Package: morse 3.3.5

morse: Modelling Reproduction and Survival Data in Ecotoxicology

Advanced methods for a valuable quantitative environmental risk assessment using Bayesian inference of survival and reproduction Data. Among others, it facilitates Bayesian inference of the general unified threshold model of survival (GUTS). See our companion paper Baudrot and Charles (2021) <doi:10.21105/joss.03200>, as well as complementary details in Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464> and Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>.

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

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
morse/json (API)

# Install 'morse' in R:
install.packages('morse', 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:
  • cadmium1 - Reproduction and survival data sets for _Daphnia magna_ exposed to cadmium during 21 days
  • cadmium2 - Reproduction and survival data sets for _Lymnaea stagnalis_ exposed to cadmium during 28 days
  • chlordan - Reproduction and survival data sets for _Daphnia magna_ exposed to chlordan during 21 days
  • copper - Reproduction and survival data sets for _Daphnia magna_ exposed to copper during 21 days
  • dichromate - Survival data set for _Daphnia magna_ exposed to dichromate during 21 days
  • FOCUSprofile - A simulated exposure profile with 11641 time points.
  • propiconazole - Survival data set for _Gammarus pulex_ exposed to propiconazole during four days
  • propiconazole_pulse_exposure - Survival data set for _Gammarus pulex_ exposed to propiconazole during 10 days with time-variable exposure concentration
  • propiconazole_split - Survival data set for _Gammarus pulex_ exposed to propiconazole during four days
  • zinc - Reproduction and survival data sets for _Daphnia magna_ exposed to zinc during 21 days

On CRAN:

Conda:

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

jagscpp

3.32 score 70 scripts 646 downloads 1 mentions 22 exports 39 dependencies

Last updated from:d19063f296. Checks:13 OK. Indexed: yes.

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linux-release-arm64OK275
linux-release-x86_64OK216
macos-release-arm64OK191
macos-release-x86_64OK293
macos-oldrel-arm64OK125
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Exports:is_exposure_constantLCxMFxMFx_odeplot_prior_postplotDoseResponseppcpredict_Nsurvpredict_Nsurv_checkpredict_Nsurv_odepredict_odepriors_distributionpriors_survDatareproDatareproDataCheckreproFitTTsurvDatasurvData_joinsurvDataChecksurvFitsurvFitTKTDsurvFitTT

Dependencies:clicodacpp11deSolvedplyrepitoolsfarvergenericsggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrpillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2rjagsrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrzoo

Models in 'morse' package
Survival toxicity tests | Analysis of target time survival toxicity tests | Modelling | Inference | Toxicokinetic-Toxicodynamic modeling | GUTS Modelling | GUTS-SD | GUTS-IT | For constant concentration exposure | Reproduction toxicity tests | Estimation of the effective observation period | Target time analysis | References
Rendered frommodelling.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2022-10-28

How to generate a Minimal Working Example
Please report any issue | Loading morse and its dependencies (JAGS, C++) | JAGS | C++ | Survival analysis | Fit | ... with plot | LCx | MFX | Predict survival probability | Predict number of survival
Rendered fromMinimalWorkingExample.Rmdusingknitr::rmarkdown

Last update: 2024-09-19
Started: 2021-01-27

Tutorial
Survival data analysis at target time (TT) | Step 1: check the structure and the data set integrity | Step 2: create a survData object | Step 3: visualize your data set | Step 4: fit an exposure-response model to the survival data at target time | Step 5: validate the model with a posterior predictive check | Survival analysis using a toxicokinetic-toxicodynamic (TKTD) model: GUTS | GUTS model with constant exposure concentrations | GUTS model "SD" | Fix background mortality | GUTS model "IT" | GUTS model under time-variable exposure concentration | Computing prediction | Robust ODE solver with deSolve | Removing background mortality in predictions | Validation criteria: EFSA recommendations | Computing predictions with number of survivors | Robust implementation with ODE solver predict_Nsurv_ode | 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 | Compute a range of multiplication factors | Multiplication factor when hb is fixed | Reproduction data analysis at target-time | Model comparison | Reproduction data and survival functions
Rendered fromtutorial.Rmdusingknitr::rmarkdown

Last update: 2024-09-19
Started: 2015-09-01

Readme and manuals

Help Manual

Help pageTopics
MOdelling tools for Reproduction and Survival data in Ecotoxicologymorse-package morse
Reproduction and survival data sets for _Daphnia magna_ exposed to cadmium during 21 dayscadmium1
Reproduction and survival data sets for _Lymnaea stagnalis_ exposed to cadmium during 28 dayscadmium2
Reproduction and survival data sets for _Daphnia magna_ exposed to chlordan during 21 dayschlordan
Reproduction and survival data sets for _Daphnia magna_ exposed to copper during 21 dayscopper
Survival data set for _Daphnia magna_ exposed to dichromate during 21 daysdichromate
A simulated exposure profile with 11641 time points.FOCUSprofile
Test in a well-formed argument to function 'survData' if the concentration is constant and different from 'NA' for each replicate (each time-serie)is_exposure_constant
Predict X% Lethal Concentration at the maximum time point (default).LCx LCx.survFit
Predict the Multiplication Factor leading to x% of reduction in survival at a specific time.MFx MFx.survFit MFx_ode MFx_ode.survFit
Create a list giving data to use in Bayesian inference.modelData modelData.survDataCstExp modelData.survDataVarExp
Generic method to plot priors and posteriors.plot_prior_post
Plot posteriors vs priorsplot_prior_post.survFit
Plotting method for 'LCx' objectsplot.LCx
Plotting method for 'MFx' objectsplot.MFx
Plotting method for 'reproData' objectsplot.reproData
Plotting method for 'reproFitTT' objectsplot.reproFitTT
Plotting method for 'survData' objectsplot.survDataCstExp
Plotting method for 'survDataVarExp' objectsplot.survDataVarExp
Plotting method for 'survFit' objectsplot.survFitCstExp
Plotting method for 'survFitPredict' objectsplot.survFitPredict
Plotting method for 'survFitPredict_Nsurv' objects.plot.survFitPredict_Nsurv
Plotting method for 'survFitTKTD' objectsplot.survFitTKTD
Plotting method for 'survFitTT' objectsplot.survFitTT
Plotting method for 'survFit' objectsplot.survFitVarExp
Plot dose-response from raw dataplotDoseResponse
Plot dose-response from 'reproData' objectsplotDoseResponse.reproData
Plot dose-response from 'survData' objectsplotDoseResponse.survDataCstExp
Posterior predictive check plotppc ppc.reproFitTT ppc.survFitCstExp ppc.survFitPredict_Nsurv ppc.survFitTKTD ppc.survFitTT ppc.survFitVarExp
Checking goodness-of-fit method for 'survFitPredict' and 'survFitPredict_Nsurv' objectspredict_Nsurv_check predict_Nsurv_check.survFitPredict_Nsurv
Predict method for 'survFit' objectspredict_ode
Predict method for 'survFit' objectspredict_ode.survFit
Predict method for 'survFit' objectspredict predict.survFit predict_Nsurv predict_Nsurv.survFit predict_Nsurv_ode predict_Nsurv_ode.survFit
Print 'msgTables' objectsprint.msgTable
Print of 'reproFitTT' objectprint.reproFitTT
Print of 'survFit' objectprint.survFitCstExp
Print of 'survFitTKTD' objectprint.survFitTKTD
Print of 'survFitTT' objectprint.survFitTT
Print of 'survFitVarExp' objectprint.survFitVarExp
Density distribution of priors.priors_distribution
Density distribution of priors from a 'survFit' object.priors_distribution.survFit
Create a list of scalars giving priors to use in Bayesian inference.priors_survData
Survival data set for _Gammarus pulex_ exposed to propiconazole during four dayspropiconazole
Survival data set for _Gammarus pulex_ exposed to propiconazole during 10 days with time-variable exposure concentration (non-standard pulsed toxicity experiments)propiconazole_pulse_exposure
Survival data set for _Gammarus pulex_ exposed to propiconazole during four dayspropiconazole_split
Creates a dataset for reproduction toxicity analysisreproData
Checks if an object can be used to perform reproduction toxicity data analysisreproDataCheck
Fits a Bayesian concentration-effect model for target-time reproduction analysisreproFitTT
Summary of 'reproData' objectsummary.reproData
Summary of 'reproFitTT' objectsummary.reproFitTT
Summary of 'survDataCstExp' objectsummary.survDataCstExp
Summary of 'survDataVarExp' objectsummary.survDataVarExp
Summary of 'survFit' objectsummary.survFit
Summary of 'survFitTKTD' objectsummary.survFitTKTD
Summary of 'survFitTT' objectsummary.survFitTT
Creates a data set for survival analysissurvData survDataCheck
Joins a concentration with a survival data set into an argument for 'survData' when the concentration varies over timesurvData_join
Fits a TKTD model for survival analysis using Bayesian inferencesurvFit survFit.survDataCstExp survFit.survDataVarExp
Fits a TKTD for survival analysis using Bayesian inference for 'survDataTKTD' objectsurvFitTKTD
Fits a Bayesian concentration-response model for target-time survival analysissurvFitTT
Fits a Bayesian concentration-response model for target-time survival analysissurvFitTT.survDataCstExp
Reproduction and survival data sets for _Daphnia magna_ exposed to zinc during 21 dayszinc