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Package: BeeGUTS 1.5.0

Carlo Romoli

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

Tools to calibrate, validate, and make predictions with the General Unified Threshold model of Survival adapted for Bee species. The model is presented in the publication from Baas, J., Goussen, B., Miles, M., Preuss, T.G., Roessing, I. (2022) <doi:10.1002/etc.5423> and Baas, J., Goussen, B., Taenzler, V., Roeben, V., Miles, M., Preuss, T.G., van den Berg, S., Roessink, I. (2024) <doi:10.1002/etc.5871>, and is based on the GUTS framework Jager, T., Albert, C., Preuss, T.G. and Ashauer, R. (2011) <doi:10.1021/es103092a>. The authors are grateful to Bayer A.G. for its financial support.

Authors:Benoit Goussen [aut], Liubov Zakharova [ctb], Carlo Romoli [aut, cre], Bayer AG [cph, fnd], ibacon GmbH [cph]

BeeGUTS_1.5.0.tar.gz
BeeGUTS_1.5.0.zip(r-4.7-x86_64)BeeGUTS_1.5.0.zip(r-4.7-arm64)BeeGUTS_1.5.0.zip(r-4.6-x86_64)BeeGUTS_1.5.0.zip(r-4.6-arm64)
BeeGUTS_1.5.0.tar.gz(r-4.7-arm64)BeeGUTS_1.5.0.tar.gz(r-4.7-x86_64)BeeGUTS_1.5.0.tar.gz(r-4.6-arm64)BeeGUTS_1.5.0.tar.gz(r-4.6-x86_64)
BeeGUTS_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BeeGUTS/json (API)

# Install 'BeeGUTS' in R:

install.packages('BeeGUTS', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ibacon-gmbh-modelling/beeguts/issues

Uses libs:

onetbb– Parallelism library for C++
c++– GNU Standard C++ Library v3

Datasets:

betacyfluthrinChronic - Survival datasets for _Honey bees_ exposed to constant concentration of Betacyfluthrin for 10 days.
fitBetacyfluthrin_Chronic - Model calibration results datasets for _Honey bees_ exposed to constant concentration of Betacyfluthrin for 10 days.
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

On CRAN:

onetbb cpp

3.00 score 355 downloads 15 exports 64 dependencies

Last updated from:3aab55f523. Checks:10 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	OK	428
linux-devel-x86_64	OK	525
source / vignettes	OK	898
linux-release-arm64	OK	470
linux-release-x86_64	OK	416
windows-devel-arm64	OK	576
windows-devel-x86_64	OK	711
windows-release-arm64	OK	557
windows-release-x86_64	OK	695
wasm-release	OK	306

Exports:concAC concAO concCst correlation_plot criteriaCheck dataGUTS fitBeeGUTS LCx ppc predict2 priorposterior_plot ShortTimeEffects traceplot TRT validate

Dependencies:abind backports BH callr checkmate cli codetools cowplot cpp11 data.table desc deSolve distributional doParallel dplyr farver foreach generics ggplot2 glue gridExtra gtable inline isoband iterators labeling lattice lifecycle loo magrittr matrixStats numDeriv odeGUTS otel pillar pkgbuild pkgconfig posterior processx ps purrr QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan rstantools S7 scales StanHeaders stringi stringr tensorA tibble tidyr tidyselect utf8 vctrs viridisLite withr zoo

Tutorial

BeeGUTS | Installation | Example | Documentation

Rendered fromTutorial.Rmdusingknitr::rmarkdown

Last update: 2024-10-23
Started: 2022-08-09

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

Package: BeeGUTS 1.5.0

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

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)