When editing an Sweave document in LaTeX (using the Noweb mode), Emacs knows to "ignore" code that is in <<>>= blocks. However, for interstitial \Sexpr{} blocks, this isn't the case. Given that R references by columns via '$' and LaTeX uses $ to set-off equations, these \Sexpr{} blocks often break the syntax highlighting, like so:
I have a very rudimentary understanding the elisp & Emacs syntax highlighting, but my hope is that it might be possible to add something to .emacs that will disable any parsing/$ detection within \Sexpr{}'s.
I thought emacs with ESS has correct syntax highlighting for Sweave?
Anyway, the easiest "fix" is to just not use the $ operator but [[ instead. For example:
foo$p.value
foo[['p.value']]
Should give the same result. I think foo$p.value is just short for foo[["p.value",exact=FALSE]]
I don't have a fix either, but I'll pass along my workaround, which is to never (well, rarely) do any processing in \Sexpr chunks but instead to store things I want to use in \Sexpr in variables, and to do so in the same chunk I do the main calculations in.
<<echo=FALSE, results=hide>>=
t1 <- chisq.test(someVar)
p1 <- formatC(t1$p.value, format="%f", digits=2)
#
\dots with a $p$-value of \Sexpr{p1}.
While there are some downsides to this, I find it helps me to better keep track of what I want to present, and how I want to present it.
As an aside, consider using formatC instead of round as it can keep significant zeros (ie, 0.10 instead of 0.1).
I have no good answer for you as I am not an Emacs hacker, so I usually do one of two things:
Either add a simple % $ comment at the of the line to "close" the math expression from $ to $,
Or rewrite the expression to not use $-based subsetting:
round(as.numeric(chisq.test(someVar)["p.value"]), 2).
Related
I work with knitr() and I wish to transform inline Latex commands like "\label" and "\ref", depending on the output target (Latex or HTML).
In order to do that, I need to (programmatically) generate valid R strings that correctly represent the backslash: for example "\label" should become "\\label". The goal would be to replace all backslashes in a text fragment with double-backslashes.
but it seems that I cannot even read these strings, let alone process them: if I define:
okstr <- function(str) "do something"
then when I call
okstr("\label")
I directly get an error "unrecognized escape sequence"
(of course, as \l is faultly)
So my question is : does anybody know a way to read strings (in R), without using the escaping mechanism ?
Yes, I know I could do it manually, but that's the point: I need to do it programmatically.
There are many questions that are close to this one, and I have spent some time browsing, but I have found none that yields a workable solution for this.
Best regards.
Inside R code, you need to adhere to R’s syntactic conventions. And since \ in strings is used as an escape character, it needs to form a valid escape sequence (and \l isn’t a valid escape sequence in R).
There is simply no way around this.
But if you are reading the string from elsewhere, e.g. using readLines, scan or any of the other file reading functions, you are already getting the correct string, and no handling is necessary.
Alternatively, if you absolutely want to write LaTeX-like commands in literal strings inside R, just use a different character for \; for instance, +. Just make sure that your function correctly handles it everywhere, and that you keep a way of getting a literal + back. Here’s a suggestion:
okstr("+label{1 ++ 2}")
The implementation of okstr then needs to replace single + by \, and double ++ by + (making the above result in \label{1 + 2}). But consider in which order this needs to happen, and how you’d like to treat more complex cases; for instance, what should the following yield: okstr("1 +++label")?
I've searched through several answers here and through Google, but I'm still not sure what's going wrong with my prompt.
According to the documentation I've read, this should work
setopt prompt_subst
autoload -U colors && colors
PROMPT="%{[00m[38;5;245m%}test %D%{[00m%}"
My prompt is the following, however:
[00m[38;5;245mtest 15-07-01[00m
Note that the date expansion actually worked, so prompt substitution is working. The ZSH man pages for prompt expansion states that %{...%} should be treated as a raw escape code, but that doesn't seem to be happening. Passing that string to print -P also results in the output above. I've found example prompts on the Internet for ZSH that also seem to indicate that the above syntax should work. See this for one example - the $FG and $FX arrays are populated with escape codes and are defined here. I've tried this example directly by merging both the files above, adding setopt prompt_subst to the beginning just to make sure it's set, then sourcing it and the prompt is a mess of escape codes.
The following works
setopt prompt_subst
autoload -U colors && colors
PROMPT=$'%{\e[00m\e[38;5;245m%}test %D%{\e[00m%}'
I get the expected result of test 15-07-01 in the proper color.
I've tested this on ZSH 5.0.5 in OSX Yosimite, 5.0.7 from MacPorts, and 4.3.17 on Debian, with the same results. I know I have provided a valid solution to my own problem here with the working example, but I'm wondering why the first syntax isn't working as it seems it should.
I think this all has to do with the timeless and perennial problem of escaping. It's worth reminding ourselves what escaping means, briefly: an escape character is an indicator to the computer that what follows should not be output literally.
So there are 2 escaping issues with:
PROMPT="%{[00m[38;5;245m%}test %D%{[00m%}"
Firstly, the colour escape sequences (eg; [00m) should all start with the control character like so \e[00m. You may have also seen it written as ^[00m and \003[00m. What I suspect has happened is one of the variations has suffered the common fate of being inadvertently escaped by either the copy/paste of the author or the website's framework stack, whether that be somewhere in a database, HTTP rendering or JS parsing. The control character (ie, ^, \e or \003), as you probably know, does not have a literal representation, say if you press it on the keyboard. That's why a web stack might decide to not display anything if it sees it in a string. So let's correct that now:
PROMPT="%{\e[00m\e[38;5;245m%}test %D%{\e[00m%}"
This actually nicely segues into the next escaping issue. Somewhat comically \e[ is actually a representation of ESC, it is therefore in itself an escape sequence marker that, yes, is in turn escaped by \. It's a riff on the old \\\\\\\\\\ sort of joke. Now, significantly, we must be clear on the difference between the escape expressions for the terminal and the string substitutions of the prompt, in pseudo code:
PROMPT="%{terminal colour stuff%}test %D%{terminal colour stuff%}"
Now what I suspect is happening, though I can't find any documentation to prove it, is that once ZSH has done its substitutions, or indeed during the substitution process, all literal characters, regardless of escape significations, are promoted to real characters¹. To yet further the farce, this promotion is likely done by escaping all the escape characters. For example if you actually want to print '\e' on the command line, you have to do echo "\\\e". So to overcome this issue, we just need to make sure the 'terminal colour stuff' escape sequences get evaluated before being assigned to PROMPT and that can be done simply with the $'' pattern, like so:
PROMPT=$'%{\e[00m\e[38;5;245m%}test %D%{\e[00m%}'
Note that $'' is of the same ilk as $() and ${}, except that its only function is to interpret escape sequences.
[1] My suspicion for this is based on the fact that you can actually do something like the following:
PROMPT='$(date)'
where $(date) serves the same purpose as %D, by printing a live version of the date for every new prompt output to the screen. What this specific examples serves to demonstrate is that the PROMPT variable should really be thought of as storage for a mini script, not a string (though admittedly there is overlap between the 2 concepts and thus stems confusion). Therefore, as a script, the string is first evaluated and then printed. I haven't looked at ZSH's prompt rendering code, but I assume such evaluation would benefit from native use of escape sequences. For example what if you wanted to pass an escape sequence as an argument to a command (a command that gets run for every prompt render) in the prompt? For example the following is functionally identical to the prompt discussed above:
PROMPT='%{$(print "\e[00m\e[38;5;245m")%}test $(date)%{$(print "\e[00m")%}'
The escape sequences are stored literally and only interpreted at the moment of each prompt rendering.
Am using the RODBC library to bring data into R. I have a long query that I want to pass a variable to, much like this SO user.
Problem is that R interprets the whitespace/carriage returns in my query as a newline '\n'.
The accepted solution for this question suggests to simply break up the text into chunks and then paste() together - which works, but ideally I'd like to keep the whitespace intact - makes it easier to test/verify the behavior of the query over in the database before pasting into R.
In other languages I'm familiar with there's a simple line continuation character - indeed, several of the comments on the accepted answer are looking for an approach similar to python's \.
I found an aside to a workaround using strwrap deep in the bowels of an R discussion lists, so in the interest of making the internet better I will post it here. However, if someone can point the direction toward a more elegant/straightforward solution, I will happily accept your answer.
I don't know if you will find this helpful or not, but I have eventually gravitated towards keeping my SQL separate from my R scripts. Keeping the query in my R script, except for very very short ones, I find gets unreadable very quickly.
These days, I tend to keep queries that are more than a single line in their own separate .sql file. Then I can keep them nice and formatted and readable in a nice text editor, and read them into R as needed via something like this:
read_sql <- function(path){
stopifnot(file.exists(path))
sql <- readChar(path,nchar = file.info(path)$size)
sql
}
For binding parameters into the queries, I just keep a %s where the parameter will go in the .sql file, and then add in the parameters in R using sprintf.
I've been much happier this way, as I was finding that cluttering up my R scripts with really long paste statements and multi-line character objects was making my code really hard to read.
R's strwrap will destroy whitespace, including newline characters, per the documentation.
Essentially, you can get the desired behavior by initially letting R introduce line breaks/newline \ns, and then immediately stripping them out.
#make query using PASTE
query_1 <- paste("SELECT map.ps_studentid
,students.first_name || ' ' || students.last_name AS full_name
,map.testritscore
,map.termname
,map.measurementscale
FROM map$comprehensive_with_growth map
JOIN students
ON map.ps_studentid = students.id
WHERE map.termname = '",map_term,"'", sep='')
#remove newline characters introduced above.
#width is an arbitrary big number-
#it just needs to be longer than your string.
query_1 <- strwrap(query_1, width=10000, simplify=TRUE)
#execute the query
map_njask <- sqlQuery(XE, query_1)
query <- gsub(pattern='\\s',replacement="",x=query)
Try using sprintf to get variable substitution, and then replacing all newlines and whitespace.
See my answer to a similar question for details.
When editing an Sweave document in LaTeX (using the Noweb mode), Emacs knows to "ignore" code that is in <<>>= blocks. However, for interstitial \Sexpr{} blocks, this isn't the case. Given that R references by columns via '$' and LaTeX uses $ to set-off equations, these \Sexpr{} blocks often break the syntax highlighting, like so:
I have a very rudimentary understanding the elisp & Emacs syntax highlighting, but my hope is that it might be possible to add something to .emacs that will disable any parsing/$ detection within \Sexpr{}'s.
I thought emacs with ESS has correct syntax highlighting for Sweave?
Anyway, the easiest "fix" is to just not use the $ operator but [[ instead. For example:
foo$p.value
foo[['p.value']]
Should give the same result. I think foo$p.value is just short for foo[["p.value",exact=FALSE]]
I don't have a fix either, but I'll pass along my workaround, which is to never (well, rarely) do any processing in \Sexpr chunks but instead to store things I want to use in \Sexpr in variables, and to do so in the same chunk I do the main calculations in.
<<echo=FALSE, results=hide>>=
t1 <- chisq.test(someVar)
p1 <- formatC(t1$p.value, format="%f", digits=2)
#
\dots with a $p$-value of \Sexpr{p1}.
While there are some downsides to this, I find it helps me to better keep track of what I want to present, and how I want to present it.
As an aside, consider using formatC instead of round as it can keep significant zeros (ie, 0.10 instead of 0.1).
I have no good answer for you as I am not an Emacs hacker, so I usually do one of two things:
Either add a simple % $ comment at the of the line to "close" the math expression from $ to $,
Or rewrite the expression to not use $-based subsetting:
round(as.numeric(chisq.test(someVar)["p.value"]), 2).
For example, in http://homepages.cwi.nl/~paulv/papers/algorithmicstatistics.pdf at the bottom of page 5 and top of page 6, he uses a plus/equal symbol and a similar plus/lessthan symbol. I can't figure out how to make that symbol, and I'd like to quote him.
Any help?
Try $\stackrel{top}{bottom}$
You'd want something like this:
$X \stackrel{+}{=} Y$
This positions the plus sign above the equals sign. For example, the following code:
$K(x,y|z) \stackrel{+}{=} K(x|z) \stackrel{+}{<} I(x:y|z)$
produces the following output:
The Comprehensive LaTeX Symbol List (from here) is a great resource, and start for questions like this. You could also contact the author, it's possible he did some LaTex voodoo (math accents and such) to get it to work.
Best of luck.
PS: isn't \pm plus-minus, not plus-equals?
Here's the list of Latex Math Symbols. I don't see the two from the PDF you linked to. Do you know what they mean? You might be able to find an equivalent in the Latex list.