Package: jagshelper 0.4.1

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
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manual.pdf |manual.html✨
card.svg |card.png
jagshelper/json (API)
NEWS

# Install 'jagshelper' in R:

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

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

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC - binary JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: * To have an engine for the BUGS language that runs on Unix * To be extensible, allowing users to write their own functions, distributions and samplers. * To be a plaftorm for experimentation with ideas in Bayesian modelling This package contains the 'jags' binary as well as the associated shared library modules loaded by the binary.
c++– GNU Standard C++ Library v3

Datasets:

asdf_jags_out - Example data: asdf jags out
asdf_prior_jags_out - Example data: asdf prior jags out
SS_data - Example data: Time series associated with SS JAGS out
SS_out - Example data: SS JAGS out

On CRAN:

jags cpp

4.72 score 104 scripts 592 downloads 35 exports 5 dependencies

Last updated from:cad36332f8. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	206
source / vignettes	OK	181
linux-release-x86_64	OK	180
macos-release-arm64	OK	94
macos-oldrel-arm64	OK	120
windows-devel	OK	119
windows-release	OK	114
windows-oldrel	OK	99
wasm-release	OK	112

Exports:caterpillar chaindens_df chaindens_jags chaindens_line check_neff check_Rhat comparecat comparedens comparepriors cor_jags crossplot envelope expit jags_df jags_plist kfold logit nbyname nparam overlayenvelope pairstrace_jags plot_postpred plotcor_jags plotdens plotRhats pull_post qq_postpred rcolors skeleton trace_df trace_jags trace_line tracedens_jags traceworstRhat ts_postpred

Dependencies:coda jagsUI lattice MASS rjags

jagshelper-vignette

Rendered fromjagshelper-vignette.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2024-10-23
Started: 2022-10-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Functions for Extracting and Visualizing Output from 'jagsUI'	jagshelper-package jagshelper
Example data: asdf jags out	asdf_jags_out
Example data: asdf prior jags out	asdf_prior_jags_out
Caterpillar plot	caterpillar
By-chain kernel density of each column of a 'data.frame'.	chaindens_df
By-chain kernel densities of 'jagsUI' object	chaindens_jags
Simple by-chain kernel density plot	chaindens_line
Quick summary of n.eff values by parameter name	check_neff
Quick summary of Rhat values by parameter name	check_Rhat
Compare Caterpillar Plots	comparecat
Compare Density	comparedens
Compare Priors	comparepriors
Correlation matrix from a JAGS object	cor_jags
Bivariate Plot of Posterior Densities	crossplot
Envelope plot	envelope
Expit, or inverse logit	expit
Extract data.frame	jags_df
Plist	jags_plist
Automated K-fold or Leave One Out Cross Validation	kfold
Logit	logit
Number of parameter nodes by parameter name	nbyname
Number of parameters	nparam
Overlay envelope plots	overlayenvelope
Pairs trace plot	pairstrace_jags
Diagnostic plots from posterior predictive distribution	plot_postpred
Plot a correlation matrix from a JAGS object	plotcor_jags
Plot kernel densities of single parameter nodes	plotdens
Plotting all Rhat values	plotRhats
Subset from posterior data.frame	pull_post
Quantile-quantile plot from posterior predictive distribution	qq_postpred
Random Colors	rcolors
Skeleton	skeleton
Example data: Time series associated with SS JAGS out	SS_data
Example data: SS JAGS out	SS_out
Trace plot of each column of a 'data.frame'.	trace_df
Trace plot of jagsUI object	trace_jags
Simple trace plot	trace_line
Combination of trace plots and by-chain kernel densities of 'jagsUI' object	tracedens_jags
Trace plots corresponding to the worst values of Rhat	traceworstRhat
Time series plot of centered posterior predictive distribution	ts_postpred