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rbioacc (version 1.3.1)

Inference and Prediction of Toxicokinetic Models

Description

Provides bioaccumulation factors from a toxicokinetic model fitted to accumulation-depuration data. It is designed to fulfil the requirements of regulators when examining applications for market authorization of active substances.

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Version

Install

install.packages('rbioacc')

Monthly Downloads

158

Version

1.3.1

License

MIT + file LICENSE

Maintainer

Virgile Baudrot

Last Published

September 26th, 2025

Functions in rbioacc (1.3.1)

exposure_names

Retrieve exposure routes names from object
psrf

Potential Scale Reduction Factors (PSRF) of the parameters
quantile_table

Quantiles of parameters
mcmcTraces

Traces of MCMC iterations
waic

Widely Applicable Information Criterion (WAIC)
modelData

Create a list giving data and parameters to use in the model inference.
fitTK

Posterior predictive check
df_ppc

PPC data.frame
equations

Equations of the mathematical model used for the fit
.index_col_exposure

Return column matching "expw", "exps", "expf", "exppw" of a data.frame
plot.predictTK

Plotting method for predictTK objects
t95

Return the time at 95% depuration of the parent component
rmMessWarn

remove message and warning
plot_exposure

Plot exposure profile
.index_col_metabolite

Return column matching "concX" of a data.frame where X is metabolite
predict.fitTK

Prediction function using fitTK object
replace_

Replace element of a vector
rbioacc-package

The 'rbioacc' package.
bioacc_metric

Biaccumulation metrics
Chiro_Creuzot

Data on Chironomus with several exposure routes.
.is_equal_rmInf

Check if two vectors x and y are equal after remove Inf
plot.fitTK

Plotting method for fitTK objects
corrMatrix

Correlations between parameters: colored matrix
corrPlot

Correlations between parameters: pairs plot
modelData_ode

Create a list giving data and parameters to use in the model inference.
plot.bioaccMetric

Plot function for object of class bioaccMetric
Male_Gammarus_Single

Bio-accumulation data set for Gammarus fossarum exposed to Hg spiked water.
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.
Gammarus_azoxistrobine_1d_Rosch2017

Data on Gammarus exposed to azoxistrobine
Chironomus_benzoapyrene

Data on Chironomus exposed to benzoapyrene
Internal_Sialis_lutaria

Data on Sialis lutaria internal time series
plot_PriorPost

Plot Posterior over Prior
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.
Oncorhynchus_two

Data on Oncorhynchus exposition
Exposure_Sialis_lutaria

Data on Sialis lutaria exposure time series
.fonte

A simple implementation of to pivot_longer of tidyr
df_PriorPost

Data frame of Posterior over Prior