Modelling Tools for Reproduction and Survival Data in Ecotoxicology


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Documentation for package ‘morse’ version 3.2.2

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morse-package MOdelling tools for Reproduction and Survival data in Ecotoxicology
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)
LCx Predict X% Lethal Concentration at the maximum time point (default).
LCx.survFit Predict x% Lethal Concentration at any specified time point for a 'survFit' object.
MFx Predict the Multiplication Factor leading to x% of reduction in survival at a specific time.
MFx.survFit Predict x% Multiplication Factor at any specified time point for a 'survFit' object.
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 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
ppc Posterior predictive check plot
ppc.reproFitTT Posterior predictive check plot for 'reproFitTT' objects
ppc.survFitCstExp Posterior predictive check plot for 'survFitCstExp' objects
ppc.survFitPredict_Nsurv Posterior predictive check plot for 'survFitPredict_Nsurv' objects
ppc.survFitTKTD Posterior predictive check plot for 'survFitTKTD' objects
ppc.survFitTT Posterior predictive check plot for 'survFitTT' objects
ppc.survFitVarExp Posterior predictive check plot for 'survFitVarExp' objects
predict.survFit Predict method for 'survFit' objects
predict_Nsurv 'Predict_Nsurv' method for 'survFit' objects
predict_Nsurv.survFit 'Predict_Nsurv' method for 'survFit' objects
predict_Nsurv_check Checking goodness-of-fit method for 'survFitPredict' and 'survFitPredict_Nsurv' objects
predict_Nsurv_check.survFitPredict_Nsurv Compute criteria to check model performance
predict_Nsurv_ode Predict method for 'survFit' 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)
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
survDataCheck Checks if an object can be used to perform 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
survFit.survDataCstExp Fits a TKTD model for survival analysis using Bayesian inference for 'survDataCstExp' object
survFit.survDataVarExp Fits a TKTD model for survival analysis using Bayesian inference for 'survDataVarExp' object
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