Inference and Prediction of ToxicoKinetic (TK) Models

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Documentation for package ‘rbioacc’ version 1.2.1

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

Help Pages

rbioacc-package	The 'rbioacc' package.
.fonte	A simple implementation of to pivot_longer of tidyr
.index_col_exposure	Return column matching "expw", "exps", "expf", "exppw" of a 'data.frame'
.index_col_metabolite	Return column matching "concX" of a 'data.frame' where X is metabolite
.is_equal_rmInf	Check if two vectors 'x' and 'y' are equal after remove 'Inf'
bioacc_metric	Biaccumulation metrics
bioacc_metric.fitTK	Biaccumulation metrics
Chironomus_benzoapyrene	Data on Chironomus exposed to benzoapyrene
Chiro_Creuzot	Data on Chironomus with several exposure routes.
corrMatrix	Correlations between parameters: colored matrix
corrPlot	Correlations between parameters: pairs plot
df_ppc	PPC data.frame
df_ppc.fitTK	PPC data.frame
df_PriorPost	Data frame of Posterior over Prior
df_PriorPost.fitTK	Data frame of Posterior over Prior
equations	Equations of the mathematical model used for the fit
exposure_names	Retrieve exposure routes names from object
Exposure_Sialis_lutaria	Data on Sialis lutaria exposure time series
fitTK	Posterior predictive check
fitTK.stanTKdataCST	Posterior predictive check
fitTK.stanTKdataVAR	Posterior predictive check
Gammarus_azoxistrobine_1d_Rosch2017	Data on Gammarus exposed to azoxistrobine
Internal_Sialis_lutaria	Data on Sialis lutaria internal time series
Male_Gammarus_Merged	Male 'Gammarus fossarum' exposed to Hg spiked water. Three exposure concentrations were tested in triplicates. The duration of the accumulation phase is 4 days for 0.0000708021 and 0.000283208 mu g.m L^{-1} exposure concentrations, and 7 days for 0.000141604 mu g.m L^{-1} exposure concentration.
Male_Gammarus_seanine_growth	Male 'Gammarus pulex' exposed to seanine spiked water. A single exposure concentration was tested. The duration of the accumulation phase is 1.417 days. Three metabolites were quantified. The growth of organism was included.
Male_Gammarus_Single	Bio-accumulation data set for _Gammarus fossarum_ exposed to Hg spiked water.
mcmcTraces	Traces of MCMC iterations
modelData	Create a list giving data and parameters to use in the model inference.
modelData.data.frame	Create a list giving data and parameters to use in the model inference.
modelData_ode	Create a list giving data and parameters to use in the model inference.
Oncorhynchus_two	Data on Oncorhynchus exposition
plot.bioaccMetric	Plot function for object of class 'bioaccMetric'
plot.fitTK	Plotting method for 'fitTK' objects
plot.predictTK	Plotting method for 'predictTK' objects
plot.predictTKstan	Plotting method for 'predictTK' objects
plot_exposure	Plot exposure profile
plot_PriorPost	Plot Posterior over Prior
plot_PriorPost.df_PP	Plot Posterior over Prior
plot_PriorPost.fitTK	Plot Posterior over Prior
ppc	PPC data.frame
ppc.fitTK	PPC data.frame
predict.fitTK	Prediction function using 'fitTK' object
predict_manual	Prediction function using 'fitTK' object
predict_stan	Prediction function using 'fitTK' object
psrf	Potential Scale Reduction Factors (PSRF) of the parameters
quantile_table	Quantiles of parameters
rbioacc	The 'rbioacc' package.
replace_	Replace element of a vector
t95	Return the time at 95% depuration of the parent component
waic	Widely Applicable Information Criterion (WAIC)