aq-level2-validation/_06-compile-reports.R at main · bcgov/aq-level2-validation · GitHub

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# _06-compile-reports.R

source("_00-setup.R")

# compile annual data validation reports for each file in preppedDAta:

root<-stringr::str_remove(dir("./prepped-data"),
                        ".rds")
                        # trs:  skookumchuk 88
                        # co: victoria topaz 107
                        # everything else (except h2s): kitimat riverlodge 51
                        # h2s: pine river gas plant 68

utils::View(root)

# stations that won't compile:

#indices in roots that won't compile:
# bugs<-c()

root_no_bugs<-root[!(1:length(root) %in% bugs)]

utils::View(root_no_bugs)

purrr::walk(root[1:length(root)],

  #compile reports for stations without bugs
  # root_no_bugs[1:length(root_no_bugs)], #%>% utils::View(.),

  # compile for roots with bugs:
  # root[bugs],

  #compile reports for specific stations:
  #root[15],
            function(r){

              # testing

              # (r<-root[1])

              # End testing
              print(paste0("Compiling for ",
                           r,
                           " ..."))

              # # RENDER ENTIRE BOOK
              bookdown::render_book(
                # this will compile all the rmd files listed in _bookdown.yml
                ".",
                "bookdown::gitbook",
                output_dir = stringr::str_c("_", r, sep = ""),
                params = list(
                  prepped_data = stringr::str_c("./prepped-data/", r, ".rds", collapse = ""),
                  year = year_to_validate
                ) #params
              ) # render_book

              # # RENDER SPECIFIC CHAPTERS
              # bookdown::preview_chapter(c("index.Rmd","05-nox.Rmd"),
              #                           output_dir = stringr::str_c("_", r, sep = ""),
              #                           params = list(
              #                             prepped_data = stringr::str_c("./prepped-data/", r, ".rds", collapse = ""),
              #                             year = year_to_validate
              #                           ))

            }

            )

# need to delete all files 404.html - don't know why these are being generated
files_to_delete <- list.files(
  #path = ".",
  # path = "R:\\WANSHARE\\EPD\\EPD_SHARED\\MAS\\Air Quality Section\\aq-level2-validation",
  path = "C:\\HagaR\\aq-level2-validation",
  pattern = "404",
  recursive = TRUE,
  full.names = TRUE
)

file.remove(files_to_delete)

# # # 2025 - what's below wasn't working for transferring files (wasn't making subdirectories)
# # # so transferred them manually

# list files in the reports
files_to_copy <- dir(
  file.path(".",
            stringr::str_c("_",
                           root)),
  all.files = TRUE,
  full.names = TRUE,
  recursive = TRUE
)

#copy files to shared drive
destination<-"R:\\WANSHARE\\EPD\\EPD_SHARED\\MAS\\Air Quality Section\\aq-level2-validation"

file.copy(from = files_to_copy,
          to=destination,
          overwrite = TRUE,
          recursive = TRUE)