R: Bayesian Inference of TKTD Models

# Bayesian Inference of TKTD Models

## Documentation for package ‘morseTKTD’ version 0.1.3

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

## Help Pages

morseTKTD-package | The 'morseTKTD' package.
build_dN | build sub-dataframe of Nsurv without NA
build_dX | build sub-dataframe of concentration without NA
build_priors | Create a list giving data to use in Bayesian inference.
build_stanData | Create a list giving data to use in Bayesian inference.
cadmium1 | Reproduction and survival data sets of chronic laboratory toxicity tests of cadmium with Daphnia
cadmium2 | Reproduction and survival data sets of chronic laboratory toxicity tests of cadmium with snails
CheckData | Set of function to test conformity of data
checking_table | Set of function to test conformity of data
check_concentration | Set of function to test conformity of data
check_concNsurv | Set of function to test conformity of data
check_Nsurv | Set of function to test conformity of data
check_time | Set of function to test conformity of data
check_TimeNsurv | Set of function to test conformity of data
chlordan | Reproduction and survival data sets of chronic laboratory toxicity tests of chlordan with Daphnia
ComputePredictSurvFit | Compute post value on object
compute_Ninit | Compute post value on object
compute_Nsurv | Compute post value on object
compute_Nsurv.SurvPredict | Compute post value on object
copper | Reproduction and survival data sets of chronic laboratory toxicity tests of copper on Daphnia
dichromate | Survival data set of chronic laboratory toxicity tests of dichromate with Daphnia
Extract | Extraction methods to recover output of fit object.
extract_Nsurv_ppc | Extraction methods to recover output of fit object.
extract_Nsurv_sim | Extraction methods to recover output of fit object.
extract_param | Extraction methods to recover output of fit object.
fit | Fits a TKTD model for survival analysis using Bayesian inference
fit.SurvDataCstExp | Fits a TKTD model for survival analysis using Bayesian inference
fit.SurvDataVarExp | Fits a TKTD model for survival analysis using Bayesian inference
FOCUSprofile | A simulated exposure profile with 11641 time points using FOCUS model.
group_array | build array with indices of rows
is.between | Set of function to test conformity of data
is_exposure_constant | Set of function to test conformity of data
LCxt | Predict Lethal Concentration at any specified time point.
lcxt | Predict Lethal Concentration at any specified time point.
lcxt.SurvFit | Predict Lethal Concentration at any specified time point.
LPxt | Lethal Profile calculation
lpxt | Lethal Profile calculation
lpxt.SurvFit | Lethal Profile calculation
ModelData | Create a list giving data to use in Bayesian inference.
modelData | Create a list giving data to use in Bayesian inference.
modelData.SurvData | Create a list giving data to use in Bayesian inference.
morseTKTD | The 'morseTKTD' package.
plot.LCxt | Plot of the LCxt object
plot.LPxt | Plot of the LPxt object
plot.PPC | Plot an object 'PPC'
plot.PriorPosterior | Plot of Prior and Posterior distributions
plot.SurvDataCstExp | Plotting method for 'survDataVar' objects
plot.SurvDataVarExp | Plotting method for 'survDataVar' objects
plot.SurvFit | Fits a TKTD model for survival analysis using Bayesian inference
plot.SurvPredict | Plotting method for 'SurvPredict' objects
PlotData | Plotting method for 'survDataVar' objects
PlotLCxt | Plot of the LCxt object
PlotLPxt | Plot of the LPxt object
PlotPPC | Plot an object 'PPC'
PlotPredictSurvFit | Plotting method for 'SurvPredict' objects
PlotPriorPosterior | Plot of Prior and Posterior distributions
PPC | Posterior predictive check methods
ppc | Posterior predictive check methods
ppc.SurvFit | Posterior predictive check methods
predict | Prediction base on 'SurvFit' objects
predict.SurvFit | Prediction base on 'SurvFit' objects
PredictSurvFit | Prediction base on 'SurvFit' objects
predict_cstIT | Prediction base on 'SurvFit' objects
predict_cstSD | Prediction base on 'SurvFit' objects
predict_SurvFitCstExp | Prediction base on 'SurvFit' objects
predict_SurvFitVarExp | Prediction base on 'SurvFit' objects
predict_varIT | Prediction base on 'SurvFit' objects
predict_varSD | Prediction base on 'SurvFit' objects
PriorPosterior | Return Prior and Posterior density of parameters of 'SurvFit' object
priorPosterior | Return Prior and Posterior density of parameters of 'SurvFit' object
priorPosterior.SurvFit | Return Prior and Posterior density of parameters of 'SurvFit' object
priors_distribution | Extraction methods to recover output of fit object.
priors_distribution.SurvFit | Extraction methods to recover output of fit object.
propiconazole | Survival data set of chronic laboratory toxicity tests of propiconazole with Gammarus pulex
propiconazole_pulse_exposure | Survival data set of chronic laboratory toxicity tests of propiconazole with Gammarus pulex
SurvData | Creates a data set for survival analysis
survData | Creates a data set for survival analysis
survData.data.frame | Creates a data set for survival analysis
SurvDataCheck | Checks if an object can be used to perform survival analysis
survDataCheck | Checks if an object can be used to perform survival analysis
SurvFit | Fits a TKTD model for survival analysis using Bayesian inference
survFit_TKTD_params | Table of posterior estimated parameters
SurvIT_cst | Internal predict function
SurvIT_var | Internal predict function
SurvSD_cst | Internal predict function
SurvSD_var | Internal predict function
update.LPxt | Lethal Profile calculation
zinc | Reproduction and survival data sets of a chronic laboratory toxicity tests of zinc with Daphnia