Release for v1.0

R/create_tables_doc.R

@@ -31,7 +31,7 @@ create_tables_doc <- function(resdir = NULL,
       add_chunk(
         paste0("rda_dir <- '", rda_dir, "/rda_files'"),
         label = "set-rda-dir-tbls",
-        eval = "false"
+        eval = "true"
         ),
       "\n"
     )
@@ -51,7 +51,7 @@ rm(rda)\n
 indices_table <- indices_table_rda$table
 indices_cap <- indices_table_rda$cap"),
         label = "tbl-indices-setup",
-        eval = "true"
+        eval = "false"
       ),
       "\n"
     )

R/create_template.R

@@ -100,19 +100,19 @@
 #' using the image included in the project's repository.
 #' @param bib_file File path to a .bib file used for citing references in
 #' the report
-#' @param rda_dir The location of the folder containing .rda files
-#' ("rda_files") already made with `satf`, or, if the user has not used
-#' `satf` to make those .rda files already, rda_dir represents the location
-#' that will contain .rda files in an "rda_files" folder. The folder would have
-#' been made with `satf::exp_all_figs_tables()`, or by exporting files
-#' by running individual `satf` figure- and table-generating functions.
-#' If you have used `satf` to generate these .rda files, you can leave
-#' the arguments below blank.
+#' @param rda_dir If the user has already created .rda files containing
+#' figures, tables, alt text, and captions with `satf`, rda_dir represents
+#' the location of the folder containing these .rda files ("rda_files").
+#' Otherwise, if the user has not used `satf` to make those .rda files already,
+#' those files will be generated automatically and placed within the "report"
+#' folder within the `file_dir`. The "rda_files" folder would have been
+#' made with `satf::exp_all_figs_tables()`, or by exporting files by running individual
+#' `satf` figure- and table-generating functions. If you have used `satf` to
+#' generate these .rda files, you can leave the arguments below blank. NOTE:
+#' If an "rda_files" folder is detected within rda_dir, .rda files will not be
+#' regenerated.
+#' @param end_year The last year of assessment. The default is year - 1.
 #' @inheritParams satf::plot_recruitment
-#' @param make_rda This argument is automatically assessed based on the presence
-#' or absence of .rda files and should be left blank. TRUE/FALSE; indicate
-#' whether to produce an .rda file containing a list with the figure/table,
-#'  caption, and alternative text (if figure) for each figure and table.
 #' @param ref_line An argument inherited from `satf::plot_spawning_biomass.R`.
 #' A string specifying the type of reference you want to
 #' compare spawning biomass to. The default is `"target"`, which looks for
@@ -146,6 +146,7 @@
 #' create_template(
 #'   new_section = "a_new_section",
 #'   section_location = "before-introduction",
+#'   rda_dir = here::here()
 #' )
 #'
 #'
@@ -163,6 +164,7 @@
 #'   model = "SS3",
 #'   new_section = "an_additional_section",
 #'   section_location = "after-introduction",
+#'   rda_dir = here::here()
 #' )
 #'
 #' asar::create_template(
@@ -177,7 +179,8 @@
 #'   new_section = c("a_new_section", "another_new_section"),
 #'   section_location = c("before-introduction", "after-introduction"),
 #'   custom = TRUE,
-#'   custom_sections = c("executive_summary", "introduction")
+#'   custom_sections = c("executive_summary", "introduction"),
+#'   rda_dir = here::here()
 #' )
 #'
 #' create_template(
@@ -216,14 +219,13 @@
 #'   rda_dir = "C:/Users/Documents",
 #'   unit_label = "metric tons",
 #'   scale_amount = 1,
-#'   end_year = NULL,
+#'   end_year = 2022,
 #'   n_projected_years = 10,
 #'   relative = FALSE,
-#'   make_rda = FALSE,
-#'   ref_line = c("target", "MSY", "msy", "unfished"),
+#'   ref_line = "target",
 #'   spawning_biomass_label = "metric tons",
 #'   recruitment_label = "metric tons",
-#'   ref_line_sb = c("target", "MSY", "msy", "unfished")
+#'   ref_line_sb = "target"
 #' )
 #' }
 #'
@@ -262,13 +264,12 @@ create_template <- function(
     add_image = FALSE,
     spp_image = NULL,
     bib_file = "asar_references.bib",
-    rda_dir = NULL,
+    rda_dir = getwd(),
     unit_label = "metric tons",
     scale_amount = 1,
     end_year = NULL,
     n_projected_years = 10,
     relative = FALSE,
-    make_rda = FALSE,
     ref_line = c("target", "MSY", "msy", "unfished"),
     spawning_biomass_label = "metric tons",
     recruitment_label = "metric tons",
@@ -279,6 +280,11 @@ create_template <- function(
     year <- format(as.POSIXct(Sys.Date(), format = "%YYYY-%mm-%dd"), "%Y")
   }
 
+  # If analyst forgets to add end year, default will be year - 1
+  if (is.null(end_year)) {
+   end_year <- as.numeric(year) - 1
+  }
+
   # Name report
   if (!is.null(type)) {
     report_name <- paste0(
@@ -420,22 +426,25 @@ create_template <- function(
       # Create tables qmd
       if (include_tables) {
         if (!is.null(resdir) | !is.null(model_results) | !is.null(model)) {
-          if (!is.null(rda_dir) & !is.null(end_year)){
+          # if there is an existing folder with "rda_files" in the rda_dir:
+          if(dir.exists(fs::path(rda_dir, "rda_files"))){
               create_tables_doc(
                 resdir = resdir,
                 model_results = model_results,
                 model = model,
                 subdir = subdir,
                 rda_dir = rda_dir
               )
-
-            } else {
-              tables_doc <- paste0(
-                "### Tables \n \n",
-                "Please refer to the `satf` package downloaded from remotes::install_github('nmfs-ost/satf') to add premade tables."
-              )
-              utils::capture.output(cat(tables_doc), file = fs::path(subdir, "08_tables.qmd"), append = FALSE)
-              warning("Rda directory and/or arguments needed to create .rda files not defined.")
+            # if there isn't an existing folder with "rda_files" in the rda_dir,
+            # and the rda_files will be placed in the subdir:
+          } else {
+            create_tables_doc(
+              resdir = resdir,
+              model_results = model_results,
+              model = model,
+              subdir = subdir,
+              rda_dir = subdir
+            )
             }
         } else {
           tables_doc <- paste0(
@@ -457,7 +466,8 @@ create_template <- function(
       # Create figures qmd
       if (include_figures) {
         if (!is.null(resdir) | !is.null(model_results) | !is.null(model)) {
-          if (!is.null(rda_dir) & !is.null(end_year)){
+          # if there is an existing folder with "rda_files" in the rda_dir:
+          if(dir.exists(fs::path(rda_dir, "rda_files"))){
               create_figures_doc(
                 resdir = resdir,
                 model_results = model_results,
@@ -466,15 +476,19 @@ create_template <- function(
                 year = year,
                 rda_dir = rda_dir
               )
-            } else {
-              figures_doc <- paste0(
-                "### Figures \n \n",
-                "Please refer to the `satf` package downloaded from remotes::install_github('nmfs-ost/satf') to add premade figures."
-              )
-              utils::capture.output(cat(figures_doc), file = fs::path(subdir, "09_figures.qmd"), append = FALSE)
-              warning("Rda directory and/or arguments needed to create .rda files not defined.")
-            }
-        } else {
+            # if there isn't an existing folder with "rda_files" in the rda_dir,
+            # and the rda_files will be placed in the subdir:
+          } else {
+            create_figures_doc(
+              resdir = resdir,
+              model_results = model_results,
+              model = model,
+              subdir = subdir,
+              year = year,
+              rda_dir = subdir
+            )
+          }
+      } else {
           figures_doc <- paste0(
             "### Figures \n \n",
             "Please refer to the `satf` package downloaded from remotes::install_github('nmfs-ost/satf') to add premade figures."
@@ -769,9 +783,9 @@ create_template <- function(
       }
 
       # run satf::exp_all_figs_tables() if rda files not premade
-      if (!is.null(rda_dir) & !is.null(end_year)){
-
-        if(!dir.exists(file.path(rda_dir, "rda_files"))){
+      # output folder: subdir
+        if(!dir.exists(fs::path(rda_dir, "rda_files"))){
+          if (!is.null(resdir) | !is.null(model_results)) {
 
         # load converted output
         output <- utils::read.csv(paste0(resdir, "/", model_results))
@@ -785,14 +799,14 @@ create_template <- function(
           n_projected_years = n_projected_years,
           relative = relative,
           make_rda = TRUE,
-          rda_dir = rda_dir,
+          rda_dir = subdir,
           ref_line = ref_line,
           spawning_biomass_label = spawning_biomass_label,
           recruitment_label = recruitment_label,
           ref_line_sb = ref_line_sb
-        )
+          )
+          }
         }
-      }
 
 
       # print("_______Standardized output data________")
@@ -821,7 +835,7 @@ create_template <- function(
           "  ", "dplyr::summarize(max_val = max(year)) |> \n",
           "  ", "dplyr::pull(max_val))-10", "\n",
           # for quantities - don't want any values that are split by factor
-          "# subset output to remove quantities that are fplit by factor \n",
+          "# subset output to remove quantities that are split by factor \n",
           "output2 <- output |> \n",
           "  ", "dplyr::filter(is.na(season), \n",
           "  ", "  ", "is.na(fleet), \n",

inst/resources/affiliation_info.csv

@@ -1,23 +1,31 @@
 affiliation,office,name,address,city,state,country,postal-code
-OST-MD,OST,Office of Science and Technology,1315 East-West Highway,Silver Spring,MD,U.S.A.,20910
+AFSC-NOR,AFSC,Alaska Fisheries Science Center,2032 SE OSU Drive Building 955,Newport,OR,U.S.A.,97365-2097
+AFSC-SWA,AFSC,Alaska Fisheries Science Center,2725 Montlake Boulevard East,Seattle,WA,U.S.A.,98112-2097
+AFSC-JAK,AFSC,Alaska Fisheries Science Center,17109 Point Lena Loop Road,Juneau,AK,U.S.A.,99801
+AFSC,AFSC,Alaska Fisheries Science Center,17109 Point Lena Loop Road,Juneau,AK,U.S.A.,99801
+AFSC-WA,AFSC,Alaska Fisheries Science Center,7600 Sand Point Way N.E.,Seattle,WA,U.S.A.,98115
+AFSC-ABL,AFSC,Alaska Fisheries Science Center,17109 Point Lena Loop Road,Juneau,AK,U.S.A.,99801
+CDFW,CDFW,California Department of Fish and Wildlife,"1123 Industrial Rd., Suite 300",San Carlos,CA,U.S.A.,94070
 NEFSC,NEFSC,Northeast Fisheries Science Center,166 Water Street,Woods Hole,MA,U.S.A.,2543
 NEFSC-WHMA,NEFSC,Northeast Fisheries Science Center,166 Water Street,Woods Hole,MA,U.S.A.,2543
 NEFSC-NRI,NEFSC,Northeast Fisheries Science Center,28 Tarzwell Drive,Narragansett,RI,U.S.A.,2882
 NEFSC-MCT,NEFSC,Northeast Fisheries Science Center,212 Rogers Avenue,Milford,CT,U.S.A.,6460
+NWFSC,NWFSC,Northwest Fisheries Science Center,2725 Montlake Boulevard East,Seattle,WA,U.S.A.,98112-2097
+NWFSC-NOR,NWFSC,Northwest Fisheries Science Center,2032 SE OSU Drive Building 955,Newport,OR,U.S.A.,97365-2097
+NWFSC-SWA,NWFSC,Northwest Fisheries Science Center,2725 Montlake Boulevard East,Seattle,WA,U.S.A.,98112-2097
+ODFW,ODFW,Oregon Department of Fish and Wildlife,2040 Southeast Marine Science Drive,Newport,OR,U.S.A.,97365
+OST-MD,OST,Office of Science and Technology,1315 East-West Highway,Silver Spring,MD,U.S.A.,20910
+PIFSC,PIFSC,Pacific Islands Fisheries Science Center,1845 Wasp Boulevard,Honolulu,HI,U.S.A.,96818
+PSMFC,NWFSC,Pacific States Marine Fisheries Commission,2725 Montlake Boulevard East,Seattle,WA,U.S.A.,98112-2097
 SEFSC,SEFSC,Southeast Fisheries Science Center,75 Virginia Beach Drive,Miami,FL,U.S.A.,33149
 SEFSC-MFL,SEFSC,Southeast Fisheries Science Center,75 Virginia Beach Drive,Miami,FL,U.S.A.,33149
 SEFSC-BNC,SEFSC,Southeast Fisheries Science Center,101 Pivers Island Road,Beaufort,NC,U.S.A.,28516
 SEFSC-PCFL,SEFSC,Southeast Fisheries Science Center,3500 Delwood Beach Road,Panama City,FL,U.S.A.,32408
 SEFSC-GTX,SEFSC,Southeast Fisheries Science Center,4700 Avenue U,Galveston,TX,U.S.A.,77551
 SEFSC-PMS,SEFSC,Southeast Fisheries Science Center,3209 Frederic Street,Pascagoula,MS,U.S.A.,39567
 SEFSC-LLA,SEFSC,Southeast Fisheries Science Center,646 Cajundome Boulevard,Lafayette,LA,U.S.A.,70506
-NWFSC,NWFSC,Northwest Fisheries Science Center,2725 Montlake Boulevard East,Seattle,WA,U.S.A.,98112-2097
-NWFSC-NOR,NWFSC,Northwest Fisheries Science Center,2032 SE OSU Drive Building 955,Newport,OR,U.S.A.,97365-2097
-NWFSC-SWA,NWFSC,Northwest Fisheries Science Center,2725 Montlake Boulevard East,Seattle,WA,U.S.A.,98112-2097
 SWFSC-LJCA,SWFSC,Southwest Fisheries Science Center,8901 La Jolla Shores Drive,La Jolla,CA,U.S.A.,92037
-AFSC-NOR,AFSC,Alaska Fisheries Science Center,2032 SE OSU Drive Building 955,Newport,OR,U.S.A.,97365-2097
-AFSC-SWA,AFSC,Alaska Fisheries Science Center,2725 Montlake Boulevard East,Seattle,WA,U.S.A.,98112-2097
-AFSC-JAK,AFSC,Alaska Fisheries Science Center,17109 Point Lena Loop Road,Juneau,AK,U.S.A.,99801
-AFSC,AFSC,Alaska Fisheries Science Center,17109 Point Lena Loop Road,Juneau,AK,U.S.A.,99801
-PIFSC,PIFSC,Pacific Islands Fisheries Science Center,1845 Wasp Boulevard,Honolulu,HI,U.S.A.,96818
-AFSC-ABL,AFSC,Alaska Fisheries Science Center,17109 Point Lena Loop Road,Juneau,AK,U.S.A.,99801
+SWFSC-SC,SWFSC,Southwest Fisheries Science Center,110 McAllister Way,Santa Cruz,CA,U.S.A.,95060
+UAF,UAF,University of Alaska Fairbanks,"Department of Fisheries at Lena Point, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Rd",Juneau,AK,U.S.A.,99801
+WCR,WCR,West Coast Region,7600 Sand Point Way N.E.,Seattle,WA,U.S.A.,98115
+WDFW,WDFW,Washington Department of Fish and Wildlife,600 Capital Way North,Olympia,WA,U.S.A.,98501

inst/resources/authorship.csv

@@ -2,77 +2,99 @@ last,first,mi,office
 Adams,Charles,,NEFSC
 Ailloud,Lisa,,SEFSC
 Allen Akselrud,Caitlin,,SWFSC-LJCA
-Berger,Aaron,M.,NWFSC-SWA
+Berger,Aaron,M.,NWFSC-NOR
+Beyer,Sabrina,,NWFSC-SWA
+Bizzarro,Joseph,J.,SWFSC-SC
 Blackhart,Kristan,,NEFSC
 Boucher,Jason,,NEFSC
 Brodziak,John,,PIFSC
 Brown,Russell,W.,NEFSC-WHMA
+Budrick,John,E.,CDFW
 Carvalho,Felipe,,PIFSC
 Chang,Jui-Han,,NEFSC
 Chute,Toni,,NEFSC
+Coates,Julia,,CDFW
 Cope,Jason,M.,NWFSC-SWA
 Correa,Giancarlo,M.,AFSC
 Curti,Kiersten,,NEFSC
 Damiano,Matt,,SEFSC
 Deary,Alison,L.,AFSC
 Deroba,Jon,,NEFSC
+Dick,E.,J.,SWFSC-SC
 Dorn,Martin,W.,AFSC
 Ducharme-Barth,Nicholas,,PIFSC
 Dunn,Alex,,NEFSC
+Feddern,Megan,L.,NWFSC-SWA
 Ferriss,Bridget,E.,AFSC
-Field,John,,SWFSC
+Field,John,,SWFSC-SC
 Fitchett,Mark,D.,PIFSC
 Forrestal,Francesca,,SEFSC-MFL
-Gertseva,Vladlena,,NWFSC
-Haltuch,Melissa,A.,AFSC-SWA
+Gertseva,Vladlena,,NWFSC-SWA
+Haltuch,Melissa,A.,AFSC-WA
 Hamel,Owen,S.,NWFSC-SWA
 Hart,Dvora,,NEFSC
+Hastie,Jim,,NWFSC-SWA
 Havron,Andrea,,OST
+Head,Melissa,A.,NWFSC-SWA
 Hendrickson,Lisa,,NEFSC
 Hennen,Dan,,NEFSC
+Hernvann,Pierre-Yves,,NWFSC-SWA
 Hill,Kevin,T.,SWFSC-LJCA
+Hillier,Lisa,K.,WDFW
+Hinton,Kristen,E.,WDFW
 Johnson,Kelli,F.,NWFSC-SWA
 Jones,Andy,,NEFSC
-Kapur,Maia,R.,PIFSC
+Kapur,Maia,S.,AFSC-WA
 Kuriyama,Peter,T.,SWFSC-LJCA
+Lam,Laurel,S.,PSMFC
 Langseth,Brian,J.,NWFSC-SWA
 Legault,Chris,,NEFSC
 Levine,Mike,,AFSC
-Marshall,Kristan,,NWFSC
+Marshall,Kristan,,NWFSC-SWA
+Matson,Sean,E.,WCR
 McGowan,David,W.,AFSC
 Methot,Richard,,NWFSC
-Monk,Melissa,,SWFSC
+Monk,Melissa,,SWFSC-SC
 Monnahan,Cole,C.,AFSC
 Nieland,Julie,,NEFSC
+Niles,Corey,B.,WDFW
 Nitschke,Paul,,NEFSC
 O'Keefe,Cate,,NEFSC
 Oken,Kiva,L.,NWFSC-SWA
 Oshima,Megumi,,PIFSC
 Perretti,Charles,,NEFSC
 Rios,Adyan,,SEFSC
 Rogers,Lauren,,AFSC
+Rogers,Tanya,L.,SWFSC-SC
+Saas,Emma,M.,SWFSC-SC
 Sagarese,Skyler,,SEFSC-MFL
 Sculley,Michelle,,PIFSC
 Shank,Burton,,NEFSC
 Shertzer,Kyle,,SEFSC-BNC
 Shotwell,S.,Kalei,AFSC
 Siegfried,Katie,,SEFSC
 Sosebee,Karson,,NEFSC
+Spies,Ingrid,,AFSC-WA
 Stawitz,Christine,,OST
-Sullivan,Jane,,AFSC
+Sullivan,Jane,Y.,AFSC
 Syslo,John,,PIFSC
 Taylor,Ian,G.,NWFSC-SWA
 Tolimieri,Nick,,NWFSC-SWA
 Traver,Michele,,NEFSC
+Tsou,Tien-Shui,,WDFW
 Tyrell,Abigail,,NEFSC
-Wassermann,Sophia,N.,AFSC-SWA
+Veron,Matthieu,,AFSC-WA
+Wallace,John,R.,NWFSC-SWA
+Wassermann,Sophia,N.,AFSC-WA
 Wetzel,Chantel,R.,NWFSC-SWA
+Whitman,Alison,D.,ODFW
 Wigley,Susan,,NEFSC
 Williams,Ben,,AFSC
 Williams,Erik,,SEFSC
 Wood,Anthony,,NEFSC
 Yau,Annie,J.,PIFSC
 Zador,Stephani,,AFSC
+Zahner,Joshua,A.,UAF
 Zwolinski,Juan,P.,SWFSC-LJCA
 Snow,John,,AFSC
 Phantom,Danny,,NEFSC