Package: BeeGUTS 1.3.0

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, cre], Liubov Zakharova [ctb], Romoli Carlo [ctb], Bayer AG [cph], ibacon GmbH [cph]

BeeGUTS_1.3.0.tar.gz
BeeGUTS_1.3.0.zip(r-4.5)BeeGUTS_1.3.0.zip(r-4.4)BeeGUTS_1.3.0.zip(r-4.3)
BeeGUTS_1.3.0.tgz(r-4.4-x86_64)BeeGUTS_1.3.0.tgz(r-4.4-arm64)BeeGUTS_1.3.0.tgz(r-4.3-x86_64)BeeGUTS_1.3.0.tgz(r-4.3-arm64)
BeeGUTS_1.3.0.tar.gz(r-4.5-noble)BeeGUTS_1.3.0.tar.gz(r-4.4-noble)
BeeGUTS.pdf |BeeGUTS.html✨
BeeGUTS/json (API)
NEWS

# Install 'BeeGUTS' in R:
install.packages('BeeGUTS', repos = c('https://bgoussen.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bgoussen/beeguts/issues

Uses libs:
  • 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.

On CRAN:

4.95 score 3 stars 6 scripts 733 downloads 15 exports 69 dependencies

Last updated 1 months agofrom:cccfc31cc6. Checks:OK: 2 NOTE: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-win-x86_64NOTENov 23 2024
R-4.5-linux-x86_64OKNov 23 2024
R-4.4-win-x86_64NOTENov 23 2024
R-4.4-mac-x86_64NOTENov 23 2024
R-4.4-mac-aarch64NOTENov 23 2024
R-4.3-win-x86_64NOTENov 23 2024
R-4.3-mac-x86_64NOTENov 23 2024
R-4.3-mac-aarch64NOTENov 23 2024

Exports:concACconcAOconcCstcorrelation_plotcriteriaCheckdataGUTSfitBeeGUTSLCxppcpredict2priorposterior_plotShortTimeEffectstraceplotTRTvalidate

Dependencies:abindbackportsBHcallrcheckmateclicodetoolscolorspacecowplotcpp11data.tabledescdeSolvedistributionaldoParalleldplyrfansifarverforeachgenericsggplot2gluegridExtragtableinlineisobanditeratorslabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivodeGUTSpillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithrzoo

Tutorial

Rendered fromTutorial.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-04-17
Started: 2021-11-05

Readme and manuals

Help Manual

Help pageTopics
'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 beesconcAC
Recalculate concentration for the acute oral tests for beesconcAO
Recalculate the concentrations for the chronic oral tests for bees from mg a.s./kg feed to mug/beeconcCst
Plotting of correlation plots for 'beeSurvFit' objectscorrelation_plot
Computes PPC and NRMSE as defined in EFSA 2018criteriaCheck
Read and format the data for the BeeGUTS modeldataGUTS
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' objectLCx
Predict the Lethal Concentration at which x\% of organisms die for any specified time-point for a 'beeSurvFit' objectLCx.beeSurvFit
Plotting method for 'beeSurvData' objectsplot.beeSurvData
Plotting method for 'beeSurvFit' objectsplot.beeSurvFit
Plotting method for 'beeSurvPred' objectsplot.beeSurvPred
Plotting method for 'beeSurvValidation' objectsplot.beeSurvValidation
Plotting method for 'ppc' objectsplot.ppc
Generates an object to be used in posterior predictive check for 'beeSurvFit', 'beeSurvPred'ppc
Posterior predictive check method for 'beeSurvFit' objectsppc.beeSurvFit
Posterior predictive check method for 'beeSurvValidation' objectsppc.beeSurvValidation
Predict method for 'beeSurvFit' objectspredict.beeSurvFit
Predict method for 'beeSurvFit' objectspredict2
Plotting of prior and posterior plots for 'beeSurvFit' objectspriorposterior_plot
Perform comparison between LLD50 at 2 days and at 10 days as for EFSA revised guideline (2023) - Section 6.6ShortTimeEffects
Calculate the presence of Time Reinforced Toxicity for the compound from the calibrated model 'beeSurvFit' object.ShortTimeEffects.beeSurvFit
Summary of 'beeSurvFit' objectssummary.beeSurvFit
Summary of 'LCx' objectssummary.LCx
Plotting method for traces and densities for 'beeSurvFit' objectstraceplot 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 GTRT
Calculate the presence of Time Reinforced Toxicity for the compound from the calibrated model 'beeSurvFit' object.TRT.beeSurvFit
Validation method for 'beeSurvFit ' objectsvalidate
Validate method for 'beeSurvFit' objectsvalidate.beeSurvFit