Package: genMCMCDiag 0.2.2.9000

Luke Duttweiler

genMCMCDiag: Generalized Convergence Diagnostics for Difficult MCMC Algorithms

Trace plots and convergence diagnostics for Markov Chain Monte Carlo (MCMC) algorithms on highly multivariate or unordered spaces. Methods outlined in a forthcoming paper.

Authors:Luke Duttweiler [aut, cre, cph]

genMCMCDiag_0.2.2.9000.tar.gz
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genMCMCDiag.pdf |genMCMCDiag.html✨
genMCMCDiag/json (API)
NEWS

# Install 'genMCMCDiag' in R:

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

Bug tracker:https://github.com/lukeduttweiler/genmcmcdiag/issues

Datasets:

bnMCMCResults - Results from a Bayesian Network MCMC algorithm on simulated data
uniMCMCResults - Results from a univariate MCMC algorithm on a simulated posterior

On CRAN:

4 exports 1.59 score 56 dependencies 1 dependents 3 scripts 236 downloads

Last updated 2 months agofrom:15d6c48bd8. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 10 2024
R-4.5-win	OK	Sep 10 2024
R-4.5-linux	OK	Sep 10 2024
R-4.4-win	OK	Sep 10 2024
R-4.4-mac	OK	Sep 10 2024
R-4.3-win	OK	Sep 10 2024
R-4.3-mac	OK	Sep 10 2024

Exports:eucDist genDiagnostic hammingDist partitionDist

Dependencies:brio callr cli coda colorspace crayon desc diffobj digest ellipse evaluate fansi farver fftwtools fs ggplot2 glue gtable highr isoband jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix mcmcse mgcv munsell nlme pillar pkgbuild pkgconfig pkgload praise processx ps R6 RColorBrewer Rcpp RcppArmadillo rematch2 rlang rprojroot scales testthat tibble utf8 vctrs viridisLite waldo withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Results from a Bayesian Network MCMC algorithm on simulated data	bnMCMCResults
DPMM Distance	dpmmDistance
Uses generic formulas and rough time estimate to estimate time it will take to evaluate the TS algorithm on a set of unique draws with the tsTransform function.	estimateTsTime
Euclidean Distance	eucDist
Helpful mini function to fit the nearest neighbor (NN) algorithm given a set and defined distance	fitNN
Generate Generalized Diagnostics for Markov Chain Monte Carlo Draws	genDiagnostic
Hamming Distance	hammingDist
Transforms a list of MCMC chains into a list of data.frames using the Lanfear transformation	lanfearTransform
Function to assign character labels to all unique objects in a list	listLabels
Partition Distance	partitionDist
Print method for mcmcDiag objects	print.mcmcDiag
Calculate the effective sample size, per chain and in total, of draws from an MCMC algorithm	sess
Calculate the Gelman-Rubin diagnostic of draws from an MCMC algorithm	sgelmanRubin
Transforms a list of MCMC chains into a list of dataframes with no modifications to values	standardTransform
Generate a traceplot of draws from a multi-chain MCMC	straceplot
Transforms a list of MCMC chains into a list of data.frames using the TS transformation	tsTransform
Results from a univariate MCMC algorithm on a simulated posterior	uniMCMCResults