Package: bayesnec 2.1.3.0

Rebecca Fisher

bayesnec: A Bayesian No-Effect- Concentration (NEC) Algorithm

Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECx' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>), 'NSEC' (see Fisher and Fox (2023)<doi:10.1002/etc.5610>), and 'N(S)EC (see Fisher et al. 2023<doi:10.1002/ieam.4809>). A full description of this package can be found in Fisher 'et al.' (2024)<doi:10.18637/jss.v110.i05>. This package expands and supersedes an original version implemented in 'R2jags' (see Su and Yajima (2020)<https://CRAN.R-project.org/package=R2jags>; Fisher et al. (2020)<doi:10.5281/ZENODO.3966864>).

Authors:Rebecca Fisher [aut, cre], Diego R. Barneche [aut], Gerard F. Ricardo [aut], David R. Fox [aut]

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bayesnec.pdf |bayesnec.html✨
bayesnec/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/open-aims/bayesnec/issues

Datasets:

On CRAN:

bayesian-inferenceconcentration-responseecotoxicologyno-effect-concentrationnon-linear-decaythreshold-derivationtoxicology

8.33 score 11 stars 360 scripts 436 downloads 28 exports 81 dependencies

Last updated 3 months agofrom:5a942a5573. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 18 2024
R-4.5-winOKOct 18 2024
R-4.5-linuxOKOct 18 2024
R-4.4-winOKOct 18 2024
R-4.4-macOKOct 18 2024
R-4.3-winOKOct 18 2024
R-4.3-macOKOct 18 2024

Exports:amendaverage_estimatesbayesnecformulabnecbnec_newdatabnfcheck_chainscheck_formulacheck_priorscompare_estimatescompare_fittedcompare_posteriordispersionecxexpand_manecexpand_necggbnec_datais_manecsummarymake_brmsformulamodelsnecnsecpull_brmsfitpull_outpull_priorsample_priorsshow_paramsstep

Dependencies:abindbackportsbayesplotBHbridgesamplingbrmsBrobdingnagcallrcheckmatechkclicodacodetoolscolorspacecpp11descdigestdistributionaldplyrevaluatefansifarverformula.toolsfuturefuture.applygenericsggplot2ggridgesglobalsgluegridExtragtableinlineisobandlabelinglatticelifecyclelistenvloomagrittrMASSMatrixmatrixStatsmgcvmunsellmvtnormnleqslvnlmenumDerivoperator.toolsparallellypillarpkgbuildpkgconfigplyrposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithr

Comparing posterior predictions

Rendered fromexample4.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-01-02
Started: 2020-11-18

Model details

Rendered fromexample2b.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-01-02
Started: 2020-11-20

Multi model usage

Rendered fromexample2.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-01-02
Started: 2020-11-03

Priors

Rendered fromexample3.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-01-02
Started: 2020-11-03

Running bayesnec

Rendered fromexample5.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-01-02
Started: 2023-05-19

Single model usage

Rendered fromexample1.Rmdusingknitr::rmarkdownon Oct 18 2024.

Last update: 2024-01-02
Started: 2020-11-03

Readme and manuals

Help Manual

Help pageTopics
The 'bayesnec' package.bayesnec-package bayesnec
Custom beta-binomial family"beta_binomial"
"Add" multiple 'bnecfit' objects into one single 'bayesmanecfit' object containing Bayesian model averaging statistics.+.bnecfit
Amends an existing 'bayesmanecfit' objectamend
bayesnec standard ggplot2 plotting methodautoplot autoplot.bayesmanecfit autoplot.bayesnecfit
average_estimatesaverage_estimates
Class 'bayesmanecfit' of models fitted with the 'brms' packagebayesmanecfit bayesmanecfit-class
Class 'bayesnecfit' of models fitted with the 'brms' packagebayesnecfit bayesnecfit-class
Set up a model formula for use in 'bayesnec'bayesnecformula bnf
bnecbnec
bnec_newdatabnec_newdata
Class 'bnecfit' of models fitted with function 'bnec'bnecfit bnecfit-class
Concatenate multiple 'bnecfit' objects into one single 'bayesmanecfit' object containing Bayesian model averaging statistics.c.bnecfit
Checking chain convergencecheck_chains check_chains.bayesmanecfit check_chains.bayesnecfit
Check if input model formula is appropriate to use with 'bayesnec'check_formula
Plots the prior and posterior parameter probability densities from an object of class 'bayesnecfit' or 'bayesmanecfit'.check_priors
compare_estimatescompare_estimates
compare_fittedcompare_fitted
compare_posteriorcompare_posterior
Posterior dispersiondispersion
Extracts the predicted ECx valueecx
Extracts a range of statistics from a list of 'prebayesnecfit' objects.expand_manec
Extracts a range of statistics from a 'prebayesnecfit' object.expand_nec
Generates mean posterior linear predictions for objects fitted by 'bnec'fitted fitted.bayesmanecfit fitted.bayesnecfit
Retrieve formulas from models fitted by 'bnec'formula formula.bayesmanecfit formula.bayesnecfit
Creates the data.frame for plotting with 'autoplot'.ggbnec_data
Herbicide phytotoxicity dataherbicide
Checks if argument is a 'manecsummary' objectis_manecsummary
Checks if argument is a 'necsummary' objectis_necsummary
Expose the final 'brmsformula'make_brmsformula
Example bayesmanecfit objectmanec_example
Class 'manecsummary' of models fitted with the 'brms' packagemanecsummary manecsummary-class
Model.frame methods in bayesnec.model.frame model.frame.bayesmanecfit model.frame.bayesnecfit model.frame.bayesnecformula
modelsmodels
Extracts the predicted NEC value as desired from an object of class 'bayesnecfit' or 'bayesmanecfit'.nec
Example data of non-linear decaynec_data
Class 'necsummary' of models fitted with the 'brms' packagenecsummary necsummary-class
Extracts the predicted NSEC value as desired from an object of class 'bayesnecfit' or 'bayesmanecfit'.nsec
Generates a plot for objects fitted by 'bnec'plot plot.bayesmanecfit plot.bayesnecfit
Generates posterior linear predictions for objects fitted by 'bnec'posterior_epred posterior_epred.bayesmanecfit posterior_epred.bayesnecfit
Generates posterior predictions for objects fitted by 'bnec'posterior_predict posterior_predict.bayesmanecfit posterior_predict.bayesnecfit
Class 'prebayesnecfit' of models fitted with the 'brms' packageprebayesnecfit prebayesnecfit-class
Generates mean posterior predictions for objects fitted by 'bnec'predict predict.bayesmanecfit predict.bayesnecfit
Prints a summary for objects fitted by 'bnec'print print.bayesmanecfit print.bayesnecfit
Extract and object of class 'brmsfit' from 'bayesnecfit' or 'bayesmanecfit'.pull_brmsfit pull_brmsfit.bayesmanecfit pull_brmsfit.bayesnecfit
pull_outpull_out
pull_priorpull_prior
Extract Diagnostic Quantities of 'brms' Modelsrhat rhat.bayesmanecfit rhat.bayesnecfit
sample_priorssample_priors
show_paramsshow_params
stepstep
Generates a summary for objects fitted by 'bnec'summary summary.bayesmanecfit summary.bayesnecfit
Update an object of class 'bnecfit' as fitted by function 'bnec'.update.bnecfit