Importing package namespace into default namespace [duplicate] - r

Question

This question already has an answer here:
How can I read the source code for an R function?
(1 answer)
Closed 9 years ago.
Frequently when I am working with R and I want to find out what the function does, I type in the name of the function and scroll through the code. However, sometimes when I type in the name of the function I get a response that does not tell me anything.
> library(limma)
> plotMDS #can't get to the code
function (x, ...)
UseMethod("plotMDS")
<environment: namespace:limma>
> limma:::plotMDS
function (x, ...)
UseMethod("plotMDS")
<environment: namespace:limma>
> heatmap #im expecting something more like this
function (x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL,
distfun = dist, hclustfun = hclust, reorderfun = function(d,
w) reorder(d, w), add.expr, symm = FALSE, revC = identical(Colv,
"Rowv"), scale = c("row", "column", "none"), na.rm = TRUE,
margins = c(5, 5), ColSideColors, RowSideColors, cexRow = 0.2 +
1/log10(nr), cexCol = 0.2 + 1/log10(nc), labRow = NULL,
labCol = NULL, main = NULL, xlab = NULL, ylab = NULL, keep.dendro = FALSE,
verbose = getOption("verbose"), ...)
{
scale <- if (symm && missing(scale))
"none"
else match.arg(scale)
/* ... many lines removed ... */
}
invisible(list(rowInd = rowInd, colInd = colInd, Rowv = if (keep.dendro &&
doRdend) ddr, Colv = if (keep.dendro && doCdend) ddc))
}
<bytecode: 0x16199b8>
<environment: namespace:stats>
Thus, I was wondering if there is a way to import a package's namespace into the default namespace so I can look at code in functions (and debug things easier). I've been reading up on namespace but most of the time it is written for developers so it is talking about how to export namespaces for packages.

Answer 1

plotMDS is the generic function. What you access via plotMDS and limma:::plotMDS is exactly the same thing, the latter just less-efficiently. What you want to get at are the methods for this generic function.
To see the list of method for plotMDS try
methods(plotMDS)
That will return a vector of function names. I can't install limma so here is what we see for the base plot generic [in my current session]:
> methods(plot)
[1] plot.acf* plot.correspondence* plot.data.frame*
[4] plot.decomposed.ts* plot.default plot.dendrogram*
[7] plot.density plot.ecdf plot.factor*
[10] plot.formula* plot.function plot.hclust*
[13] plot.histogram* plot.HoltWinters* plot.isoreg*
[16] plot.lda* plot.lm plot.mca*
[19] plot.medpolish* plot.mlm plot.ppr*
[22] plot.prcomp* plot.princomp* plot.profile*
[25] plot.profile.nls* plot.ridgelm* plot.spec
[28] plot.stepfun plot.stl* plot.table*
[31] plot.ts plot.tskernel* plot.TukeyHSD
Non-visible functions are asterisked
To access the code of non-starred functions we just enter the full function name, e.g.
> plot.density
function (x, main = NULL, xlab = NULL, ylab = "Density", type = "l",
zero.line = TRUE, ...)
{
....
To see the code for starred functions/methods you need the pkg:::function structure, e.g. for the plot.data.frame method
> plot.data.frame
Error: object 'plot.data.frame' not found
> graphics:::plot.data.frame
function (x, ...)
{
....
If you don't know which namespace a method belongs to, then use getAnywhere, e.g.
> getAnywhere(plot.data.frame)
A single object matching ‘plot.data.frame’ was found
It was found in the following places
registered S3 method for plot from namespace graphics
namespace:graphics
with value
function (x, ...)
{
....
The printed results indicate the relevant namespace (in this case graphics) plus return the value of the function, or the code.

Answer 2

This is a really crude alternative, but it does what was requested:
Firstly, copy the contents of the namespace to a list in the global environment:
L <- as.list(asNamespace("yourpackage"))
Now you can either navigate L or copy all its contents to equally named objects in the global environment with this:
invisible(lapply(names(L), function(x) eval(parse(text=paste0(x,"<-L[['",x,"']]")), globalenv())))
warning: this will overwrite whatever object you have defined with the same name! So use with care.