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morse

Modelling Tools for Reproduction and Survival Data in Ecotoxicology

Tools for ecotoxicologists and regulators dedicated to the mathematical and statistical modelling of toxicity test data. They use advanced and innovative methods for a valuable quantitative environmental risk assessment. See also Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>. and Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464>.

Functions (63)

FOCUSprofile

A simulated exposure profile with 11641 time points.

LCX

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

MFx

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

PPC

Posterior predictive check plot

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

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)

modelData

Create a list giving data to use in Bayesian inference.

modelData.survDataCstExp

Create a data set to analyse a survDataCstExp object.

modelData.survDataVarExp

Create a data set to analyse a survDataVarExp object.

morse-package

MOdelling tools for Reproduction and Survival data in Ecotoxicology

plot.LCx

Plotting method for LCx objects

plot.MFx

Plotting method for MFx objects

plot.reproData

Plotting method for reproData objects

plot.reproFitTT

Plotting method for reproFitTT objects

plot.survDataCstExp

Plotting method for survData objects

plot.survDataVarExp

Plotting method for survDataVarExp objects

plot.survFitCstExp

Plotting method for survFit objects

plot.survFitPredict

Plotting method for survFitPredict objects

plot.survFitPredict_Nsurv

Plotting method for survFitPredict_Nsurv objects.

plot.survFitTKTD

Plotting method for survFitTKTD objects

plot.survFitTT

Plotting method for survFitTT objects

plot.survFitVarExp

Plotting method for survFit objects

plotDoseResponse

Plot dose-response from raw data

plotDoseResponse.reproData

Plot dose-response from reproData objects

plotDoseResponse.survDataCstExp

Plot dose-response from survData objects

plot_prior_post

Generic method to plot priors and posteriors.

plot_prior_post.survFit

Plot posteriors vs priors

predict

Predict method for survFit objects

predict_check

Checking goodness-of-fit method for survFitPredict and survFitPredict_Nsurv objects

predict_ode

Predict method for survFit objects

predict_ode.survFit

Predict method for survFit objects

print.reproFitTT

Print of reproFitTT object

print.survFitCstExp

Print of survFit object

print.survFitTKTD

Print of survFitTKTD object

print.survFitTT

Print of survFitTT object

print.survFitVarExp

Print of survFitVarExp object

priors_distribution

Density distribution of priors.

priors_distribution.survFit

Density distribution of priors from a survFit object.

priors_survData

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

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 (non-standard pulsed toxicity experiments)

propiconazole_split

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

reproData

Creates a dataset for reproduction toxicity analysis

reproDataCheck

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

reproFitTT

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

summary.reproData

Summary of reproData object

summary.reproFitTT

Summary of reproFitTT object

summary.survDataCstExp

Summary of survDataCstExp object

summary.survDataVarExp

Summary of survDataVarExp object

summary.survFit

Summary of survFit object

summary.survFitTKTD

Summary of survFitTKTD object

summary.survFitTT

Summary of survFitTT object

survData

Creates a data set for survival analysis

survData_join

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

survFit

Fits a TKTD model for survival analysis using Bayesian inference

survFitTKTD

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

survFitTT

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

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

morse

Modelling Tools for Reproduction and Survival Data in Ecotoxicology

v3.3.1

GPL (>= 2)

Authors

Virgile Baudrot [aut], 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 [aut], Alexander Singer [ctb], Philippe Veber [aut]

Initial release

morse

Functions (63)

morse

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