Package: morseDR 0.1.2

morseDR: Bayesian Inference of Binary, Count and Continuous Data in Toxicology

Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of several type of toxicological data. 'binary' (e.g., survival, mobility), 'count' (e.g., reproduction) and 'continuous' (e.g., growth as length, weight). Estimation procedures can be used without a deep knowledge of their underlying probabilistic model or inference methods. Rather, they were designed to behave as well as possible without requiring a user to provide values for some obscure parameters. That said, models can also be used as a first step to tailor new models for more specific situations.

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

morseDR_0.1.2.tar.gz
morseDR_0.1.2.zip(r-4.7)morseDR_0.1.2.zip(r-4.6)morseDR_0.1.2.zip(r-4.5)
morseDR_0.1.2.tgz(r-4.6-any)morseDR_0.1.2.tgz(r-4.5-any)
morseDR_0.1.2.tar.gz(r-4.7-any)morseDR_0.1.2.tar.gz(r-4.6-any)
morseDR_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
morseDR/json (API)

# Install 'morseDR' in R:
install.packages('morseDR', repos = c('https://virgile-baudrot.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • cadmium_daphnia - Continuous response of toxicity test of cadmium on Daphnia
  • 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
  • chlordan_daphnia - Continuous response of toxicity test of chlordan on Daphnia
  • copper - Reproduction and survival data sets of chronic laboratory toxicity tests of copper on Daphnia
  • copper_daphnia - Continuous response of toxicity test of copper on Daphnia
  • dichromate - Survival data set of chronic laboratory toxicity tests of dichromate with Daphnia
  • plant01 - Continuous response of toxicity test on plants
  • plant02 - Continuous response of toxicity test on plants
  • plant03 - Continuous response of toxicity test on plants
  • plant04 - Continuous response of toxicity test on plants
  • plant05 - Continuous response of toxicity test on plants
  • plant06 - Continuous response of toxicity test on plants
  • plant07 - Continuous response of toxicity test on plants
  • plant08 - Continuous response of toxicity test on plants
  • plant09 - Continuous response of toxicity test on plants
  • plant10 - Continuous response of toxicity test on plants
  • propiconazole - Survival data set of chronic laboratory toxicity tests of propiconazole with Gammarus pulex
  • reco27 - Continuous response of toxicity test
  • subst01_lymnaea - Continuous response of toxicity test on snails
  • zinc - Reproduction and survival data sets of a chronic laboratory toxicity tests of zinc with Daphnia
  • zinc_daphnia - Continuous response of toxicity test of zinc on Daphnia

On CRAN:

Conda:

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

jagscpp

3.00 score 3 scripts 520 downloads 15 exports 20 dependencies

Last updated from:c4a4ecc1e6. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK154
source / vignettesOK356
linux-release-x86_64OK150
macos-release-arm64OK130
macos-oldrel-arm64OK147
windows-develOK130
windows-releaseOK100
windows-oldrelOK101
wasm-releaseOK110

Exports:binaryDatabinaryDataCheckcontinuousDatacontinuousDataCheckcountDatacountDataCheckdoseResponseextract_simfitmodelDataposteriorppcpredictpriorPosteriorxcx

Dependencies:clicodacpp11farverggplot2gluegtableisobandlabelinglatticelifecycleR6RColorBrewerrjagsrlangS7scalesvctrsviridisLitewithr

Dose-Response models in the morseDR package
DR modelling of binary data | Target-time DR analysis of binary data | Modelling | Inference | DR modelling of count data | Estimation of the effective observation period | Target-time DR analysis of count data | DR modelling of quantitative continuous data | Target-time DR analysis of quantitative continuous data

Last update: 2025-05-29
Started: 2025-05-29

Tutorial
Binary data analysis | Step 1: check the structure and the dataset integrity | Step 2: create a BinaryData object | Step 3: visualise the raw data | Step 4: fit an exposure-response model to the survival data at target time | Plot fitting results | Step 5: the posterior predictive check as a goodness-of-fit criterion | Prior Posterior representation | Correlation plot | Goodness of Fit | Count data analysis | Model comparison | Count data versus binary data dedicated functions | Quantitative continuous data analysis | Load growth data | Dose-response plot of quantitative conitnuous data | Inference | Posterior Predictive Check (PPC)

Last update: 2025-05-29
Started: 2025-05-29

Readme and manuals

Help Manual

Help pageTopics
Continuous response of toxicity test of cadmium on Daphniacadmium_daphnia
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
Checking object structure for analysisbinaryDataCheck CheckData continuousDataCheck countDataCheck
Reproduction and survival data sets of chronic laboratory toxicity tests of chlordan with Daphniachlordan
Continuous response of toxicity test of chlordan on Daphniachlordan_daphnia
Reproduction and survival data sets of chronic laboratory toxicity tests of copper on Daphniacopper
Continuous response of toxicity test of copper on Daphniacopper_daphnia
Survival data set of chronic laboratory toxicity tests of dichromate with Daphniadichromate
Prepare data for Dose-ReponseDoseResponse doseResponse doseResponse.BinaryData doseResponse.ContinuousData doseResponse.CountData
Extract simulation from the fitextract_sim
Fits a Bayesian concentration-response model for target-timefit fit.BinaryData fit.ContinuousData fit.CountData FitTT
Creates a data set for binary data analysisbinaryData binaryData.data.frame continuousData continuousData.data.frame countData countData.data.frame ModelData modelData modelData.data.frame
Continuous response of toxicity test on plantsplant01
Continuous response of toxicity test on plantsplant02
Continuous response of toxicity test on plantsplant03
Continuous response of toxicity test on plantsplant04
Continuous response of toxicity test on plantsplant05
Continuous response of toxicity test on plantsplant06
Continuous response of toxicity test on plantsplant07
Continuous response of toxicity test on plantsplant08
Continuous response of toxicity test on plantsplant09
Continuous response of toxicity test on plantsplant10
Plotting method for 'BinaryData', 'CountData' or 'ContinuousData'.plot.BinaryData plot.ContinuousData plot.CountData PlotData
Plot dose-response from 'DoseResponse' objectsplot.BinaryDoseResponse plot.ContinuousDoseResponse plot.CountDoseResponse plot.DoseResponse PlotDoseResponse
Plotting method for 'FitTT' objects.plot.BinaryFitTT plot.ContinuousFitTT plot.CountFitTT PlotFitTT
Plot the Posterior Predictive Chack on an object 'PPC'plot.PPC PlotPPC
Plot an object 'XCX'plot.XCX PlotRiskMeasure
Posterior Predictive Check data.frame for 'FitTT' objectsPPC ppc ppc.BinaryFitTT ppc.ContinuousFitTT ppc.CountFitTT
Prediction base on 'FitTT'Predict predict predict.BinaryFitTT predict.ContinuousFitTT predict.CountFitTT
Return Prior and Posterior density of parameters of 'FitTT' objectplot.PriorPosterior posterior posterior.FitTT PriorPosterior priorPosterior priorPosterior.BinaryFitTT priorPosterior.ContinuousFitTT priorPosterior.CountFitTT
Survival data set of chronic laboratory toxicity tests of propiconazole with Gammarus pulexpropiconazole
Continuous response of toxicity testreco27
Predict X% Concentration at the target time (default).RiskMeasure xcx xcx.FitTT
Continuous response of toxicity test on snailssubst01_lymnaea
Summary of 'FitTT' objectSummary summary.BinaryFitTT summary.ContinuousFitTT summary.CountFitTT summary.PPC
Reproduction and survival data sets of a chronic laboratory toxicity tests of zinc with Daphniazinc
Continuous response of toxicity test of zinc on Daphniazinc_daphnia