# General Unified Threshold Model of Survival for Bees using Bayesian Inference

## Documentation for package ‘BeeGUTS’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BeeGUTS-package | 'BeeGUTS' package; a package to perform GUTS modelling for Bee experiments.
BeeGUTS | 'BeeGUTS' package; a package to perform GUTS modelling for Bee experiments.
betacyfluthrinChronic | Survival datasets for _Honey bees_ exposed to constant concentration of Betacyfluthrin for 10 days.
concAC | Recalculate the concentrations for the acute contact tests for bees
concAO | Recalculate concentration for the acute oral tests for bees
concCst | Recalculate the concentrations for the chronic oral tests for bees from mg a.s./kg feed to mug/bee
correlation_plot | Plotting of correlation plots for 'beeSurvFit' objects
criteriaCheck | Computes PPC and NRMSE as defined in EFSA 2018
dataGUTS | Read and format the data for the BeeGUTS model
fitBeeGUTS | Fit a GUTS model for bees survival analysis using Bayesian Inference (stan)
fitBetacyfluthrin_Chronic | Model calibration results datasets for _Honey bees_ exposed to constant concentration of Betacyfluthrin for 10 days.
LCx | Predict the Lethal Concentration method at which x\% of organisms die for any specified time-point for a 'beeSurvFit' object
LCx.beeSurvFit | Predict the Lethal Concentration at which x\% of organisms die for any specified time-point for a 'beeSurvFit' object
plot.beeSurvData | Plotting method for 'beeSurvData' objects
plot.beeSurvFit | Plotting method for 'beeSurvFit' objects
plot.beeSurvPred | Plotting method for 'beeSurvPred' objects
plot.beeSurvValidation | Plotting method for 'beeSurvValidation' objects
plot.ppc | Plotting method for 'ppc' objects
ppc | Generates an object to be used in posterior predictive check for 'beeSurvFit', 'beeSurvPred'
ppc.beeSurvFit | Posterior predictive check method for 'beeSurvFit' objects
ppc.beeSurvValidation | Posterior predictive check method for 'beeSurvValidation' objects
predict.beeSurvFit | Predict method for 'beeSurvFit' objects
predict2 | Predict method for 'beeSurvFit' objects
priorposterior_plot | Plotting of prior and posterior plots for 'beeSurvFit' objects
ShortTimeEffects | Perform comparison between LLD50 at 2 days and at 10 days as for EFSA revised guideline (2023) - Section 6.6
ShortTimeEffects.beeSurvFit | Calculate the presence of Time Reinforced Toxicity for the compound from the calibrated model 'beeSurvFit' object.
summary.beeSurvFit | Summary of 'beeSurvFit' objects
summary.LCx | Summary of 'LCx' objects
traceplot | Plotting method for traces and densities for 'beeSurvFit' objects
traceplot.beeSurvFit | Plotting method for traces and densities for 'beeSurvFit' objects
TRT | Perform the extrapolation of the LDD50 to 27 days and check the presence of reinforced toxicity as for EFSA revised guideline (2023) - Annex G
TRT.beeSurvFit | Calculate the presence of Time Reinforced Toxicity for the compound from the calibrated model 'beeSurvFit' object.
valBetacyfluthrinChronic | Pre-calculated validation results for _Honey bees_ exposed to constant concentration of Betacyfluthrin for 10 days. This is a toy example that uses the calibrated model of the object fitBetacyfluthrin_Chronic and the dataset betacyfluthrinChronic
validate | Validation method for 'beeSurvFit ' objects
validate.beeSurvFit | Validate method for 'beeSurvFit' objects