# Inference and Prediction of ToxicoKinetic (TK) Models

## 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)