FLR

While its not strictly a bug, I note that there are two sets of code for the plot() method for an FLIndex object in FLIndex.r.

The first instance is on line 242...

## plot::FLIndex {{{
setMethod("plot", signature(x="FLIndex",y="missing"),
function(x, type=c("splom"), ...) {

plotinternal <- function(x, ... ) {
pfun <- function(x,y,...){
panel.xyplot(x,y, ...)
if (length(x) > 1) panel.lmline(x,y, lty=1)
}

The second on line 379...

# plot (FLIndex) {{{
# Author: Mark Payne, DIFRES
setMethod("plot", signature(x="FLIndex",y="missing"),
function(x, type=c("splom"), ...)
{
# The body of the plot method
validObject(x)
type <- type[1]

res <- switch(type,
"splom" = plotinternal(x=x, ... ),
"ts" = plotts(x=x, ... ),
"pairwise"=pairwiseConsistency(idx=x,...),
"internal"=plotInternalConsistency(idx=x,...),
cat("type must be 'splom', 'ts', 'pairwise' or 'internal'!\n"))
# Return result invisibly
invisible(res)
}
) # }}}

The first instance is probably overriden by the second, and therefore is probably redundant (???).

The structuring (and documentation) of these plotting functions could also probably be improved.