It has something to do with the default inline hook, I realize that and I have tried getting at it (the hook) and also read this thread and Yihui's page about hooks, but I haven't been able to solve my issue. I even tried this suggestion from Sacha Epskamp, but it didn't do this trick in my case.
I'm using \Sexpr and doing something along the lines of \Sexpr{load("meta.data.saved"); meta.data[1,7]} to print a keyword in my report, the problem is that people writing these keywords (people I can't control) are using special LaTeX characters ($, &, %, # etc.) and when they are passed to my .tex file without an \ I'm having a bad time.
I have an .Rnw file with this code,
\documentclass{article}
\begin{document}
Look \Sexpr{foo <- "me&you"; foo} at this.
\end{document}
Thsi creates an .tex file with an illegal LaTeX character. Like this,
<!-- Preamble omitted for this example. -->
\begin{document}
Look me&you at this.
\end{document}
I'm interested to get an output that looks like this,
<!-- Preamble omitted for this example. -->
\begin{document}
Look me\&you at this.
\end{document}
Sorry for the simple question, but can someone help me, and maybe others, getting starting on how to modify the default inline hook for \Sexpr?
The solution provided by #agstudy has shown the basic idea, and here is a more robust version:
hook_inline = knit_hooks$get('inline')
knit_hooks$set(inline = function(x) {
if (is.character(x)) x = knitr:::escape_latex(x)
hook_inline(x)
})
It only modifies the default inline hook when the inline result is character (otherwise just use the default hook). I have an internal function escape_latex() which hopefully escapes all special LaTeX characters correctly.
Hooking works in this case. I customize it like this :
inline_hook <- function(x) {
x <- gsub("\\&", "\\\\&", x)
x <- gsub("\\$", "\\\\$", x)
## good luck for all Latex special character
## $ % _ { } & ~ ^ < > | \
}
knit_hooks$set(inline = inline_hook)
Then
knit(input='report.Rnw')
Will reproduce your report.tex.
PS: I think it is better to not to allow users do what they want.
Related
Say I have an .Rmd file like this:
The total number of steps per day can also be calculated
using `tapply`.
```{r}
tapply(d$steps, INDEX=d$date, FUN=sum)[1:5]
```
What seems to be different is that, per default, `xtabs`
returns 0 for `NA` values and `tapply` returns `NA`.
In my terminal window, this looks like this:
It would be great if somehow I could inform vim that the R chunk is actually R code which it could highlight just as it does when working in an actual .R file.
Is this possible?
Yes you can. This code is taken from here.
Put this in the ~/.vim/r.vim file (if any of these files do not exist, create them)
function! TextEnableCodeSnip(filetype,start,end,textSnipHl) abort
let ft=toupper(a:filetype)
let group='textGroup'.ft
if exists('b:current_syntax')
let s:current_syntax=b:current_syntax
" Remove current syntax definition, as some syntax files (e.g. cpp.vim)
" do nothing if b:current_syntax is defined.
unlet b:current_syntax
endif
execute 'syntax include #'.group.' syntax/'.a:filetype.'.vim'
try
execute 'syntax include #'.group.' after/syntax/'.a:filetype.'.vim'
catch
endtry
if exists('s:current_syntax')
let b:current_syntax=s:current_syntax
else
unlet b:current_syntax
endif
execute 'syntax region textSnip'.ft.'
\ matchgroup='.a:textSnipHl.'
\ start="'.a:start.'" end="'.a:end.'"
\ contains=#'.group
endfunction
Now you can use
:call TextEnableCodeSnip( 'r', '```{r}', '```', 'SpecialComment')
As long as there is an r.vim syntax file.
You could also automatically call this method every time you open a .Rmd file:
autocmd BufNewFile,BufRead *.Rmd :call TextEnableCodeSnip( 'r', '```{r}', '```', 'SpecialComment')
If you wanted to highlight with r followed by any number of characters you can use regular expressions:
:call TextEnableCodeSnip( 'r', '```{r.*}', '```', 'SpecialComment')
Or in your .vimrc:
autocmd BufNewFile,BufRead *.Rmd :call TextEnableCodeSnip( 'r', '```{r.*}', '```', 'SpecialComment')
The .* regular expression means any repeating character. So r.* means r followed by any number of characters.
Therefore this will work with
```{r whatever you want to put here}`
Some r code here
```
You might also be interested in my SyntaxRange plugin, which is based on the Vim Tip in #Zach's answer. It simplifies the setup of such syntax regions.
The setup would be like this (e.g. in ~/.vim/ftplugin/markdown.vim):
call SyntaxRange#Include('^````{r}', '^````', 'r', 'SpecialComment')
How can I find how did I first declare a certain variable when I am a few hundred
lines down from where I first declared it. For example, I have declared the following:
a <- c(vectorA,vectorB,vectorC)
and now I want to see how I declared it. How can I do that?
Thanks.
You could try using the history command:
history(pattern = "a <-")
to try to find lines in your history where you assigned something to the variable a. I think this matches exactly, though, so you may have to watch out for spaces.
Indeed, if you type history at the command line, it doesn't appear to be doing anything fancier than saving the current history in a tempfile, loading it back in using readLines and then searching it using grep. It ought to be fairly simple to modify that function to include more functionality...for example, this modification will cause it to return the matching lines so you can store it in a variable:
myHistory <- function (max.show = 25, reverse = FALSE, pattern, ...)
{
file1 <- tempfile("Rrawhist")
savehistory(file1)
rawhist <- readLines(file1)
unlink(file1)
if (!missing(pattern))
rawhist <- unique(grep(pattern, rawhist, value = TRUE,
...))
nlines <- length(rawhist)
if (nlines) {
inds <- max(1, nlines - max.show):nlines
if (reverse)
inds <- rev(inds)
}
else inds <- integer()
#file2 <- tempfile("hist")
#writeLines(rawhist[inds], file2)
#file.show(file2, title = "R History", delete.file = TRUE)
rawhist[inds]
}
I will assume you're using the default R console. If you're on Windows, you can File -> Save history and open the file in your fav text browser, or you can use function savehistory() (see help(savehistory)).
What you need to do is get a (good) IDE, or at least a decent text editor. You will benevit from code folding, syntax coloring and much more. There's a plethora of choices, from Tinn-R, VIM, ESS, Eclipse+StatET, RStudio or RevolutionR among others.
You can run grep 'a<-' .Rhistory from terminal (assuming that you've cdd to your working directory). ESS has several very useful history-searching functions, like (comint-history-isearch-backward-regexp) - binded to M-r by default.
For further info, consult ESS manual: http://ess.r-project.org/Manual/ess.html
When you define a function, R stores the source code of the function (preserving formatting and comments) in an attribute named "source". When you type the name of the function, you will get this content printed.
But it doesn't do this with variables. You can deparse a variable, which generates an expression that will produce the variable's value but this doesn't need to be the original expression. For example when you have b <- c(17, 5, 21), deparse(b) will produce the string "c(17, 5, 21)".
In your example, however, the result wouldn't be "c(vectorA,vectorB,vectorC)", it would be an expression that produces the combined result of your three vectors.
I am trying to add a table of contents for my LaTex document. The issue I am having is that this line:
\subsubsection{The expectation of \(X^2\)}
Causes an error in the file that contains the table of contents
\contentsline {subsubsection}{\numberline {1.2.3}
The expectation of \relax $X^2\relax \GenericError { }{
LaTeX Error: Bad math environment delimiter}{
See the LaTeX manual or LaTeX Companion for explanation.}
{Your command was ignored.\MessageBreak Type I <command> <return>
to replace it with another command,\MessageBreak or <return> to
continue without it.}}{5}
Which causes the document not to be generated.
Does anyone have a solution to having maths in sections while still having the table of contents
You should use the Amsmath inline math delimiter $ instead of \( and \). Thus:
\subsubsection{The expectation of $X^2$}
Note: be sure to remove the currently generated .toc file first, otherwise the error will not go away.
If you wish to continue using \(...\) as your math delimiters, you can load the (officially supported) fixltx2e package. This is where fixes to LaTeX go that cannot be integrated into the main sources because of the possibility of backwards compatibility problems.
(In short, your problem is that \( and \) by default aren't "robust" and hence can't be used in places like section headings and captions; the fixltx2e package fixes this.)
Could you try again with putting the $ signs around the expression? What error do you get?
I (sort of) already know the answer to this question. But I figured it is one that gets asked so frequently on the R Users list, that there should be one solid good answer. To the best of my knowledge there is no multiline comment functionality in R. So, does anyone have any good workarounds?
While quite a bit of work in R usually involves interactive sessions (which casts doubt on the need for multiline comments), there are times when I've had to send scripts to colleagues and classmates, much of which involves nontrivial blocks of code. And for people coming from other languages it is a fairly natural question.
In the past I've used quotes. Since strings support linebreaks, running an R script with
"
Here's my multiline comment.
"
a <- 10
rocknroll.lm <- lm(blah blah blah)
...
works fine. Does anyone have a better solution?
You can do this easily in RStudio:
select the code and click CTR+SHIFT+C
to comment/uncomment code.
This does come up on the mailing list fairly regularly, see for example this recent thread on r-help. The consensus answer usually is the one shown above: that given that the language has no direct support, you have to either
work with an editor that has region-to-comment commands, and most advanced R editors do
use the if (FALSE) constructs suggested earlier but note that it still requires complete parsing and must hence be syntactically correct
A neat trick for RStudio I've just discovered is to use #' as this creates an self-expanding comment section (when you return to new line from such a line or insert new lines into such a section it is automatically comment).
[Update] Based on comments.
# An empty function for Comments
Comment <- function(`#Comments`) {invisible()}
#### Comments ####
Comment( `
# Put anything in here except back-ticks.
api_idea <- function() {
return TRUE
}
# Just to show api_idea isn't really there...
print( api_idea )
`)
####
#### Code. ####
foo <- function() {
print( "The above did not evaluate!")
}
foo()
[Original Answer]
Here's another way... check out the pic at the bottom. Cut and paste the code block into RStudio.
Multiline comments that make using an IDE more effective are a "Good Thing", most IDEs or simple editors don't have highlighting of text within simple commented -out blocks; though some authors have taken the time to ensure parsing within here-strings. With R we don't have multi-line comments or here-strings either, but using invisible expressions in RStudio gives all that goodness.
As long as there aren't any backticks in the section desired to be used for a multiline comments, here-strings, or non-executed comment blocks then this might be something worth-while.
#### Intro Notes & Comments ####
invisible( expression( `
{ <= put the brace here to reset the auto indenting...
Base <- function()
{ <^~~~~~~~~~~~~~~~ Use the function as a header and nesting marker for the comments
that show up in the jump-menu.
--->8---
}
External <- function()
{
If we used a function similar to:
api_idea <- function() {
some_api_example <- function( nested ) {
stopifnot( some required check here )
}
print("Cut and paste this into RStudio to see the code-chunk quick-jump structure.")
return converted object
}
#### Code. ####
^~~~~~~~~~~~~~~~~~~~~~~~~~ <= Notice that this comment section isnt in the jump menu!
Putting an apostrophe in isn't causes RStudio to parse as text
and needs to be matched prior to nested structure working again.
api_idea2 <- function() {
} # That isn't in the jump-menu, but the one below is...
api_idea3 <- function() {
}
}
# Just to show api_idea isn't really there...
print( api_idea )
}`) )
####
#### Code. ####
foo <- function() {
print( "The above did not evaluate and cause an error!")
}
foo()
## [1] "The above did not evaluate and cause an error!"
And here's the pic...
I can think of two options. The first option is to use an editor that allows to block comment and uncomment (eg. Eclipse). The second option is to use an if statement. But that will only allow you to 'comment' correct R syntax. Hence a good editor is the prefered workaround.
if(FALSE){
#everything in this case is not executed
}
If find it incredible that any language would not cater for this.
This is probably the cleanest workaround:
anything="
first comment line
second comment line
"
Apart from using the overkilled way to comment multi-line codes just by installing RStudio, you can use Notepad++ as it supports the syntax highlighting of R
(Select multi-lines) -> Edit -> Comment/Uncomment -> Toggle Block Comment
Note that you need to save the code as a .R source first (highlighted in red)
I use vim to edit the R script.
Let's say the R script is test.R, containing say "Line 1", "Line 2", and "Line 3" on 3 separate lines.
I open test.R on the command line with Vim by typing "vim test.R".
Then I go to the 1st line I want to comment out, type "Control-V", down arrow to the last line I want to comment out, type a capital I i.e. "I" for insert, type "# ", and then hit the Escape key to add "# " to every line that I selected by arrowing down. Save the file in Vim and then exit Vim by typing ":wq". Changes should show up in Rstudio.
To delete the comments in Vim, start at the first line on top of the character "#" you want to delete, again do "Control-V", and arrow down to the last line you want to delete a "#" from. Then type "dd". The "#" signs should be deleted.
There's seconds-worth of lag time between when changes to test.R in Vim are reflected in Rstudio.
Now there is a workaround, by using package ARTofR or bannerCommenter
Examples here:
In RStudio an easy way to do this is to write your comment and once you have used CTRL + Shift + C to comment your line of code, then use CTRL + SHIFT + / to reflow you comment onto multiple lines for ease of reading.
In RStudio you can use a pound sign and quote like this:
#' This is a comment
Now, every time you hit return you don't need to add the #', RStudio will automatically put that in for you.
Incidentally, for adding parameters and items that are returned, for standardization if you type an # symbol inside those comment strings, RStudio will automatically show you a list of codes associated with those comment parameters:
#' #param tracker_df Dataframe of limit names and limits
#' #param invoice_data Dataframe of invoice data
#' #return return_list List of scores for each limit and rejected invoice rows
I have to hand in a software project that requires either a paper or .pdf copy of all the code included.
One solution I have considered is grouping classes by context and doing a cat *.extension > out.txt to provide all the code, then by catting the final text files I should have a single text file that has classes grouped by context. This is not an ideal solution; there will be no page breaks.
Another idea I had was a shell script to inject latex page breaks in between files to be joined, this would be more acceptable. Although I'm not too adept at scripting or latex.
Are there any tools that will do this for me?
Take a look at enscript (or nenscript), which will convert to Postscript, render in columns, add headers/footers and perform syntax highlighting. If you want to print code in a presentable fashion, this works very nicely.
e.g. here's my setting (within a zsh function)
# -2 = 2 columns
# -G = fancy header
# -E = syntax filter
# -r = rotated (landscape)
# syntax is picked up from .enscriptrc / .enscript dir
enscript -2GrE $*
For a quick solution, see a2ps, followed by ps2pdf. For a nicer, more complex solution I would go for a simple script that puts each file in a LaTeX listings environment and combines the result.