Bayesian Inference of TKTD Models


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Documentation for package ‘morseTKTD’ version 0.1.3

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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