Output Analysis and Diagnostics for MCMC

Provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.


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install.packages("coda")

0.19-2 by Martyn Plummer, 6 months ago


Browse source code at https://github.com/cran/coda


Authors: Martyn Plummer [aut, cre, trl] , Nicky Best [aut] , Kate Cowles [aut] , Karen Vines [aut] , Deepayan Sarkar [aut] , Douglas Bates [aut] , Russell Almond [aut] , Arni Magnusson [aut]


Documentation:   PDF Manual  


Task views: Bayesian Inference, gRaphical Models in R


GPL (>= 2) license


Imports lattice


Imported by AHMbook, BAMBI, BANOVA, BDWreg, BEST, BNSP, BPEC, BRugs, BSL, BTSPAS, BTYDplus, BaBooN, BaM, BayesBinMix, BayesComm, BayesFM, BayesRS, BayesSingleSub, BayesX, BayesianTools, Bayesrel, Bchron, Bergm, BiProbitPartial, CARBayes, CARBayesST, CaliCo, DeLorean, DrBats, EasyMARK, GERGM, HLSM, IFP, IRATER, JointAI, LAM, MCMCvis, MPTmultiverse, MRH, MSEtool, MSGARCH, MetaLandSim, MfUSampler, MixSIAR, MplusAutomation, NestedCategBayesImpute, PANICr, POUMM, PVAClone, R2OpenBUGS, R2admb, R2jags, RMark, RcmdrPlugin.RMTCJags, SAVE, SIBER, SeqFeatR, TAM, TBSSurvival, TreeBUGS, Zelig, agRee, apTreeshape, apollo, arm, auRoc, bairt, bamp, bayesGARCH, bayesLife, bayesTFR, bayescount, bayeslm, bayesmix, bcgam, bdpopt, bfa, bfw, bgsmtr, blavaan, bridgesampling, brms, broom.mixed, bsam, bssm, btergm, circglmbayes, conting, ctmcd, dalmatian, dcmle, deBInfer, diagis, eggCounts, eiPack, eiwild, emdbook, ergm, ergm.ego, evolqg, evolvability, ewoc, fabMix, fdasrvf, geiger, geoBayes, glmBfp, greta, hSDM, hierarchicalDS, hmi, immer, jagsUI, latentnet, list, llbayesireg, lvmcomp, marked, mcmcabn, mcmcr, mdmb, metaBMA, miWQS, mixAK, morse, multimark, nLTT, networkTomography, nimble, nse, pcnetmeta, phytools, plotMCMC, polySegratioMM, pomp, ptycho, qrjoint, r4ss, ratematrix, rbacon, redist, ref.ICAR, rjmcmc, rr, runjags, rwty, scape, shinyrecap, simmr, sirt, slfm, sns, spBayesSurv, spTDyn, spTimer, sparsereg, spatialreg, spdep, spikeSlabGAM, sspse, statnet.common, stocc, tRophicPosition, telefit, tergm, tidybayes, tuts, wiqid, zic, zooaRchGUI.

Depended on by AdjBQR, ArchaeoChron, ArchaeoPhases, B2Z, BAYSTAR, BMAmevt, BayLum, BayesFactor, BayesLCA, BayesSAE, BayesTwin, DPP, EpiILM, EpiILMCT, FME, HelpersMG, HybridMC, ICBayes, ISEtools, InSilicoVA, MBSP, MCMC.OTU, MCMC.qpcr, MCMCglmm, MCMCpack, MCMCtreeR, MasterBayes, PhaseType, R2WinBUGS, Rlda, RxCEcolInf, SPACECAP, TESS, Ultimixt, WMCapacity, adaptMCMC, adaptsmoFMRI, anominate, bamlss, bayesDccGarch, bayesSurv, bayespref, bayou, bhm, bmk, boral, c212, coalescentMCMC, codadiags, cplm, cubfits, dclone, endorse, gemtc, hzar, iFad, icenReg, lira, mcgibbsit, mcmcplots, mcsm, motmot.2.0, ocomposition, phase1PRMD, phase1RMD, popReconstruct, prevalence, ramps, relevent, rjags, robustsae, siar, spBayes, spNNGP, spatial.gev.bma, stochvol, superdiag, zoib.

Suggested by AdMit, BBMV, BGGE, BayHaz, CARrampsOcl, DiffusionRgqd, DiffusionRimp, DiffusionRjgqd, HDInterval, Luminescence, R2BayesX, SALTSampler, airGR, amen, bayesImageS, bcp, bnormnlr, broom, embryogrowth, emmeans, gap, geoCount, geoRglm, ggmcmc, glmmTMB, glmmfields, icensBKL, ltbayes, miceadds, nmathresh, outbreaker2, phybreak, polyfreqs, pscl, rase, rbi, season, shinystan, spCP, surveillance, systemicrisk, womblR, zoo.


See at CRAN