code injection with match.fun/do.call Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
…or-functions Add comprehensive README and refactor poorly coded R functions
The /tests folder contained ad-hoc scripts from 2007-2009 that were development artifacts, not proper package tests: - No testing framework (no testthat, no RUnit) - No assertions or expected output comparisons - seedGerminationMods.R was 100% commented out - test2.r was mostly commented out since May 2009 - Old commented-out Windows absolute paths - No other package files reference the tests/ folder Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
…lder Remove /tests folder (development artifacts)
Can be safely removed. Not needed for the package dev
… remove redundant reference files Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
Update .gitignore and .Rbuildignore with standard R package settings
…md, _pkgdown.yml Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
Remove obsolete base-level files
First dev merge to main
Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
…ws-file Add news file entry summarizing all fork changes from upstream
Summarize all fork changes in news file
…s, add missing Imports Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
…pace-files Fix DESCRIPTION format: add Encoding, fix Authors@R, remove deprecated fields
…>'e2' in ursa, 'contain'->'contents' in EDcomp, 'mising'->'missing' and 'reponses'->'responses' in drm.Rd, 'reponse'->'response' in CRS.5a.Rd Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
Add roxygen2 comment blocks before the function definitions in drm() and drmc(), based on the existing hand-written .Rd man pages. Only comments are added; no function code is modified. No @export tags are included since the package uses a hand-written NAMESPACE file. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Add roxygen2 headers (#' comments) before function definitions in four R source files based on their corresponding .Rd man pages: - R/ED.drc.R: ED generic and ED.drc method with full param/details docs - R/EDcomp.R: EDcomp with full docs; fieller, splitInd, createsifct marked as @Keywords internal - R/compParm.R: compParm with full param/return/examples docs - R/comped.r: comped with full param/return/examples docs No @export tags added. No function code modified. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Add roxygen2 headers (#' comments) before function definitions in: - plot.drc.R: main plot.drc function with full param/details/examples - predict.drc.R: predict.drc function - summary.drc.R: summary.drc function - anova.drc.R: main anova.drc function - coef.drc.R: coef.drc function - confint.drc.R: confint.drc function - fitted.drc.R: fitted.drc function - residuals.drc.R: residuals.drc function - logLik.drc.R: logLik.drc function - vcov.drc.R: main vcov.drc function Documentation derived from corresponding .Rd man pages. No @export tags added. Function code unchanged. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Add roxygen2 headers (#' comments) before function definitions in: - update.drc.R: update.drc function - print.drc.R: print.drc function - print.summary.drc.R: print.summary.drc function - hatvalues.drc.R: hatvalues.drc function - cooks.distance.drc.R: cooks.distance.drc function (undocumented) - boxcox.drc.R: boxcox.drc main function only - sandwich.r: estfun.drc and bread.drc functions - modelFit.R: modelFit function only - mselect.r: mselect function - noEffect.R: noEffect function Documentation derived from corresponding .Rd man pages. No @export tags added. No function code modified. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
…utput Verify drm() output matches drm_legacy() with comprehensive tests
Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
…overview Update README: Add CRS.4/CRS.5/CRS.6 models and fix dependencies
Updated installation instructions for the drc package.
…d=TRUE Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
… p-values Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
…mprehensive anova tests Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
Fix mselect lack-of-fit always zero and handle negative F statistics in anova
Updated installation instructions for CRAN and GitHub.
Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
…uthors Add Hannes Reinwald as package author
…026-03-11) Co-authored-by: hreinwald <115988583+hreinwald@users.noreply.github.com>
Add missing news entries for dev branch changes (2026-03-09 through 2026-03-11)
Added new changes and updates to the 'drc' package, including bug fixes, new features, and documentation improvements.
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This pull request introduces a comprehensive update to the package, including new model functions, improvements to documentation, expanded export/imports, and updates to package metadata. The main themes are: expanding dose-response modeling capabilities, improving documentation and usability, updating package infrastructure, and enhancing compatibility with modern R standards.
Dose-response modeling enhancements:
Added new model functions such as
CRS.6(generalized Cedergreen-Ritz-Streibig model for hormesis), additional variants for Cedergreen models, and new helper/model functions for effective dose calculations (ED.drc,ED.lin,EDhelper) and relative potency comparisons (EDcomp,fieller,splitInd,createsifct). All new functions are documented with roxygen comments for clarity and usability. [1] [2] [3] [4] [5] [6] [7] [8]Expanded the list of exported functions in
NAMESPACEto include new and previously unexported models and utilities, improving accessibility for users.Documentation and usability improvements:
Package infrastructure and compatibility:
Updated
DESCRIPTIONfor new version (3.3.0), new author, modern R dependency (>=4.0.0), updated URLs, encoding, roxygen version, testthat configuration, and additional suggested packages.Improved
.Rbuildignoreto exclude more files and folders, and removed.travis.ymlfor modern CI compatibility. [1] [2]Namespace and S3 methods updates:
mrdrcclass and additional confint, plot, print, ED methods, and improved imports for graphics, MASS, sandwich, lifecycle, and utils.These changes collectively modernize the package, expand its modeling capabilities, and improve its usability and maintainability for dose-response analysis in R.