Tutorial"

In BeeGUTS: General Unified Threshold Model of Survival for Bees using Bayesian Inference

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BeeGUTS

The goal of BeeGUTS is to analyse the survival toxicity tests performed for bee species. It can be used to fit a Toxicokinetic-Toxicodynamic (TKTD) model adapted for bee standard studies (acute oral, acute contact, and chronic oral studies). The TKTD model used is the General Unified Threshold model of Survival (GUTS).

Installation

You can install the released version of BeeGUTS from CRAN with:

install.packages("BeeGUTS")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("bgoussen/BeeGUTS")

Example

This is a basic example which shows you how to solve a common problem. Beware that for space constrains with CRAN, the fit has been limited to a single chain, but more chains can be used.

library(BeeGUTS)
file_location <- system.file("extdata", "betacyfluthrin_chronic_ug.txt", package = "BeeGUTS") # Load the path to one of the example file
lsData <- dataGUTS(file_location = file_location, test_type = 'Chronic_Oral', cstConcCal = FALSE) # Read the example file
plot(lsData) # Plot the data
fit <- fitBeeGUTS(lsData, modelType = "SD", nIter = 2000, nChains = 1) # Fit a SD model. This can take some time...
traceplot(fit) # Produce a diagnostic plot of the fit
plot(fit) # Plot the fit results
summary(fit) # Gives a summary of the results
validation <- validate(fit, lsData) # produce a validation of the fit (here it uses the same dataset as calibration as an example, so not relevant…)
plot(validation) # plot the validation results
dataPredict <- data.frame(time = c(1:5, 1:15), conc = c(rep(5, 5), rep(15, 15)),  replicate = c(rep("rep1", 5), rep("rep3", 15))) # Prepare data for forwards prediction
prediction <- predict(fit, dataPredict) # Perform forwards prediction. At the moment, no concentration recalculation is performed in the forwards prediction. The concentrations are taken as in a chronic test
plot(prediction) # Plot of the prediction results

Documentation

For the complete documentation, refer to the github page

BeeGUTS documentation built on Oct. 30, 2024, 9:14 a.m.