#' Trace plots
#'
#' Use reader.exe to view .psv file and create a more complete parampost.out
#' file (THK) Traces
#'
#' @export
#'
Trace_posterior <- function(stock, source.dir, target.dir = source.dir[1])
{
# How many chains are we plotting?
Nchain <- length(source.dir)
data <- NULL
for (Chain in 1:Nchain)
{
parameter <- read.table(paste(source.dir[Chain], "/parampost.out", sep = ""), header = TRUE, as.is = TRUE)
nam1 <- as.character(scan(paste(source.dir[Chain], "/parampost.out", sep = ""), nlines = 1, what = "character", quiet = TRUE))
indicators <- read.table(paste(source.dir[Chain], "/indicpost.out", sep = ""), header = TRUE, as.is = TRUE)
nam2 <- as.character(scan(paste(source.dir[Chain], "/indicpost.out", sep = ""), nlines = 1, what = "character", quiet = TRUE))
Nsim <- nrow(parameter)
d1 <- data.frame(parameter, indicators, as.factor(Chain), 1:Nsim)
names(d1) <- c(nam1, nam2, "Chain", "sample")
data <- rbind(data, d1)
}
# Delete constant columns/parameters
loc.del <- c()
for ( datacol in 1:ncol(data) )
{
if ( length(unique(data[[datacol]])) == 1 & names(data[datacol]) != "Chain" )
{
loc.del <- c(loc.del,datacol)
}
}
if (!is.null(loc.del)) data <- data[,-loc.del]
nam <- names(data)
Nsim <- nrow(data)
dfm <- melt(data, id.vars = c("Chain","sample"))
# Add a running mean line but only if a single chain is being plotted
if (Nchain == 1)
{
i <- which(!names(data) %in% c("Chain","sample"))
ma <- apply(data[,i], 2, moving.average, n = MCMCOptions$running.mean)
ma <- melt(ma)
dfm$ma <- ma$value
#dfm$variable <- factor(rep(nam, each = Nsim))
}
# Do the plots
Nplots <- ceiling(ncol(data) / MCMCOptions$n.post)
for ( pp in 1:Nplots )
{
PlotType(paste(target.dir, "/", stock, "Trace_posterior", pp, sep = ""),
width = 1.6*PlotOptions$plotsize[1], height = 1.5*PlotOptions$plotsize[2])
cvars <- nam[((MCMCOptions$n.post * (pp - 1)) + 1):(MCMCOptions$n.post * pp)]
dat <- subset(dfm, subset = variable %in% cvars)
p <- ggplot(data = dat, aes(x = sample, y = value, colour = Chain)) +
geom_line(alpha = 0.7) +
scale_colour_manual(values = PlotOptions$colourPalette) +
facet_wrap( ~ variable, nrow = 6, ncol = 2, scales = "free_y", drop = TRUE) +
xlab("\nSample") + ylab(NULL) + theme_lobview(PlotOptions)
if (Nsim == 1) p <- p + geom_line(aes(x = sample, y = ma), colour = PlotOptions$colourPalette[2])
print(p)
dev.off()
}
}
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