regex replace parts/groups of a string in R - r

Question

Trying to postprocess the LaTeX (pdf_book output) of a bookdown document to collapse biblatex citations to be able to sort them chronologically using \usepackage[sortcites]{biblatex} later on. Thus, I need to find }{ after \\autocites and replace it with ,. I am experimenting with gsub() but can't find the correct incantation.
# example input
testcase <- "text \\autocites[cf.~][]{foxMapping2000}{wattPattern1947}{runkleGap1990} text {keep}{separate}"
# desired output
"text \\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990} text {keep}{separate}"
A simple approach was to replace all }{
> gsub('\\}\\{', ',', testcase, perl=TRUE)
[1] "text \\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990} text {keep,separate}"
But this also collapses {keep}{separate}.
I was then trying to replace }{ within a 'word' (string of characters without whitspace) starting with \\autocites by using different groups and failed bitterly:
> gsub('(\\\\autocites)([^ \f\n\r\t\v}{}]+)((\\}\\{})+)', '\\1\\2\\3', testcase, perl=TRUE)
[1] "text \\autocites[cf.~][]{foxMapping2000}{wattPattern1947}{runkleGap1990} some text {keep}{separate}"
Addendum:
The actual document contains more lines/elements than the testcase above. Not all elements contain \\autocites and in rare cases one element has more than one \\autocites. I didn't originally think this was relevant. A more realistic testcase:
testcase2 <- c("some text",
"text \\autocites[cf.~][]{foxMapping2000}{wattPattern1947}{runkleGap1990} text {keep}{separate}",
"text \\autocites[cf.~][]{foxMapping2000}{wattPattern1947}{runkleGap1990} text {keep}{separate} \\autocites[cf.~][]{foxMapping2000}{wattPattern1947}")

Answer 1

A single gsub call is enough:
gsub("(?:\\G(?!^)|\\\\autocites)\\S*?\\K}{", ",", testcase, perl=TRUE)
## => [1] "text \\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990} text {keep}{separate}"
See the regex demo. Here, (?:\G(?!^)|\\autocites) matches the end of the previous match or \autocites string, then it matches any 0 or more non-whitespace chars, but as few as possible, then \K discards the text from the current match buffer and consumes the }{ substring that is eventually replaced with a comma.
There is also a very readable solution with one regex and one fixed text replacements using stringr::str_replace_all:
library(stringr)
str_replace_all(testcase, "\\\\autocites\\S+", function(x) gsub("}{", ",", x, fixed=TRUE))
# => [1] "text \\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990} text {keep}{separate}"
Here, \\autocites\S+ matches \autocites and then 1+ non-whitespace chars, and gsub("}{", ",", x, fixed=TRUE) replaces (very fast) each }{ with , in the matched text.

Answer 2

Not the prettiest solution, but it works. This repeatedly replaces }{ with , but only if it follows autocities with no intervening blanks.
while(length(grep('(autocites\\S*)\\}\\{', testcase, perl=TRUE))) {
testcase = sub('(autocites\\S*)\\}\\{', '\\1,', testcase, perl=TRUE)
}
testcase
[1] "text \\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990} text {keep}{separate}"

Answer 3

I'll make the input string slightly bigger to make the algorithm more clear.
str <- "
text \\autocites[cf.~][]{foxMapping2000}{wattPattern1947}{runkleGap1990} text {keep}{separate}
text \\autocites[cf.~][]{wattPattern1947}{foxMapping2000}{runkleGap1990} text {keep}{separate}
"
We will firstly extract all the citation blocks, replace "}{" with "," in them and then put them back into the string.
# pattern for matching citation blocks
pattern <- "\\\\autocites(\\[[^\\[\\]]*\\])*(\\{[[:alnum:]]*\\})+"
cit <- str_extract_all(str, pattern)[[1]]
cit
#> [1] "\\autocites[cf.~][]{foxMapping2000}{wattPattern1947}{runkleGap1990}"
#> [2] "\\autocites[cf.~][]{wattPattern1947}{foxMapping2000}{runkleGap1990}"
Replace in citation blocks:
newcit <- str_replace_all(cit, "\\}\\{", ",")
newcit
#> [1] "\\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990}"
#> [2] "\\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990}"
Break the original string in the places where citation block was found
strspl <- str_split(str, pattern)[[1]]
strspl
#> [1] "\ntext " " text {keep}{separate}\ntext " " text {keep}{separate}\n"
Insert modified citation blocks:
combined <- character(length(strspl) + length(newcit))
combined[c(TRUE, FALSE)] <- strspl
combined[c(FALSE, TRUE)] <- newcit
combined
#> [1] "\ntext "
#> [2] "\\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990}"
#> [3] " text {keep}{separate}\ntext "
#> [4] "\\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990}"
#> [5] " text {keep}{separate}\n"
Paste it together to finalize:
newstr <- paste(combined, collapse = "")
newstr
#> [1] "\ntext \\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990} text {keep}{separate}\ntext \\autocites[cf.~][]{foxMapping2000,wattPattern1947,runkleGap1990} text {keep}{separate}\n"
I suspect there could be a more elegant fully-regex solution based on the same idea, but I wasn't able to find one.

Answer 4

I found an incantation that works. It's not pretty:
gsub("\\\\autocites[^ ]*",
gsub("\\}\\{",",",
gsub(".*(\\\\autocites[^ ]*).*","\\\\\\1",testcase) #all those extra backslashes are there because R is ridiculous.
),
testcase)
I broke it in to lines to hopefully make it a little more intelligible. Basically, the innermost gsub extracts just the autocites (anything that follows \\autocites up to the first space), then the middle gsub replaces the }{s with commas, and the outermost gsub replaces the result of the middle one for the pattern extracted in the innermost one.
This will only work with a single autocites in a string, of course.
Also, fortune(365).