Package: compareMCMCs 0.6.0

Perry de Valpine

compareMCMCs: Compare MCMC Efficiency from 'nimble' and/or Other MCMC Engines

Manages comparison of MCMC performance metrics from multiple MCMC algorithms. These may come from different MCMC configurations using the 'nimble' package or from other packages. Plug-ins for JAGS via 'rjags' and Stan via 'rstan' are provided. It is possible to write plug-ins for other packages. Performance metrics are held in an MCMCresult class along with samples and timing data. It is easy to apply new performance metrics. Reports are generated as html pages with figures comparing sets of runs. It is possible to configure the html pages, including providing new figure components.

Authors:Perry de Valpine [aut, cre], Sally Paganin [aut], Daniel Turek [aut], Christopher Paciorek [aut]

compareMCMCs_0.6.0.tar.gz
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compareMCMCs_0.6.0.tgz(r-4.6-any)compareMCMCs_0.6.0.tgz(r-4.5-any)
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compareMCMCs_0.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
compareMCMCs/json (API)

# Install 'compareMCMCs' in R:

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

Bug tracker:https://github.com/nimble-dev/comparemcmcs/issues

On CRAN:

4.46 score 1 stars 29 scripts 252 downloads 26 exports 38 dependencies

Last updated from:47eef9c0c4. Checks:7 OK, 2 NOTE. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	234
source / vignettes	OK	261
linux-release-x86_64	OK	235
macos-release-arm64	NOTE	183
macos-oldrel-arm64	NOTE	127
windows-devel	OK	215
windows-release	OK	221
windows-oldrel	OK	277
wasm-release	OK	146

Exports:addMetrics applyConversions clearMetrics combineMetrics compareMCMCs getMetrics getPageComponents make_MCMC_comparison_pages MCMCdef_dummy MCMCdef_jags MCMCdef_stan MCMCmetric_CI95 MCMCmetric_CI95low MCMCmetric_CI95upp MCMCmetric_efficiency MCMCmetric_ESS MCMCmetric_mean MCMCmetric_median MCMCmetric_sd MCMCresult registerMCMCengine registerMetrics registerPageComponents renameMCMC unregisterMetric unregisterPageComponents

Dependencies:cli coda cpp11 dplyr farver generics ggplot2 glue gtable igraph isoband labeling lattice lifecycle magrittr Matrix nimble numDeriv pillar pkgconfig plyr pracma R6 RColorBrewer Rcpp reshape2 rlang S7 scales stringi stringr tibble tidyselect utf8 vctrs viridisLite withr xtable

Overview of compareMCMCs

Rendered fromcompareMCMCs.Rmdusingknitr::rmarkdown

Last update: 2024-10-02
Started: 2019-06-30

Help page	Topics
Apply a set of parameter conversions to MCMC output	applyConversions
Combine all metrics from a list of 'MCMCresult' objects.	combineMetrics
Run a set of MCMCs for performance comparison	compareMCMCs
Create html output with comparisons of MCMC results	make_MCMC_comparison_pages
MCMC plugins that come with the compareMCMCs package	builtin_MCMCs MCMCdef_dummy MCMCdef_jags MCMCdef_stan
R6 class to hold MCMC samples, timing results, and metrics	MCMCresult
Built-in metrics for 'MCMCresult' objects	MCMCmetric_CI95 MCMCmetric_CI95low MCMCmetric_CI95upp MCMCmetric_efficiency MCMCmetric_ESS MCMCmetric_mean MCMCmetric_median MCMCmetric_sd metrics
Manipulate metrics in one or more 'MCMCresult' object(s)	addMetrics clearMetrics modifyMetrics
Register, unregister and access page components used by 'make_MCMC_comparison_pages'	getPageComponents pageComponents registerPageComponents unregisterPageComponents
Register an MCMC function for use by compareMCMCs	registerMCMCengine
Register, unregister, or access registered MCMC metric functions for use by 'compareMCMCs' or 'addMetrics'	getMetrics registerMetrics unregisterMetric
Rename an MCMC method throughout a list of 'MCMCresult' objects	renameMCMC

Package: compareMCMCs 0.6.0

compareMCMCs: Compare MCMC Efficiency from 'nimble' and/or Other MCMC Engines

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Help Manual

Usage by other packages (reverse dependencies)