Package: extras 0.8.0.9000

Nicole Hill

extras: Helper Functions for Bayesian Analyses

Functions to 'numericise' 'R' objects (coerce to numeric objects), summarise 'MCMC' (Monte Carlo Markov Chain) samples and calculate deviance residuals as well as 'R' translations of some 'BUGS' (Bayesian Using Gibbs Sampling), 'JAGS' (Just Another Gibbs Sampler), 'STAN' and 'TMB' (Template Model Builder) functions.

Authors:Nicole Hill [aut, cre], Joe Thorley [aut], Kirill Müller [ctb], Nadine Hussein [ctb], Poisson Consulting [cph, fnd]

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

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

Bug tracker:https://github.com/poissonconsulting/extras/issues

Pkgdown site:https://poissonconsulting.github.io

On CRAN:

Conda:

8.49 score 9 stars 16 packages 15 scripts 691 downloads 130 exports 5 dependencies

Last updated 2 months agofrom:6be3d8a8e9. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 15 2025
R-4.5-winOKMar 15 2025
R-4.5-macOKMar 15 2025
R-4.5-linuxOKMar 15 2025
R-4.4-winOKMar 15 2025
R-4.4-macOKMar 15 2025
R-4.4-linuxOKMar 15 2025
R-4.3-winOKMar 15 2025
R-4.3-macOKMar 15 2025

Exports:as_listas_list_unnamedchk_indexchk_indiceschk_parsdberndev_berndev_beta_binomdev_binomdev_gammadev_gamma_poisdev_gamma_pois_zidev_lnormdev_neg_binomdev_normdev_poisdev_pois_zidev_skewnormdev_studentdskewnormexp10exp2fabsfill_allfill_nailogilog10ilog2ilogitinv_logitinv_oddsinvlogitkurtosislog_lik_bernlog_lik_beta_binomlog_lik_binomlog_lik_gammalog_lik_gamma_poislog_lik_gamma_pois_zilog_lik_lnormlog_lik_neg_binomlog_lik_normlog_lik_poislog_lik_pois_zilog_lik_skewnormlog_lik_studentlog_oddslog_odds_ratiolog_odds_ratio2log_odds<-log<-log10<-log2<-logitlogit<-lowernumericisenumericizeoddsodds_ratioodds_ratio2odds<-par_patternparamspbernpextremephipowproportional_changeproportional_change2proportional_differenceproportional_difference2pskewnormpvaluepzerosqbernqskewnormran_bernran_beta_binomran_binomran_gammaran_gamma_poisran_gamma_pois_ziran_lnormran_neg_binomran_normran_poisran_pois_ziran_skewnormran_studentrbernres_bernres_beta_binomres_binomres_gammares_gamma_poisres_gamma_pois_zires_lnormres_neg_binomres_normres_poisres_pois_zires_skewnormres_studentrskewnormsens_betasens_expsens_gammasens_gamma_poissens_gamma_pois_zisens_lnormsens_neg_binomsens_normsens_poissens_skewnormsens_studentsextremeskewnessstepsvalueuppervariancevld_indexvld_indicesvld_parsxtr_meanxtr_medianxtr_sdzeroszscore

Dependencies:chkcligluelifecyclerlang

Beta-binomial Deviance Residuals

Rendered frombeta-binomial-deviance-residuals.Rmdusingknitr::rmarkdownon Mar 15 2025.

Last update: 2024-09-17
Started: 2022-11-25

Deviance Residuals

Rendered fromdeviance-residuals.Rmdusingknitr::rmarkdownon Mar 15 2025.

Last update: 2022-10-30
Started: 2022-10-25

Readme and manuals

Help Manual

Help pageTopics
As Listas_list as_list.default
As Listas_list_unnamed as_list_unnamed.default
Check Indexchk_index vld_index
Check Indiceschk_indices vld_indices
Check Parameter Nameschk_pars vld_pars
Bernoulli Distributiondbern pbern qbern rbern
Bernoulli Deviancesdev_bern
Beta-Binomial Deviancesdev_beta_binom
Binomial Deviancesdev_binom
Gamma Deviancesdev_gamma
Gamma-Poisson Deviancesdev_gamma_pois
Zero-Inflated Gamma-Poisson Deviancesdev_gamma_pois_zi
Log-Normal Deviancesdev_lnorm
Negative Binomial Deviancesdev_neg_binom
Normal Deviancesdev_norm
Poisson Deviancesdev_pois
Zero-Inflated Poisson Deviancesdev_pois_zi
Skew Normal Deviancesdev_skewnorm
Student's t Deviancesdev_student
Skew-Normal Distributiondskewnorm pskewnorm qskewnorm rskewnorm
Exponential Transformation of Base 10exp10
Exponential Transformation of Base 2exp2
Absolutefabs
Fill All Valuesfill_all fill_all.character fill_all.integer fill_all.logical fill_all.numeric
Fill Missing Valuesfill_na fill_na.character fill_na.integer fill_na.logical fill_na.numeric
Inverse Log Transformationilog
Inverse Log Base 10 Transformationilog10
Inverse Log Base 2 Transformationilog2
Inverse Logistic Transformationilogit
Inverse Logistic Transformationinv_logit
Inverse Oddsinv_odds
Inverse Logistic Transformationinvlogit
Kurtosiskurtosis
Bernoulli Log-Likelihoodlog_lik_bern
Beta-Binomial Log-Likelihoodlog_lik_beta_binom
Binomial Log-Likelihoodlog_lik_binom
Gamma Log-Likelihoodlog_lik_gamma
Gamma-Poisson Log-Likelihoodlog_lik_gamma_pois
Zero-Inflated Gamma-Poisson Log-Likelihoodlog_lik_gamma_pois_zi
Log-Normal Log-Likelihoodlog_lik_lnorm
Negative Binomial Log-Likelihoodlog_lik_neg_binom
Normal Log-Likelihoodlog_lik_norm
Poisson Log-Likelihoodlog_lik_pois
Zero-Inflated Poisson Log-Likelihoodlog_lik_pois_zi
Skew Normal Log-Likelihoodlog_lik_skewnorm
Student's t Log-Likelihoodlog_lik_student
Log Oddslog_odds
Log-Odds Ratiolog_odds_ratio
Log Odds Ratio2log_odds_ratio2
Inverse Log Odds Transformationlog_odds<-
Log Transformationlog<-
Log Base 10 Transformationlog10<-
Log Base 2 Transformationlog2<-
Logistic Transformationlogit
Logistic Transformationlogit<-
Lower Credible Limitlower
Numericise (or Numericize)numericise numericise.array numericise.data.frame numericise.Date numericise.double numericise.factor numericise.hms numericise.integer numericise.logical numericise.matrix numericise.POSIXct numericize
Oddsodds
Odds Ratioodds_ratio
Odds Ratio2odds_ratio2
Inverse Odds Transformationodds<-
Parameter Patternpar_pattern
Extreme Probabilitypextreme
Phiphi
Powerpow
Proportional Changeproportional_change
Proportional Change2proportional_change2
Proportional Differenceproportional_difference
Proportional Difference2proportional_difference2
Bayesian P-Valuepvalue
Proportion of Zerospzeros
Bernoulli Random Samplesran_bern
Beta-Binomial Random Samplesran_beta_binom
Binomial Random Samplesran_binom
Gamma Random Samplesran_gamma
Gamma-Poisson Random Samplesran_gamma_pois
Zero-Inflated Gamma-Poisson Random Samplesran_gamma_pois_zi
Log-Normal Random Samplesran_lnorm
Negative Binomial Random Samplesran_neg_binom
Normal Random Samplesran_norm
Poisson Random Samplesran_pois
Zero-Inflated Poisson Random Samplesran_pois_zi
Skew Normal Random Samplesran_skewnorm
Student's t Random Samplesran_student
Bernoulli Residualsres_bern
Beta-Binomial Residualsres_beta_binom
Binomial Residualsres_binom
Gamma Residualsres_gamma
Gamma-Poisson Residualsres_gamma_pois
Zero-Inflated Gamma-Poisson Residualsres_gamma_pois_zi
Log-Normal Residualsres_lnorm
Negative Binomial Residualsres_neg_binom
Normal Residualsres_norm
Poisson Residualsres_pois
Zero-Inflated Poisson Residualsres_pois_zi
Skew Normal Residualsres_skewnorm
Student's t Residualsres_student
Adjust Beta Distribution Parameters for Sensitivity Analysessens_beta
Adjust Exponential Distribution Parameters for Sensitivity Analysessens_exp
Adjust Gamma Distribution Parameters for Sensitivity Analysessens_gamma
Adjust Gamma-Poisson Distribution Parameters for Sensitivity Analysessens_gamma_pois
Adjust Zero-Inflated Gamma-Poisson Distribution Parameters for Sensitivity Analysessens_gamma_pois_zi
Adjust Log-Normal Distribution Parameters for Sensitivity Analysissens_lnorm
Adjust Negative Binomial Distribution Parameters for Sensitivity Analysessens_neg_binom
Adjust Normal Distribution Parameters for Sensitivity Analysessens_norm
Adjust Poisson Distribution Parameters for Sensitivity Analysessens_pois
Adjust Skew Normal Distribution Parameters for Sensitivity Analysessens_skewnorm
Adjust Student's t Distribution Parameters for Sensitivity Analysessens_student
Extreme Surprisalsextreme
Skewnessskewness
Stepstep
Surprisal Valuesvalue
Upper Credible Limitupper
Variancevariance
Meanxtr_mean
Medianxtr_median
Standard Deviationxtr_sd
Zeroszeros
Z-Scorezscore