Modelling Reproduction and Survival Data in Ecotoxicology

Documentation for package ‘morse’ version 3.3.2

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 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
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.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_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