I want to be able to convert markdown italics and boldface to latex versions on the fly (i.e., give a text string(s) return a text string(s)). I thought easy. Wrong! (Which it still may be). See the sill buisness and error I tried at the bottom.
What I have (note the starting asterisk that's been escaped as in markdown):
x <- "\\*note: I *like* chocolate **milk** too ***much***!"
What I would like:
"*note: I \\emph{like} chocolate \\textbf{milk} too \\textbf{\\emph{much}}!"
I'm not attached to regex but would prefer a base solution (though not essential).
Silly business:
helper <- function(ins, outs, x) {
gsub(paste0(ins[1], ".+?", ins[2]), paste0(outs[1], ".+?", outs[2]), x)
}
helper(rep("***", 2), c("\\textbf{\\emph{", "}}"), x)
Error in gsub(paste0(ins[1], ".+?", ins[2]), paste0(outs[1], ".+?", outs[2]), :
invalid regular expression '***.+?***', reason 'Invalid use of repetition operators'
I have this toy that Ananda Mahto helped me make if it's helpful. You could access it from reports via wheresPandoc <- reports:::wheresPandoc
EDIT Per Ben's comments I tried:
action <- paste0(" echo ", x, " | ", wheresPandoc(), " -t latex ")
system(action)
*note: I *like* chocolate **milk** too ***much***! | C:\PROGRA~2\Pandoc\bin\pandoc.exe -t latex
EDIT2 Per Dason's comments I tried:
out <- paste("echo", shQuote(x), "|", wheresPandoc(), " -t latex"); system(out)
system(out, intern = T)
> system(out, intern = T)
\*note: I *like* chocolate **milk** too ***much***! | C:\PROGRA~2\Pandoc\bin\pandoc.exe -t latex
The lack of pipes on Windows made this tricky, but you can get around it using input to provide the stdin:
> x = system("pandoc -t latex", intern=TRUE, input="\\*note: I *like* chocolate **milk** too ***much***!")
> x
[1] "*note: I \\emph{like} chocolate \\textbf{milk} too \\textbf{\\emph{much}}!"
Noting I am working on windows and from ?system
This means that redirection, pipes, DOS internal commands, ... cannot be used
and the note from ?system2
Note
system2 is a more portable and flexible interface than system,
introduced in R 2.12.0. It allows redirection of output without
needing to invoke a shell on Windows, a portable way to set
environment variables for the execution of command, and finer control
over the redirection of stdout and stderr. Conversely, system (and
shell on Windows) allows the invocation of arbitrary command lines.
Using system2
system2('pandoc', '-t latex', input = '**em**', stdout = TRUE)
I'm running into a problem with the MNP package which I've traced to an unfortunate call to deparse (whose maximum width is limited to 500 characters).
Background (easily skippable if you're bored)
Because mnp uses a somewhat idiosyncratic syntax to allow for varying choice sets (you include cbind(choiceA,choiceB,...) in the formula definition), the left hand side of my formula call is 1700 characters or so when model.matrix.default calls deparse on it. Since deparse supports a maximum width.cutoff of 500 characters, the sapply(attr(t, "variables"), deparse, width.cutoff = 500)[-1L] line in model.matrix.default has as its first element:
[1] "cbind(plan1, plan2, plan3, plan4, plan5, plan6, plan7, plan8, plan9, plan10, plan11, plan12, plan13, plan14, plan15, plan16, plan17, plan18, plan19, plan20, plan21, plan22, plan23, plan24, plan25, plan26, plan27, plan28, plan29, plan30, plan31, plan32, plan33, plan34, plan35, plan36, plan37, plan38, plan39, plan40, plan41, plan42, plan43, plan44, plan45, plan46, plan47, plan48, plan49, plan50, plan51, plan52, plan53, plan54, plan55, plan56, plan57, plan58, plan59, plan60, plan61, plan62, plan63, "
[2] " plan64, plan65, plan66, plan67, plan68, plan69, plan70, plan71, plan72, plan73, plan74, plan75, plan76, plan77, plan78, plan79, plan80, plan81, plan82, plan83, plan84, plan85, plan86, plan87, plan88, plan89, plan90, plan91, plan92, plan93, plan94, plan95, plan96, plan97, plan98, plan99, plan100, plan101, plan102, plan103, plan104, plan105, plan106, plan107, plan108, plan109, plan110, plan111, plan112, plan113, plan114, plan115, plan116, plan117, plan118, plan119, plan120, plan121, plan122, plan123, "
[3] " plan124, plan125, plan126, plan127, plan128, plan129, plan130, plan131, plan132, plan133, plan134, plan135, plan136, plan137, plan138, plan139, plan140, plan141, plan142, plan143, plan144, plan145, plan146, plan147, plan148, plan149, plan150, plan151, plan152, plan153, plan154, plan155, plan156, plan157, plan158, plan159, plan160, plan161, plan162, plan163, plan164, plan165, plan166, plan167, plan168, plan169, plan170, plan171, plan172, plan173, plan174, plan175, plan176, plan177, plan178, plan179, "
[4] " plan180, plan181, plan182, plan183, plan184, plan185, plan186, plan187, plan188, plan189, plan190, plan191, plan192, plan193, plan194, plan195, plan196, plan197, plan198, plan199, plan200, plan201, plan202, plan203, plan204, plan205, plan206, plan207, plan208, plan209, plan210, plan211, plan212, plan213, plan214, plan215, plan216, plan217, plan218, plan219, plan220, plan221, plan222, plan223, plan224, plan225, plan226, plan227, plan228, plan229, plan230, plan231, plan232, plan233, plan234, plan235, "
[5] " plan236, plan237, plan238, plan239, plan240, plan241, plan242, plan243, plan244, plan245, plan246, plan247, plan248, plan249, plan250, plan251, plan252, plan253, plan254, plan255, plan256, plan257, plan258, plan259, plan260, plan261, plan262, plan263, plan264, plan265, plan266, plan267, plan268, plan269, plan270, plan271, plan272, plan273, plan274, plan275, plan276, plan277, plan278, plan279, plan280, plan281, plan282, plan283, plan284, plan285, plan286, plan287, plan288, plan289, plan290, plan291, "
[6] " plan292, plan293, plan294, plan295, plan296, plan297, plan298, plan299, plan300, plan301, plan302, plan303, plan304, plan305, plan306, plan307, plan308, plan309, plan310, plan311, plan312, plan313)"
When model.matrix.default tests this against the variables in the data.frame, it returns an error.
The problem
To get around this, I've written a new deparse function:
deparse <- function (expr, width.cutoff = 60L, backtick = mode(expr) %in%
c("call", "expression", "(", "function"), control = c("keepInteger",
"showAttributes", "keepNA"), nlines = -1L) {
ret <- .Internal(deparse(expr, width.cutoff, backtick, .deparseOpts(control), nlines))
paste0(ret,collapse="")
}
However, when I run mnp again and step through, it returns the same error for the same reason (base::deparse is being run, not my deparse).
This is somewhat surprising to me, as what I expect is more typified by this example, where the user-defined function temporarily over-writes the base function:
> print <- function() {
+ cat("user-defined print ran\n")
+ }
> print()
user-defined print ran
I realize the right way to solve this problem is to rewrite model.matrix.default, but as a tool for debugging I'm curious how to force it to use my deparse and why the anticipated (by me) behavior is not happening here.
The functions fixInNamespace and assignInNamespace are provided to allow editing of existing functions. You could try ... but I will not since mucking with deparse looks too dangerous:
assignInNamespace("deparse",
function (expr, width.cutoff = 60L, backtick = mode(expr) %in%
c("call", "expression", "(", "function"), control = c("keepInteger",
"showAttributes", "keepNA"), nlines = -1L) {
ret <- .Internal(deparse(expr, width.cutoff, backtick, .deparseOpts(control), nlines))
paste0(ret,collapse="")
} , "base")
There is an indication on the help page that the use of such functions has restrictions and I would not be surprised that such core function might have additional layers of protection. Since it works via side-effect, you should not need to assign the result.
This is how packages with namespaces search for functions, as described in Section 1.6, Package Namespaces of Writing R Extensions
Namespaces are sealed once they are loaded. Sealing means that imports
and exports cannot be changed and that internal variable bindings
cannot be changed. Sealing allows a simpler implementation strategy
for the namespace mechanism. Sealing also allows code analysis and
compilation tools to accurately identify the definition corresponding
to a global variable reference in a function body.
The namespace controls the search strategy for variables used by
functions in the package. If not found locally, R searches the package
namespace first, then the imports, then the base namespace and then
the normal search path.