Package: jagshelper 0.4.1

Matt Tyers

jagshelper: Extracting and Visualizing Output from 'jagsUI'

Tools are provided to streamline Bayesian analyses in 'JAGS' using the 'jagsUI' package. Included are functions for extracting output in simpler format, functions for streamlining assessment of convergence, and functions for producing summary plots of output. Also included is a function that provides a simple template for running 'JAGS' from 'R'. Referenced materials can be found at <doi:10.1214/ss/1177011136>.

Authors:Matt Tyers [aut, cre]

jagshelper_0.4.1.tar.gz
jagshelper_0.4.1.tar.gz(r-4.5-noble)jagshelper_0.4.1.tar.gz(r-4.4-noble)
jagshelper_0.4.1.tgz(r-4.4-emscripten)jagshelper_0.4.1.tgz(r-4.3-emscripten)
jagshelper.pdf |jagshelper.html✨
jagshelper/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/mbtyers/jagshelper/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:

4.63 score 85 scripts 463 downloads 35 exports 5 dependencies

Last updated 17 days agofrom:f15cbdc5d7. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-linuxOKNov 08 2024

Exports:caterpillarchaindens_dfchaindens_jagschaindens_linecheck_neffcheck_Rhatcomparecatcomparedenscomparepriorscor_jagscrossplotenvelopeexpitjags_dfjags_plistkfoldlogitnbynamenparamoverlayenvelopepairstrace_jagsplot_postpredplotcor_jagsplotdensplotRhatspull_postqq_postpredrcolorsskeletontrace_dftrace_jagstrace_linetracedens_jagstraceworstRhatts_postpred

Dependencies:codajagsUIlatticeMASSrjags

jagshelper-vignette

Rendered fromjagshelper-vignette.Rmdusingknitr::rmarkdownon Nov 08 2024.

Last update: 2024-11-07
Started: 2022-10-14

Readme and manuals

Help Manual

Help pageTopics
Functions for Extracting and Visualizing Output from 'jagsUI'jagshelper-package jagshelper
Example data: asdf jags outasdf_jags_out
Example data: asdf prior jags outasdf_prior_jags_out
Caterpillar plotcaterpillar
By-chain kernel density of each column of a 'data.frame'.chaindens_df
By-chain kernel densities of 'jagsUI' objectchaindens_jags
Simple by-chain kernel density plotchaindens_line
Quick summary of n.eff values by parameter namecheck_neff
Quick summary of Rhat values by parameter namecheck_Rhat
Compare Caterpillar Plotscomparecat
Compare Densitycomparedens
Compare Priorscomparepriors
Correlation matrix from a JAGS objectcor_jags
Bivariate Plot of Posterior Densitiescrossplot
Envelope plotenvelope
Expit, or inverse logitexpit
Extract data.framejags_df
Plistjags_plist
Automated K-fold or Leave One Out Cross Validationkfold
Logitlogit
Number of parameter nodes by parameter namenbyname
Number of parametersnparam
Overlay envelope plotsoverlayenvelope
Pairs trace plotpairstrace_jags
Diagnostic plots from posterior predictive distributionplot_postpred
Plot a correlation matrix from a JAGS objectplotcor_jags
Plot kernel densities of single parameter nodesplotdens
Plotting all Rhat valuesplotRhats
Subset from posterior data.framepull_post
Quantile-quantile plot from posterior predictive distributionqq_postpred
Random Colorsrcolors
Skeletonskeleton
Example data: Time series associated with SS JAGS outSS_data
Example data: SS JAGS outSS_out
Trace plot of each column of a 'data.frame'.trace_df
Trace plot of jagsUI objecttrace_jags
Simple trace plottrace_line
Combination of trace plots and by-chain kernel densities of 'jagsUI' objecttracedens_jags
Trace plots corresponding to the worst values of RhattraceworstRhat
Time series plot of centered posterior predictive distributionts_postpred