Bayesian Inference of TKTD Models

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Documentation for package ‘morseTKTD’ version 0.1.3

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

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