Package: morseTKTD 0.1.3

morseTKTD: Bayesian Inference of TKTD Models

Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of survival Data with toxicokinetics toxicodynamics (TKTD) models. Among others, it facilitates Bayesian inference of the general unified threshold model of survival (GUTS). See models description in Jager et al. (2011) <doi:10.1021/es103092a> and implementation using Bayesian inference in Baudrot and Charles (2019) <doi:10.1038/s41598-019-47698-0>.

Authors:Virgile Baudrot [aut, cre], Sandrine Charles [aut], Marie Laure Delignette-Muller [aut], Benoit Goussen [ctb], Nils Kehrein [ctb], Guillaume Kon-Kam-King [ctb], Christelle Lopes [ctb], Alexander Singer [ctb], Philippe Veber [aut]

morseTKTD_0.1.3.tar.gz
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morseTKTD_0.1.3.tgz(r-4.6-x86_64)morseTKTD_0.1.3.tgz(r-4.6-arm64)morseTKTD_0.1.3.tgz(r-4.5-x86_64)morseTKTD_0.1.3.tgz(r-4.5-arm64)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
morseTKTD/json (API)

# Install 'morseTKTD' in R:
install.packages('morseTKTD', repos = c('https://virgile-baudrot.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • cadmium1 - Reproduction and survival data sets of chronic laboratory toxicity tests of cadmium with Daphnia
  • cadmium2 - Reproduction and survival data sets of chronic laboratory toxicity tests of cadmium with snails
  • chlordan - Reproduction and survival data sets of chronic laboratory toxicity tests of chlordan with Daphnia
  • copper - Reproduction and survival data sets of chronic laboratory toxicity tests of copper on Daphnia
  • dichromate - Survival data set of chronic laboratory toxicity tests of dichromate with Daphnia
  • FOCUSprofile - A simulated exposure profile with 11641 time points using FOCUS model.
  • propiconazole - Survival data set of chronic laboratory toxicity tests of propiconazole with Gammarus pulex
  • propiconazole_pulse_exposure - Survival data set of chronic laboratory toxicity tests of propiconazole with Gammarus pulex
  • zinc - Reproduction and survival data sets of a chronic laboratory toxicity tests of zinc with Daphnia

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

3.00 score 6 scripts 258 downloads 24 exports 62 dependencies

Last updated from:b02e0105e5. Checks:12 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK360
linux-devel-x86_64OK421
source / vignettesOK592
linux-release-arm64OK366
linux-release-x86_64OK433
macos-release-arm64OK218
macos-release-x86_64OK699
macos-oldrel-arm64OK302
macos-oldrel-x86_64OK743
windows-develOK504
windows-releaseOK505
windows-oldrelOK498
wasm-releaseFAIL209

Exports:build_priorscompute_Ninitcompute_Nsurvextract_Nsurv_ppcextract_Nsurv_simextract_paramfitis_exposure_constantis.betweenlcxtlpxtmodelDatappcpredictpredict_cstITpredict_cstSDpredict_SurvFitCstExppredict_SurvFitVarExppredict_varITpredict_varSDpriorPosteriorpriors_distributionsurvDatasurvDataCheck

Dependencies:abindbackportsBHbriocallrcheckmateclicpp11crayondescdeSolvediffobjdistributionalevaluatefarverfsgenericsggplot2gluegridExtragtableinlineisobandjsonlitelabelinglatticelifecycleloomagrittrmatrixStatsnumDerivotelpillarpkgbuildpkgconfigpkgloadposteriorpraiseprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrprojrootrstanrstantoolsS7scalesStanHeaderstensorAtestthattibbleutf8vctrsviridisLitewaldowithrzoo

Models
Survival toxicity tests | Toxicokinetic-Toxicodynamic modeling | GUTS Modelling | GUTS-SD | GUTS-IT | For constant concentration exposure | Inference
Rendered frommodels.Rmdusingknitr::rmarkdown

Last update: 2025-06-04
Started: 2025-06-04

Tutorial
Survival analysis using a toxicokinetic-toxicodynamic (TKTD) model: GUTS | GUTS model with constant exposure concentrations | GUTS model "SD" | Extract Nsurv | Fix background mortality | GUTS model "IT" | Computing prediction | Computing Nsurv on prediction | Removing background mortality in predictions | Validation criteria: EFSA recommendations | Computing predictions with number of survivors | Validation criteria | Plot and PPC of predict_Nsurv objects | Additional options for EFSA user | Lethal concentration | Multiplication factors: 'margin of safety' | Change the level of multiplication factor | Change the default time of multiplication factor assessment
Rendered fromtutorial.Rmdusingknitr::rmarkdown

Last update: 2025-06-04
Started: 2025-06-04

Readme and manuals

Help Manual

Help pageTopics
The 'morseTKTD' package.morseTKTD-package morseTKTD
build sub-dataframe of Nsurv without NAbuild_dN
build sub-dataframe of concentration without NAbuild_dX
Reproduction and survival data sets of chronic laboratory toxicity tests of cadmium with Daphniacadmium1
Reproduction and survival data sets of chronic laboratory toxicity tests of cadmium with snailscadmium2
Set of function to test conformity of dataCheckData checking_table check_concentration check_concNsurv check_Nsurv check_time check_TimeNsurv is.between is_exposure_constant
Reproduction and survival data sets of chronic laboratory toxicity tests of chlordan with Daphniachlordan
Compute post value on objectComputePredictSurvFit compute_Ninit compute_Nsurv compute_Nsurv.SurvPredict
Reproduction and survival data sets of chronic laboratory toxicity tests of copper on Daphniacopper
Survival data set of chronic laboratory toxicity tests of dichromate with Daphniadichromate
Extraction methods to recover output of fit object.Extract extract_Nsurv_ppc extract_Nsurv_sim extract_param priors_distribution priors_distribution.SurvFit
A simulated exposure profile with 11641 time points using FOCUS model.FOCUSprofile
build array with indices of rowsgroup_array
Predict Lethal Concentration at any specified time point.LCxt lcxt lcxt.SurvFit
Lethal Profile calculationLPxt lpxt lpxt.SurvFit update.LPxt
Create a list giving data to use in Bayesian inference.build_priors build_stanData ModelData modelData modelData.SurvData
Plotting method for 'survDataVar' objectsplot.SurvDataCstExp plot.SurvDataVarExp PlotData
Plot of the LCxt objectplot.LCxt PlotLCxt
Plot of the LPxt objectplot.LPxt PlotLPxt
Plot an object 'PPC'plot.PPC PlotPPC
Plotting method for 'SurvPredict' objectsplot.SurvPredict PlotPredictSurvFit
Plot of Prior and Posterior distributionsplot.PriorPosterior PlotPriorPosterior
Posterior predictive check methodsPPC ppc ppc.SurvFit
Prediction base on 'SurvFit' objectspredict predict.SurvFit PredictSurvFit predict_cstIT predict_cstSD predict_SurvFitCstExp predict_SurvFitVarExp predict_varIT predict_varSD
Return Prior and Posterior density of parameters of 'SurvFit' objectPriorPosterior priorPosterior priorPosterior.SurvFit
Survival data set of chronic laboratory toxicity tests of propiconazole with Gammarus pulexpropiconazole
Survival data set of chronic laboratory toxicity tests of propiconazole with Gammarus pulexpropiconazole_pulse_exposure
Creates a data set for survival analysisSurvData survData survData.data.frame
Checks if an object can be used to perform survival analysisSurvDataCheck survDataCheck
Fits a TKTD model for survival analysis using Bayesian inferencefit fit.SurvDataCstExp fit.SurvDataVarExp plot.SurvFit SurvFit
Table of posterior estimated parameterssurvFit_TKTD_params
Internal predict functionSurvIT_cst
Internal predict functionSurvIT_var
Internal predict functionSurvSD_cst
Internal predict functionSurvSD_var
Reproduction and survival data sets of a chronic laboratory toxicity tests of zinc with Daphniazinc