Parsing R files

funspotr is already set-up to parse all the unique functions and packages from R or Rmd files.

r_gists <- brshallo_gists %>% 
  filter(funspotr:::str_detect_r_rmd(contents))

r_gists_parsed <- funspotr::github_spot_funs(custom_urls = r_gists)

r_gists_unnested <- r_gists_parsed %>% 
  funspotr::unnest_github_results()
r_gists_unnested
## # A tibble: 474 x 5
##    funs                  pkgs      in_multiple_pkgs contents      urls          
##    <chr>                 <chr>     <lgl>            <chr>         <chr>         
##  1 library               base      FALSE            funspotr-gis~ https://gist.~
##  2 github_gists          funspotr  FALSE            funspotr-gis~ https://gist.~
##  3 filter                dplyr     TRUE             funspotr-gis~ https://gist.~
##  4 str_detect_r_rmd      (unknown) FALSE            funspotr-gis~ https://gist.~
##  5 github_spot_funs      funspotr  FALSE            funspotr-gis~ https://gist.~
##  6 unnest_github_results funspotr  FALSE            funspotr-gis~ https://gist.~
##  7 library               base      FALSE            custom-ggplo~ https://gist.~
##  8 ggplot                ggplot    FALSE            custom-ggplo~ https://gist.~
##  9 aes                   ggplot    FALSE            custom-ggplo~ https://gist.~
## 10 geom_point            ggplot    FALSE            custom-ggplo~ https://gist.~
## # ... with 464 more rows

Parsing markdown files

To parse my .md files, I wrote a function here extract_code_md() that…

• reads in a file
• extracts the text in code chunks⁴
• saves it to a temporary file
• returns the file path of the temporary file

subset_even <- function(x) x[!seq_along(x) %% 2]

extract_code_md <- function(file_path){
  
  lines <- readr::read_file(file_path) %>% 
    stringr::str_split("```.*", simplify = TRUE) %>%
    subset_even() %>% 
    stringr::str_flatten("\n## new chunk \n")
  
  file_output <- tempfile(fileext = ".R")
  writeLines(lines, file_output)
  file_output
}

I map extract_code_md() on all the .md gists and then parse the files using funspotr.

# display output was weird here so just copied code and set eval = FALSE
md_gists <- brshallo_gists %>% 
  filter(!funspotr:::str_detect_r_rmd(contents))

md_gists_local <- md_gists %>% 
# name urls because that's what funspotr::githup_spot_funs() expects
  mutate(urls = map_chr(urls, extract_code_md))

md_gists_parsed <- funspotr::github_spot_funs(custom_urls = md_gists_local)

md_gists_unnested <- md_gists_parsed %>% 
  funspotr::unnest_github_results()
md_gists_unnested
## # A tibble: 1,061 x 5
##    funs           pkgs    in_multiple_pkgs contents                 urls        
##    <chr>          <chr>   <lgl>            <chr>                    <chr>       
##  1 library        base    FALSE            grouped-nested-t-test.md "C:\\Users\~
##  2 require        base    FALSE            grouped-nested-t-test.md "C:\\Users\~
##  3 install_github remotes FALSE            grouped-nested-t-test.md "C:\\Users\~
##  4 na.omit        stats   FALSE            grouped-nested-t-test.md "C:\\Users\~
##  5 t.test         stats   FALSE            grouped-nested-t-test.md "C:\\Users\~
##  6 tidy           broom   FALSE            grouped-nested-t-test.md "C:\\Users\~
##  7 pull           dplyr   FALSE            grouped-nested-t-test.md "C:\\Users\~
##  8 group_by       dplyr   FALSE            grouped-nested-t-test.md "C:\\Users\~
##  9 summarise      dplyr   FALSE            grouped-nested-t-test.md "C:\\Users\~
## 10 list           base    FALSE            grouped-nested-t-test.md "C:\\Users\~
## # ... with 1,051 more rows

Note that I’m assuming all the code snippets are R code⁵.

Binding files together

I bind these files together and then arrange them based on the initial order in brshallo_gists⁶.

gists_unnested <- bind_rows(
  r_gists_unnested,
  md_gists_unnested
) %>% 
  # got this arranging by a vector trick from SO:
  # https://stackoverflow.com/questions/52216341/how-to-sort-rows-of-a-data-frame-based-on-a-vector-using-dplyr-pipe
  arrange(match(contents, brshallo_gists$contents)) %>% 
  # add back-in links to url's where files are rather than urls column being
  # local paths for .md snippets
  select(-urls) %>% 
  left_join(brshallo_gists, by = "contents")

gists_unnested %>% 
  DT::datatable(rownames = FALSE,
            class = 'cell-border stripe',
            filter = 'top',
            escape = FALSE,
            options = list(pageLength = 20))