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morse (version 3.3.4)

Modelling Reproduction and Survival Data in Ecotoxicology

Description

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) , as well as complementary details in Baudrot et al. (2018) and Delignette-Muller et al. (2017) .

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Install

install.packages('morse')

Monthly Downloads

599

Version

3.3.4

License

MIT + file LICENSE

Maintainer

Virgile Baudrot

Last Published

September 18th, 2024

Functions in morse (3.3.4)

plotDoseResponse

Plot dose-response from raw data
plotDoseResponse.reproData

Plot dose-response from reproData objects
plot_prior_post

Generic method to plot priors and posteriors.
plotDoseResponse.survDataCstExp

Plot dose-response from survData objects
predict_Nsurv_check

Checking goodness-of-fit method for survFitPredict and survFitPredict_Nsurv objects
predict.survFit

Predict method for survFit objects
plot_prior_post.survFit

Plot posteriors vs priors
predict_ode

Predict method for survFit objects
plot.survFitTT

Plotting method for survFitTT objects
priors_distribution

Density distribution of priors.
print.survFitTT

Print of survFitTT object
plot.survFitVarExp

Plotting method for survFit objects
print.survFitTKTD

Print of survFitTKTD object
print.survFitVarExp

Print of survFitVarExp object
plot.survFitPredict

Plotting method for survFitPredict objects
propiconazole_split

Survival data set for Gammarus pulex exposed to propiconazole during four days
print.survFitCstExp

Print of survFit object
summary.survFitTT

Summary of survFitTT object
print.reproFitTT

Print of reproFitTT object
propiconazole

Survival data set for Gammarus pulex exposed to propiconazole during four days
plot.survFitPredict_Nsurv

Plotting method for survFitPredict_Nsurv objects.
plot.survFitTKTD

Plotting method for survFitTKTD objects
predict_ode.survFit

Predict method for survFit objects
print.msgTable

Print msgTables objects
propiconazole_pulse_exposure

Survival data set for Gammarus pulex exposed to propiconazole during 10 days with time-variable exposure concentration (non-standard pulsed toxicity experiments)
reproDataCheck

Checks if an object can be used to perform reproduction toxicity data analysis
summary.reproData

Summary of reproData object
summary.survFitTKTD

Summary of survFitTKTD object
summary.survFit

Summary of survFit object
summary.reproFitTT

Summary of reproFitTT object
survFitTT.survDataCstExp

Fits a Bayesian concentration-response model for target-time survival analysis
zinc

Reproduction and survival data sets for Daphnia magna exposed to zinc during 21 days
reproData

Creates a dataset for reproduction toxicity analysis
survData

Creates a data set for survival analysis
summary.survDataCstExp

Summary of survDataCstExp object
summary.survDataVarExp

Summary of survDataVarExp object
priors_distribution.survFit

Density distribution of priors from a survFit object.
survFit

Fits a TKTD model for survival analysis using Bayesian inference
survData_join

Joins a concentration with a survival data set into an argument for 'survData' when the concentration varies over time
priors_survData

Create a list of scalars giving priors to use in Bayesian inference.
survFitTT

Fits a Bayesian concentration-response model for target-time survival analysis
survFitTKTD

Fits a TKTD for survival analysis using Bayesian inference for survDataTKTD object
reproFitTT

Fits a Bayesian concentration-effect model for target-time reproduction analysis
LCx

Predict \(X\)% Lethal Concentration at the maximum time point (default).
dichromate

Survival data set for Daphnia magna exposed to dichromate during 21 days
MFx

Predict the Multiplication Factor leading to x% of reduction in survival at a specific time.
is_exposure_constant

Test in a well-formed argument to function 'survData' if the concentration is constant and different from NA for each replicate (each time-serie)
ppc

Posterior predictive check plot
copper

Reproduction and survival data sets for Daphnia magna exposed to copper during 21 days
FOCUSprofile

A simulated exposure profile with 11641 time points.
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
cadmium1

Reproduction and survival data sets for Daphnia magna exposed to cadmium during 21 days
plot.survDataVarExp

Plotting method for survDataVarExp objects
modelData

Create a list giving data to use in Bayesian inference.
plot.survFitCstExp

Plotting method for survFit objects
plot.MFx

Plotting method for MFx objects
plot.LCx

Plotting method for LCx objects
plot.survDataCstExp

Plotting method for survData objects
plot.reproData

Plotting method for reproData objects
plot.reproFitTT

Plotting method for reproFitTT objects
morse-package

MOdelling tools for Reproduction and Survival data in Ecotoxicology