Nothing
## plot methods (coda and lattice)
.plot_mcmc_list <- function (x, trace = TRUE, density = TRUE,
smooth = TRUE, bwf, auto.layout = TRUE, ask = par("ask"), ...) {
.set_mfrow <- function (Nchains = 1, Nparms = 1,
nplots = 1, sepplot = FALSE) {
mfrow <- if (sepplot && Nchains > 1 && nplots == 1) {
if (Nchains == 2) {
switch(min(Nparms, 5), c(1, 2), c(2, 2), c(3, 2),
c(4, 2), c(3, 2))
}
else if (Nchains == 3) {
switch(min(Nparms, 5), c(2, 2), c(2, 3), c(3, 3),
c(2, 3), c(3, 3))
}
else if (Nchains == 4) {
if (Nparms == 1)
c(2, 2)
else c(4, 2)
}
else if (any(Nchains == c(5, 6, 10, 11, 12)))
c(3, 2)
else if (any(Nchains == c(7, 8, 9)) || Nchains >= 13)
c(3, 3)
}
else {
if (nplots == 1) {
mfrow <- switch(min(Nparms, 13), c(1, 1), c(1, 2),
c(2, 2), c(2, 2), c(3, 2), c(3, 2), c(3, 3),
c(3, 3), c(3, 3), c(3, 2), c(3, 2), c(3, 2),
c(3, 3))
}
else {
mfrow <- switch(min(Nparms, 13), c(1, 2), c(2, 2),
c(3, 2), c(4, 2), c(3, 2), c(3, 2), c(4, 2),
c(4, 2), c(4, 2), c(3, 2), c(3, 2), c(3, 2),
c(4, 2))
}
}
return(mfrow)
}
oldpar <- NULL
on.exit(par(oldpar))
if (auto.layout) {
mfrow <- .set_mfrow(Nchains = nchain(x), Nparms = nvar(x),
nplots = trace + density)
oldpar <- par(mfrow = mfrow)
}
for (i in 1:nvar(x)) {
if (trace)
traceplot(x[, i, drop = FALSE], smooth = smooth,
...)
if (density) {
if (missing(bwf))
densplot(x[, i, drop = FALSE], ...)
else densplot(x[, i, drop = FALSE], bwf = bwf, ...)
}
if (i == 1)
oldpar <- c(oldpar, par(ask = ask))
}
}
setMethod("plot", signature(x="MCMClist", y="missing"), function(x, ...)
.plot_mcmc_list(as(x, "mcmc.list"), ...))
setMethod("plot", signature(x="codaMCMC", y="missing"), function(x, ...)
plot(as(x, "MCMClist"), ...))
setMethod("plot", signature(x="dcmle", y="missing"), function(x, ...)
plot(as(x, "MCMClist"), ...))
#setGeneric("traceplot", function(x, ...) standardGeneric("traceplot"))
setMethod("traceplot", "MCMClist", function(x, ...)
coda::traceplot(x, ...))
setMethod("traceplot", "codaMCMC", function(x, ...)
traceplot(as(x, "MCMClist"), ...))
setMethod("traceplot", "dcmle", function(x, ...)
traceplot(as(x, "MCMClist"), ...))
#setGeneric("densplot", function(x, ...) standardGeneric("densplot"))
setMethod("densplot", "MCMClist", function(x, ...)
coda::densplot(x, ...))
setMethod("densplot", "codaMCMC", function(x, ...)
densplot(as(x, "MCMClist"), ...))
setMethod("densplot", "dcmle", function(x, ...)
densplot(as(x, "MCMClist"), ...))
#setGeneric("pairs", function(x, ...) standardGeneric("pairs"))
setMethod("pairs", "MCMClist", function(x, ...)
dclone::pairs.mcmc.list(x, ...))
setMethod("pairs", "codaMCMC", function(x, ...)
pairs(as(x, "MCMClist")))
setMethod("pairs", "dcmle", function(x, ...)
pairs(as(x, "MCMClist")))
#setGeneric("densityplot", function(x, ...) standardGeneric("densityplot"))
setMethod("densityplot", "MCMClist",
function(x, data, ...)
lattice::densityplot(as(x, "mcmc.list"), data, ...))
setMethod("densityplot", "codaMCMC",
function(x, data, ...)
densityplot(as(x, "MCMClist"), data, ...))
setMethod("densityplot", "dcmle",
function(x, data, ...)
densityplot(as(x, "MCMClist"), data, ...))
#setGeneric("qqmath", function(x, ...) standardGeneric("qqmath"))
setMethod("qqmath", "MCMClist",
function(x, data, ...)
lattice::qqmath(as(x, "mcmc.list"), data, ...))
setMethod("qqmath", "codaMCMC",
function(x, data, ...)
qqmath(as(x, "MCMClist"), data, ...))
setMethod("qqmath", "dcmle",
function(x, data, ...)
qqmath(as(x, "MCMClist"), data, ...))
#setGeneric("xyplot", function(x, ...) standardGeneric("xyplot"))
setMethod("xyplot", "MCMClist",
function(x, data, ...)
lattice::xyplot(as(x, "mcmc.list"), data, ...))
setMethod("xyplot", "codaMCMC",
function(x, data, ...)
xyplot(as(x, "MCMClist"), data, ...))
setMethod("xyplot", "dcmle",
function(x, data, ...)
xyplot(as(x, "MCMClist"), data, ...))
#setGeneric("acfplot", function(x, ...) standardGeneric("acfplot"))
setMethod("acfplot", "MCMClist",
function(x, data, ...)
coda::acfplot(as(x, "mcmc.list"), data, ...))
setMethod("acfplot", "codaMCMC",
function(x, data, ...)
acfplot(as(x, "MCMClist"), data, ...))
setMethod("acfplot", "dcmle",
function(x, data, ...)
acfplot(as(x, "MCMClist"), data, ...))
## this plots only mcmc (one chain at a time)
#setGeneric("levelplot", function(x, ...) standardGeneric("levelplot"))
#setMethod("levelplot", "MCMClist",
# function(x, ...)
# coda:::levelplot.mcmc.list(x, ...))
#setMethod("levelplot", "dcmle",
# function(x, ...)
# levelplot(as(x, "MCMClist"), data, ...))
setGeneric("crosscorr.plot", function(x, ...)
standardGeneric("crosscorr.plot"))
setMethod("crosscorr.plot", "dcmle", function(x, ...)
crosscorr.plot(as(x, "MCMClist"), ...))
setMethod("crosscorr.plot", "codaMCMC", function(x, ...)
crosscorr.plot(as(x, "MCMClist"), ...))
setMethod("crosscorr.plot", "MCMClist", function(x, ...)
coda::crosscorr.plot(x, ...))
setGeneric("gelman.plot", function(x, ...)
standardGeneric("gelman.plot"))
setMethod("gelman.plot", "dcmle", function(x, ...)
gelman.plot(as(x, "MCMClist"), ...))
setMethod("gelman.plot", "codaMCMC", function(x, ...)
gelman.plot(as(x, "MCMClist"), ...))
setMethod("gelman.plot", "MCMClist", function(x, ...)
coda::gelman.plot(x, ...))
setGeneric("cumuplot", function(x, ...)
standardGeneric("cumuplot"))
setMethod("cumuplot", "MCMClist", function(x, ...)
coda::cumuplot(x, ...))
setMethod("cumuplot", "codaMCMC", function(x, ...)
cumuplot(as(x, "MCMClist"), ...))
setMethod("cumuplot", "dcmle", function(x, ...)
cumuplot(as(x, "MCMClist"), ...))
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