Package: tcplfit2 0.1.7

Jason Brown

tcplfit2: A Concentration-Response Modeling Utility

The tcplfit2 R package performs basic concentration-response curve fitting. The original tcplFit() function in the tcpl R package performed basic concentration-response curvefitting to 3 models. With tcplfit2, the core tcpl concentration-response functionality has been expanded to process diverse high-throughput screen (HTS) data generated at the US Environmental Protection Agency, including targeted ToxCast, high-throughput transcriptomics (HTTr) and high-throughput phenotypic profiling (HTPP). tcplfit2 can be used independently to support analysis for diverse chemical screening efforts.

Authors:Thomas Sheffield [aut], Richard S Judson [ctb], Jason Brown [cre], Sarah E. Davidson [ctb], Zhihui Zhao [ctb], Madison Feshuk [ctb], Katie Paul Friedman [ctb]

tcplfit2_0.1.7.tar.gz
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tcplfit2.pdf |tcplfit2.html✨
tcplfit2/json (API)
NEWS

# Install 'tcplfit2' in R:
install.packages('tcplfit2', repos = c('https://usepa.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/usepa/comptox-toxcast-tcplfit2/issues

Datasets:
  • mc0 - Sample multi-concentration data set from invitrodb
  • mc3 - Sample concentration-response data set from invitrodb
  • signatures - Sample concentration-response data set from HTTR

On CRAN:

comptoxord

6.76 score 2 stars 1 packages 24 scripts 489 downloads 43 exports 34 dependencies

Last updated 7 days agofrom:f7828db298. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winOKNov 14 2024
R-4.5-linuxOKNov 14 2024
R-4.4-winOKNov 14 2024
R-4.4-macOKNov 14 2024
R-4.3-winOKNov 14 2024
R-4.3-macOKNov 14 2024

Exports:acgnlsobjacybmdboundsbmdobjcnstconcRespCoreconcRespPlotconcRespPlot2exp2exp3exp4exp5fitcnstfitexp2fitexp3fitexp4fitexp5fitgnlsfithillfitpoly1fitpoly2fitpowget_AUCgnlsgnlsderivobjhillfnhitconthitcontinnerhitlogichitloginnerloggnlsloghillnestselectplot_allcurvespoly1poly2poly2bmdspost_hit_AUCpowtcplfit2_coretcplhit2_coretcplObjtoplikelihood

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmenumDerivpillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

tcplfit2: A Concentration-Response Modeling Utility

US EPA's Center for Computational Toxicology and Exposure [email protected]

Rendered fromtcplfit2-vignette.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-09-23
Started: 2020-01-07

Readme and manuals

Help Manual

Help pageTopics
AC GNLS Objective Functionacgnlsobj
Activity Concentration yacy
BMD Boundsbmdbounds
BMD Objective Functionbmdobj
Constant Modelcnst
Concentration Response CoreconcRespCore
Concentration Response PlotconcRespPlot
Concentration Response Plot - ggplot2concRespPlot2
Exponential 2 Modelexp2
Exponential 3 Modelexp3
Exponential 4 Modelexp4
Exponential 5 Modelexp5
Constant Model Fitfitcnst
Exponential 2 Model Fitfitexp2
Exponential 3 Model Fitfitexp3
Exponential 4 Model Fitfitexp4
Exponential 5 Model Fitfitexp5
Gain-Loss Model Fitfitgnls
Hill Model Fitfithill
Polynomial 1 (Linear) Model Fitfitpoly1
Polynomial 2 (Quadratic) Model Fitfitpoly2
Power Model Fitfitpow
Calculate Area Under the Curve (AUC)get_AUC
Gain-Loss Modelgnls
GNLS Derivative Objective Functiongnlsderivobj
Hill Modelhillfn
Continuous Hitcallshitcont
Continuous Hitcalls Innerhitcontinner
Hit Logic (Discrete)hitlogic
Hit Logic Inner (Discrete)hitloginner
Log Gain-Loss Modelloggnls
Log Hill Modelloghill
Sample multi-concentration data set from invitrodbmc0
Sample concentration-response data set from invitrodbmc3
Nest Selectnestselect
Plot All Curves Fit with tcplfit2_core - ggplot2plot_allcurves
Polynomial 1 Modelpoly1
Polynomial 2 Modelpoly2
Polynomial 2 Model (BMDS)poly2bmds
Calculate Area Under the Curve After Hit-callingpost_hit_AUC
Power Modelpow
Sample concentration-response data set from HTTRsignatures
Concentration-response curve fittingtcplfit2_core
Hitcalling Functiontcplhit2_core
Concentration Response Objective FunctiontcplObj
Top Likelihoodtoplikelihood