autocorrdiag.R
autocorr.diag.mcmc (method for the mcmc class)
depends on:
autocorr() defined in "output.R"
batchSE.R codamenu.R cumuplot.R gelman.R gelman.diag as.mcmc.list (mcmclist.R) mcmc.list (mcmclist.R) nchain (mcextractor.R) start (start.mcmc, mcmc.R) end (end.mcmc, mcmc.R) window (window.mcmc mcmc.R) (window.mcmc.list mcmclist.R) niter (mcextractor.R) varnames (mcextractor.R) matrix (base) array(base) var (stats) t (base) is.R (base) chol, The Choleski Decomposition (base) eigen (stats) matrix Spectral decomp backsolve (base) solve upper/lower trian system matrix (base) qr.solve (base, see "qr" in general) eigen (base) eigen uses the LAPACK routines DSYEVR, DGEEV, ZHEEV and ZGEEV sqrt (base) diag (base) var(base) t() class (get class attribute)
gelman.transform
is.R
options (base)
getOption (base)
data.frame (base)
min (base)
max (base)
log (base)
gelman.mv.diag
matrix
var
eigen
qr
print.gelman.diag
print, cat, format
gelman.plot
as.mcmc.list
par
matplot
gelman.preplot
array (base, nice consturctions)
geman.diag (this file)
geweke.R
heidel.R
HPDinterval.R
jags.R
mcextractor.R
mcmc.R
"[.mcmc" access the sample array
"as.mcmc" (generic)
"as.mcmc.default"
"as.ts.mcmc"
ts(x, start, ebd, deltat=thin)
set attr "mcpar" to zero
"start.mcmc"
mcpar(as.mcmc(x))[1]
"end.mcmc"
mcpar(as.mcmc(x))[2]
"fequency.mcmc" 1/thin.mcmc(x)
"thin.mcmc"
TODO: what is "thinning" in mcmc lingo
"is.mcmc" somewhere in the class hierarchy is "mcmc"
"mcmc" construct mcmc object
"print.mcmc" its like a toString()
"as.matrix.mcmc" <- dimnames(y)
"time.mcmc" <- convert to ts object with actual time values as data
"window.mcmc" <- slice an mcmc object
"mcmcUpgrade" <- upgrade in format not known to you
"head.mcmc" <- usus window.mcmc
"tail.mcmc" <- usus window.
mcmclist.R "[.mcmc.list" subsetting mcmc.list, not needed "mcmc.list" compose an r-list of several mcmc objects "start.mcmc.list" just get the "start" of the first one in the list "end.mcmc.list" just get then "end" of the first one in the list "thin.mcmc.list" get the first "thin" in the list "plot.mcmc.list" NA "summary.mcmc.list" NA "as.matrix.mcmc.list" 'algamation of the data into a single matrix" "as.mcmc.mcmc.list" nchain(x)==1 otherwise error "time.mcmc.list" get the time of the first elt "window.mcmc.list" get the window of the first elt "window.mcmc.list" --> applies "window.mcmc" "head.mcmc.list" --> applies "head.mcmc" "tail.mcmc.list" --> applies "tail.mcmc" "as.mcmc.list" --> S3 generic "as.mcmc.list.default" --> identity "as.array.mcmc.list" nchain array drop (delete the extentions of an array that have only 1 level) output.R raftery.R rejectionRate.R thin.R trellisplots.R util.R
ls(getNamespace("coda"),all.names=TRUE) [1] ".Coda.Options.Default" ".NAMESPACE." [3] ".S3MethodsTable." ".packageName" [5] "HPDinterval" "HPDinterval.mcmc" [7] "HPDinterval.mcmc.list" "[.mcmc"
operator overloading mcmc[..][9] "[.mcmc.list" "acfplot" [11] "acfplot.mcmc" "acfplot.mcmc.list" [13] "as.array.mcmc.list" "as.data.frame.mcmc" [15] "as.matrix.mcmc" "as.matrix.mcmc.list" [17] "as.mcmc" "as.mcmc.default" [19] "as.mcmc.list" "as.mcmc.list.default" [21] "as.mcmc.mcmc.list" "as.ts.mcmc" [23] "autocorr" "autocorr.diag" [25] "autocorr.diag.mcmc" "autocorr.diag.mcmc.list" [27] "autocorr.plot" "batchSE" [29] "batchSE.mcmc" "batchSE.mcmc.list" [31] "bugs2jags" "chanames" [33] "chanames<-" "change.tfoption" [35] "coda.env" "coda.options" [37] "codamenu" "codamenu.anal" [39] "codamenu.diags" "codamenu.diags.autocorr" [41] "codamenu.diags.crosscorr" "codamenu.diags.gelman" [43] "codamenu.diags.geweke" "codamenu.diags.heidel" [45] "codamenu.diags.raftery" "codamenu.main" [47] "codamenu.options" "codamenu.options.data" [49] "codamenu.options.diag" "codamenu.options.gelman" [51] "codamenu.options.geweke.bin" "codamenu.options.geweke.win" [53] "codamenu.options.heidel" "codamenu.options.plot" [55] "codamenu.options.plot.kernel" "codamenu.options.raftery" [57] "codamenu.options.stats" "codamenu.output.header" [59] "codamenu.ps" "crosscorr" [61] "crosscorr.plot" "cumuplot" [63] "densityplot.mcmc" "densityplot.mcmc.list" [65] "densplot" "display.coda.options" [67] "display.working.data" "do.spectrum0" [69] "effectiveSize" "end.mcmc" [71] "end.mcmc.list" "frequency.mcmc" [73] "gelman.diag" "gelman.mv.diag" [75] "gelman.plot" "gelman.preplot" [77] "gelman.transform" "geweke.diag" [79] "geweke.plot" "head.mcmc" [81] "head.mcmc.list" "heidel.diag" [83] "is.mcmc" "is.mcmc.list" [85] "levelplot.mcmc" "mcmc" [87] "mcmc.list" "mcmcUpgrade" [89] "mcpar" "multi.menu" [91] "nchain" "niter" [93] "nvar" "panel.acfplot" [95] "pcramer" "plot.mcmc" [97] "plot.mcmc.list" "pretty.discrete" [99] "print.gelman.diag" "print.geweke.diag" [101] "print.heidel.diag" "print.mcmc" [103] "print.raftery.diag" "print.summary.mcmc" [105] "qqmath.mcmc" "qqmath.mcmc.list" [107] "raftery.diag" "read.and.check" [109] "read.coda" "read.coda.interactive" [111] "read.jags" "read.openbugs" [113] "read.yesno" "rejectionRate" [115] "rejectionRate.mcmc" "rejectionRate.mcmc.list" [117] "safespec0" "set.mfrow" [119] "spectrum0" "spectrum0.ar" [121] "splom.mcmc" "start.mcmc" [123] "start.mcmc.list" "summary.mcmc" [125] "summary.mcmc.list" "tail.mcmc" [127] "tail.mcmc.list" "thin" [129] "thin.mcmc" "thin.mcmc.list" [131] "thinned.indices" "time.mcmc" [133] "time.mcmc.list" "traceplot" [135] "varnames" "varnames<-" [137] "window.mcmc" "window.mcmc.list" [139] "xyplot.mcmc" "xyplot.mcmc.list"