{"id":10834,"date":"2018-05-29T07:42:06","date_gmt":"2018-05-29T12:42:06","guid":{"rendered":"https:\/\/rud.is\/b\/?p=10834"},"modified":"2018-05-29T07:42:06","modified_gmt":"2018-05-29T12:42:06","slug":"the-fix-is-in-finding-infix-functions-inside-contributed-r-package-utilities-files","status":"publish","type":"post","link":"https:\/\/rud.is\/b\/2018\/05\/29\/the-fix-is-in-finding-infix-functions-inside-contributed-r-package-utilities-files\/","title":{"rendered":"The Fix Is In: Finding infix functions inside contributed R package &#8220;utilities&#8221; files"},"content":{"rendered":"<p>Regular readers will recall the &#8220;<a href=\"https:\/\/rud.is\/b\/2018\/04\/08\/dissecting-r-package-utility-belts\/\">utility belt<\/a>&#8221; post from back in April of this year. This is a follow-up to a request made asking for a list of all the <code>%<\/code> infix functions in those files.<\/p>\n<p>We&#8217;re going to:<\/p>\n<ul>\n<li>collect up all of the sources<\/li>\n<li>parse them<\/li>\n<li>find all the definitions of <code>%<\/code> infix functions<\/li>\n<li>write them to a file<\/li>\n<\/ul>\n<p>We&#8217;ll start by grabbing the data from the previous post and look at it as a refresher:<\/p>\n<pre><code class=\"language-r\">\nlibrary(stringi)\nlibrary(tidyverse)\n\nutils <- read_rds(url(\"https:\/\/rud.is\/dl\/utility-belt.rds\"))\n\nutils\n## # A tibble: 1,746 x 13\n##    permsissions links owner     group      size month day   year_hr path   date       pkg   fil   file_src             \n##  1 -rw-r--r--       0 hornik    users      1658 Jun   05    2016    AHR\/R\u2026 2016-06-05 AHR   util\u2026 \"## \\\\int f(x)dg(x) \u2026\n##  2 -rw-r--r--       0 ligges    users     12609 Dec   13    2016    ALA4R\u2026 2016-12-13 ALA4R util\u2026 \"## some utility fun\u2026\n##  3 -rw-r--r--       0 hornik    users         0 Feb   24    2017    AWR.K\u2026 2017-02-24 AWR.\u2026 util\u2026 \"\"                   \n##  4 -rw-r--r--       0 ligges    users      4127 Aug   30    2017    Alpha\u2026 2017-08-30 Alph\u2026 util\u2026 \"#\\n#' Assign API ke\u2026\n##  5 -rw-r--r--       0 ligges    users       121 Jan   19    2017    Amylo\u2026 2017-01-19 Amyl\u2026 util\u2026 \"make_decision <- fu\u2026\n##  6 -rw-r--r--       0 herbrandt herbrandt    52 Aug   10    2017    BANES\u2026 2017-08-10 BANE\u2026 util\u2026 \"#' @importFrom dply\u2026\n##  7 -rw-r--r--       0 ripley    users     36977 Jan   06    2015    BEQI2\u2026 2015-01-06 BEQI2 util\u2026 \"#' \\tRemove Redunda\u2026\n##  8 -rw-r--r--       0 hornik    users     34198 May   10    2017    BGDat\u2026 2017-05-10 BGDa\u2026 util\u2026 \"# A more memory-eff\u2026\n##  9 -rwxr-xr-x       0 ligges    users      3676 Aug   14    2016    BGLR\/\u2026 2016-08-14 BGLR  util\u2026 \"\\n readBinMat=funct\u2026\n## 10 -rw-r--r--       0 ripley    users      2547 Feb   04    2015    BLCOP\u2026 2015-02-04 BLCOP util\u2026 \"###################\u2026\n## # ... with 1,736 more rows\n<\/code><\/pre>\n<p>Note that we somewhat expected the file source to potentially come in handy at a later date and also expected the need to revisit that post, so the <a href=\"https:\/\/rud.is\/dl\/utility-belt.rds\">R data file<\/a> [\u2190<em>direct link to RDS<\/em>] included a <code>file_src<\/code> column.<\/p>\n<p>Now, let's find all the source files with at least one infix definition, collect them together and parse them so we can do more code spelunking:<\/p>\n<pre><code class=\"language-r\">\nfilter(utils, stri_detect_fixed(file_src, \"`%\")) %>% # only find sources with infix definitions\n  pull(file_src) %>%\n  paste0(collapse=\"\\n\\n\") %>%\n  parse(text = ., keep.source=TRUE) -> infix_src\n\nstr(infix_src, 1)\n## length 1364 expression(dplyr::`%>%`, `%||%` <- function(a, b) if (is.null(a)) b else a, get_pkg_path <- function(ctx) {  pkg_| __truncated__ ...\n##  - attr(*, \"srcref\")=List of 1364\n##  - attr(*, \"srcfile\")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7fbfc4339940> \n##  - attr(*, \"wholeSrcref\")= 'srcref' int [1:8] 1 0 15768 0 0 0 1 15768\n##   ..- attr(*, \"srcfile\")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7fbfc4339940>\n<\/code><\/pre>\n<p>We can now take all of that lovely parsed source and tokenize it to work with the discrete elements in a very tidy manner:<\/p>\n<pre><code class=\"language-r\">\ninfix_parsed <- tbl_df(getParseData(infix_src)) # tbl_df() is mainly for pretty printing \n\ninfix_parsed\n## # A tibble: 118,242 x 9\n##    line1  col1 line2  col2    id parent token          terminal text      \n##  1     1     1     1    24     1    -10 COMMENT        TRUE     #' @impor\u2026\n##  2     2     1     2    10     4    -10 COMMENT        TRUE     #' @export\n##  3     3     1     3    12    10      0 expr           FALSE    \"\"        \n##  4     3     1     3     5     7     10 SYMBOL_PACKAGE TRUE     dplyr     \n##  5     3     6     3     7     8     10 NS_GET         TRUE     ::        \n##  6     3     8     3    12     9     10 SYMBOL         TRUE     `%>%`     \n##  7     5     1     5    49    51      0 expr           FALSE    \"\"        \n##  8     5     1     5     6    16     18 SYMBOL         TRUE     `%||%`    \n##  9     5     1     5     6    18     51 expr           FALSE    \"\"        \n## 10     5     8     5     9    17     51 LEFT_ASSIGN    TRUE     <-        \n## # ... with 118,232 more rows\n<\/code><\/pre>\n<p>We just need to find a sequence of tokens that make up a function definition, then whittle those down to ones that look like our <code>%<\/code> infix names:<\/p>\n<pre><code class=\"language-r\">\npat <- c(\"SYMBOL\", \"expr\", \"LEFT_ASSIGN\", \"expr\", \"FUNCTION\") # pattern for function definition\n\n# find all of ^^ sequences (there's a good twitter discussion on this abt a month ago)\nidx <- which(infix_parsed$token == pat[1]) # find location of match of start of seq\n\n# look for the rest of the sequences starting at each idx position\nmap_lgl(idx, ~{\n  all(infix_parsed$token[.x:(.x+(length(pat)-1))] == pat)\n}) -> found\n\nf_defs <- idx[found] # starting indices of all the places where functions are defined\n\n# filter ^^ to only find infix ones\ninfix_defs <- f_defs[stri_detect_regex(infix_parsed$text[f_defs], \"^`\\\\%\")]\n\n# there aren't too many, but remember we're just searching `util` functions\nlength(infix_defs)\n## [1] 106\n<\/code><\/pre>\n<p>Now, write it out to a file so we can peruse the infix functions:<\/p>\n<pre><code class=\"language-r\">\n# nuke a file and fill it with the function definition\ncat(\"\", sep=\"\", file=\"infix_functions.R\")\nwalk2(\n  getParseText(infix_parsed, infix_parsed$id[infix_defs]),     # extract the infix name\n  getParseText(infix_parsed, infix_parsed$id[infix_defs + 3]), # extract the function definition body\n  ~{\n    cat(.x, \" <- \", .y, \"\\n\\n\", sep=\"\", file=\"infix_functions.R\", append=TRUE)\n  }\n)\n<\/code><\/pre>\n<p>There are 106 of them so you can find the extracted ones <a href=\"https:\/\/gist.github.com\/hrbrmstr\/58b827dea95a7adf0f0e751b44b75b0c\">in this gist<\/a>.<\/p>\n<p>Here's an overview of what you can expect to find:<\/p>\n<pre>\n# A tibble: 39 x 2\n   name                 n\n 1 `%||%`              47\n 2 `%+%`                7\n 3 `%AND%`              4\n 4 `%notin%`            4\n 5 `%:::%`              3\n 6 `%==%`               3\n 7 `%!=%`               2\n 8 `%*diag%`            2\n 9 `%diag*%`            2\n10 `%nin%`              2\n11 `%OR%`               2\n12 `%::%`               1\n13 `%??%`               1\n14 `%.%`                1\n15 `%@%`                1\n16 `%&&%`               1\n17 `%&%`                1\n18 `%+&%`               1\n19 `%++%`               1\n20 `%+|%`               1\n21 `%<<%`               1\n22 `%>>%`               1\n23 `%~~%`               1\n24 `%assert_class%`     1\n25 `%contains%`         1\n26 `%din%`              1\n27 `%fin%`              1\n28 `%identical%`        1\n29 `%In%`               1\n30 `%inr%`              1\n31 `%M%`                1\n32 `%notchin%`          1\n33 `%or%`               1\n34 `%p%`                1\n35 `%pin%`              1\n36 `%R%`                1\n37 `%s%`                1\n38 `%sub_in%`           1\n39 `%sub_nin%`          1\n<\/pre>\n<h3>FIN<\/h3>\n<p>If any of those are useful, feel free to PR them in to <a href=\"https:\/\/github.com\/hrbrmstr\/freebase\/blob\/master\/inst\/templates\/infix-helpers.R\">https:\/\/github.com\/hrbrmstr\/freebase\/blob\/master\/inst\/templates\/infix-helpers.R<\/a> (and add yourself to the <code>DESCRIPTION<\/code> if you do).<\/p>\n<p>Hopefully this provided some further inspiration to continue to use R not only as your language of choice but also as a fun data source.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Regular readers will recall the &#8220;utility belt&#8221; post from back in April of this year. This is a follow-up to a request made asking for a list of all the % infix functions in those files. We&#8217;re going to: collect up all of the sources parse them find all the definitions of % infix functions [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":3,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":""},"categories":[91],"tags":[],"class_list":["post-10834","post","type-post","status-publish","format-standard","hentry","category-r"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.2 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>The Fix Is In: Finding infix functions inside contributed R package &quot;utilities&quot; files - rud.is<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/rud.is\/b\/2018\/05\/29\/the-fix-is-in-finding-infix-functions-inside-contributed-r-package-utilities-files\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Fix Is In: Finding infix functions inside contributed R package &quot;utilities&quot; files - rud.is\" \/>\n<meta property=\"og:description\" content=\"Regular readers will recall the &#8220;utility belt&#8221; post from back in April of this year. 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