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.


Reference manual

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0.19-2 by Martyn Plummer, 4 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, 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, ggdmc, glmBfp, greta, hSDM, hierarchicalDS, hmi, immer, jagsUI, latentnet, list, lvmcomp, marked, mcmcr, mdmb, metaBMA, miWQS, miceadds, 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, spdep, spikeSlabGAM, sspse, statnet.common, stocc, 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, MasterBayes, PhaseType, R2WinBUGS, Rlda, SPACECAP, TESS, Ultimixt, WMCapacity, adaptMCMC, adaptsmoFMRI, anominate, bamlss, bayesDccGarch, bayesSurv, bayespref, bayou, bhm, bisoreg, 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, AnaCoDa, 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, nmathresh, outbreaker2, phybreak, polyfreqs, pscl, rase, rbi, season, shinystan, spCP, surveillance, systemicrisk, womblR, zoo.

See at CRAN