# Modelling Reproduction and Survival Data in Ecotoxicology

## Documentation for package ‘morse’ version 3.3.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
FOCUSprofile | A simulated exposure profile with 11641 time points.
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 the maximum time point (default).
MFx | Predict the Multiplication Factor leading to x% of reduction in survival at a specific time.
MFx.survFit | Predict the Multiplication Factor leading to x% of reduction in survival at a specific time.
MFx_ode | Predict the Multiplication Factor leading to x% of reduction in survival at a specific time.
MFx_ode.survFit | Predict the Multiplication Factor leading to x% of reduction in survival at a specific time.
modelData | Create a list giving data to use in Bayesian inference.
modelData.survDataCstExp | Create a list giving data to use in Bayesian inference.
modelData.survDataVarExp | Create a list giving data to use in Bayesian inference.
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
ppc.survFitCstExp | Posterior predictive check plot
ppc.survFitPredict_Nsurv | Posterior predictive check plot
ppc.survFitTKTD | Posterior predictive check plot
ppc.survFitTT | Posterior predictive check plot
ppc.survFitVarExp | Posterior predictive check plot
predict | Predict method for 'survFit' objects
predict.survFit | Predict method for 'survFit' objects
predict_Nsurv | Predict method for 'survFit' objects
predict_Nsurv.survFit | Predict method for 'survFit' objects
predict_Nsurv_check | Checking goodness-of-fit method for 'survFitPredict' and 'survFitPredict_Nsurv' objects
predict_Nsurv_check.survFitPredict_Nsurv | Checking goodness-of-fit method for 'survFitPredict' and 'survFitPredict_Nsurv' objects
predict_Nsurv_ode | Predict method for 'survFit' objects
predict_Nsurv_ode.survFit | Predict method for 'survFit' objects
predict_ode | Predict method for 'survFit' objects
predict_ode.survFit | Predict method for 'survFit' objects
print.msgTable | Print 'msgTables' 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
survDataCheck | 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
survFit.survDataCstExp | Fits a TKTD model for survival analysis using Bayesian inference
survFit.survDataVarExp | 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