Reorder skeleton (#59)

* update(template): add changes for debugging and issue - Added options for english and removed the old czech lang the in-header doc - changed the chunks for figs and tabs not to render while development is occurring * update(template): add changes for debugging and issue - Added options for english and removed the old czech lang the in-header doc - changed the chunks for figs and tabs not to render while development is occurring * Attempt to inherit custom_sections parameter from asar::create_template() * Changed remaining x's (former argument) into custom_sections (new argument), and removed the parameter definition * Clarified argument definitions for create_title.R * Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy. Questions for Sam: Please check/edit the "parameters" parameter's definition. What does it mean, and how should it be defined? Is it ever false? Please check/edit the "param_values" parameter's definition. What does it mean, and how should it be defined? Please check/edit the "convert_output" parameter's definition for accuracy. * Clarified argument definitions in convert_output.R and updated documentation. * update(create_figures_doc): add example of where caption will go Integration of the other captions once written and alt. text will form adjustments to here * refactor: Changed names of sections in create_template to those voted on by steering committee (as of Sept 2024) * deleted files with outdated names (i.e., without numbers before descriptions * updated test-create_template.R to avoid merge conflict * Remove test folder pushed to repo * fix(custom section op): change base_section, add_section, and test - changes in both naming of arguments and templates were fixed - test-add_section was adjusted so expected values were correct * fix(assessment spelling): change file name and will now pass test * delete(assessment_gloassaries.tex) * fix(test-add_section): spelling error in test * deleted files with outdated names (i.e., without numbers before descriptions * updated test-create_template.R to avoid merge conflict * Remove test folder pushed to repo * fix(assessment spelling): change file name and will now pass test * fix(test-add_section): change file names in test and adjust fxns to meet test expectations * fix(test-create_template): add to resdir to remove warning in test * delete(utils): remove add_base_section from utils * Attempt to inherit custom_sections parameter from asar::create_template() * Changed remaining x's (former argument) into custom_sections (new argument), and removed the parameter definition * Clarified argument definitions for add_child.R * Clarified argument definitions for add_chunk.R * Clarified argument definitions for add_section.R. Note: The text previously referenced an argument that was missing from the function ('title'). In my update, I changed it to 'sec_names'. Please verify that this was an accurate assumption. * Clarified argument definitions for create_citation.R * Clarified argument definitions for create_figures_doc.R * Clarified argument definitions for create_title.R * Clarified argument definitions for export_object.R * Clarified argument definitions for format_quarto.R * Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy. Questions for Sam: Please check/edit the "parameters" parameter's definition. What does it mean, and how should it be defined? Is it ever false? Please check/edit the "param_values" parameter's definition. What does it mean, and how should it be defined? Please check/edit the "convert_output" parameter's definition for accuracy. * Updated documentation * Clarified argument definitions in convert_output.R and updated documentation. * Update(affiliation_info.csv): add country * update(create_figures_doc): add example of where caption will go Integration of the other captions once written and alt. text will form adjustments to here * Attempt to inherit custom_sections parameter from asar::create_template() * Changed remaining x's (former argument) into custom_sections (new argument), and removed the parameter definition * Clarified argument definitions for create_title.R * Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy. Questions for Sam: Please check/edit the "parameters" parameter's definition. What does it mean, and how should it be defined? Is it ever false? Please check/edit the "param_values" parameter's definition. What does it mean, and how should it be defined? Please check/edit the "convert_output" parameter's definition for accuracy. * Clarified argument definitions in convert_output.R and updated documentation. * refactor: Changed names of sections in create_template to those voted on by steering committee (as of Sept 2024) * deleted files with outdated names (i.e., without numbers before descriptions * updated test-create_template.R to avoid merge conflict * Remove test folder pushed to repo * fix(custom section op): change base_section, add_section, and test - changes in both naming of arguments and templates were fixed - test-add_section was adjusted so expected values were correct * fix(assessment spelling): change file name and will now pass test * delete(assessment_gloassaries.tex) * fix(test-add_section): spelling error in test * deleted files with outdated names (i.e., without numbers before descriptions * updated test-create_template.R to avoid merge conflict * Remove test folder pushed to repo * fix(assessment spelling): change file name and will now pass test * fix(test-add_section): change file names in test and adjust fxns to meet test expectations * fix(test-create_template): add to resdir to remove warning in test * delete(utils): remove add_base_section from utils * Fix naming in create_template --------- Co-authored-by: Schiano-NOAA <[email protected]>
nmfs-ost · Oct 16, 2024 · 0c49a05 · 0c49a05
1 parent 91642c9
commit 0c49a05
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Showing 30 changed files with 311 additions and 625 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -18,9 +18,11 @@ Imports:
     gridExtra,
     gt,
     naniar,
+    nmfspalette,
     officer,
     openxlsx,
     prodlim,
+    r4ss,
     satf,
     stats,
     stringr,
@@ -40,7 +42,8 @@ VignetteBuilder:
     knitr
 Remotes:
     nmfs-ost/satf,
-    r4ss/r4ss
+    r4ss/r4ss,
+    nmfs-fish-tools/nmfspalette
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 Encoding: UTF-8

diff --git a/R/add_base_section.R b/R/add_base_section.R
@@ -11,12 +11,12 @@ add_base_section <- function(custom_sections) {
   section_list <- list()
   for (i in 1:length(sec_sel)) {
     sec_file <- grep(
-      custom_sections = list.files(system.file("templates", "skeleton", package = "asar")),
+      list.files(system.file("templates", "skeleton", package = "asar")),
       pattern = sec_sel[i],
       value = TRUE
     )
     if (identical(sec_file, character(0))) stop("One or more section name(s) does not exist. Please check the spelling or if you are tring to add a section that is not in the default template, please use parameter 'custom_sections' and refer to documentation. To check which sections are in the base template please run list.files(system.file('templates', 'skeleton', package = 'ASAR')) in your console")
-    sec_file -> section_list[i]
+    sec_file -> section_list[[i]]
   }
-  section_list
+  as.list(unlist(section_list))
 }
diff --git a/R/add_section.R b/R/add_section.R
@@ -26,7 +26,7 @@ add_section <- function(
   # after-section
   # in-section (will always append to the end of the section)
   for (i in 1:length(new_section)) {
-    section_i_name <- paste0(gsub(" ", "_", new_section[i]), ".qmd")
+    section_i_name <- paste0(gsub(" ", "_", tolower(new_section[i])), ".qmd")
     local_section <- forstringr::str_extract_part(section_location[i], "-", before = FALSE)
     local_section_prev <- forstringr::str_extract_part(section_location[i - 1], "-", before = FALSE)
 
@@ -39,7 +39,7 @@ add_section <- function(
     }
 
     section_i <- paste0(
-      "## ", stringr::str_to_title(sub("_", " ", new_section[i])), "\n",
+      "## ", stringr::str_to_title(sub("_", " ", tolower(new_section[i]))), "\n",
       "\n",
       "[Insert text here]", "\n",
       "\n",
@@ -51,9 +51,9 @@ add_section <- function(
       custom_sections <- append(custom_sections, section_i_name, after = (which(grepl(local_section, custom_sections)) - 1))
     } else if (locality == "after") {
       if (locality %in% locality_prev & local_section %in% local_section_prev) {
-        custom_sections <- append(custom_sections, section_i_name, after = which(grepl(gsub(" ", "_", new_section[i - 1]), custom_sections)))
+        custom_sections <- append(custom_sections, section_i_name, after = which(grepl(gsub(" ", "_", tolower(new_section[i - 1])), custom_sections)))
       } else {
-        custom_sections <- append(custom_sections, section_i_name, after = which(grepl(local_section, custom_sections)))
+        custom_sections <- append(custom_sections, section_i_name, after = max(which(grepl(local_section, custom_sections))))
       }
     } else if (locality == "in") {
       stop("No available option for adding a new section 'in' another quarto document.", call. = FALSE)

diff --git a/R/create_figures_doc.R b/R/create_figures_doc.R
@@ -28,6 +28,7 @@ create_figures_doc <- function(resdir = NULL,
       add_chunk(
         paste0("satf::plot_recruitment(dat = '", resdir, "/", model_results, "', model = '", model, "')"),
         label = "recruitment",
+        eval = "false",
         add_option = TRUE,
         chunk_op = "fig-cap: 'this is the caption for the figure.'"
       ),
@@ -41,13 +42,13 @@ create_figures_doc <- function(resdir = NULL,
     )
     figures_doc <- paste0(
       figures_doc,
-      add_chunk(plot_code, label = "spawn_bio"),
+      add_chunk(plot_code, label = "spawn_bio", eval = "false"),
       "\n"
     )
   } else {
     # add option for only adding specified tables
   }
 
   # Save tables doc to template folder
-  utils::capture.output(cat(figures_doc), file = paste0(subdir, "/", "figures.qmd"), append = FALSE)
+  utils::capture.output(cat(figures_doc), file = paste0(subdir, "/", "09_figures.qmd"), append = FALSE)
 }
diff --git a/R/create_tables_doc.R b/R/create_tables_doc.R
@@ -26,7 +26,8 @@ create_tables_doc <- function(resdir = NULL,
         paste0(
           "satf::table_indices(dat = '", resdir, "/", model_results, "', model = '", model, "')"
         ),
-        label = "indices"
+        label = "indices",
+        eval = "false"
       )
     )
 
@@ -44,5 +45,7 @@ create_tables_doc <- function(resdir = NULL,
   }
 
   # Save tables doc to template folder
-  utils::capture.output(cat(tables_doc), file = paste0(subdir, "/", "tables.qmd"), append = FALSE)
+  utils::capture.output(cat(tables_doc),
+                        file = paste0(subdir, "/", "08_tables.qmd"),
+                        append = FALSE)
 }
diff --git a/R/create_template.R b/R/create_template.R
@@ -276,15 +276,15 @@ create_template <- function(
             "### 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, "tables.qmd"), append = FALSE)
+          utils::capture.output(cat(tables_doc), file = fs::path(subdir, "08_tables.qmd"), append = FALSE)
           warning("Results file or model name not defined.")
         }
       } else {
         tables_doc <- paste0(
           "### Tables \n \n",
           "Please refer to the `satf` package downloaded from remotes::install_github('nmfs-ost/satf') to add premade figures"
         )
-        utils::capture.output(cat(tables_doc), file = fs::path(subdir, "tables.qmd"), append = FALSE)
+        utils::capture.output(cat(tables_doc), file = fs::path(subdir, "08_tables.qmd"), append = FALSE)
       }
       # Create figures qmd
       if (include_figures) {
@@ -298,12 +298,12 @@ create_template <- function(
           )
         } else {
           figures_doc <- paste0("## Figures \n")
-          utils::capture.output(cat(figures_doc), file = fs::path(subdir, "figures.qmd"), append = FALSE)
+          utils::capture.output(cat(figures_doc), file = fs::path(subdir, "09_figures.qmd"), append = FALSE)
           warning("Results file or model name not defined.")
         }
       } else {
         figures_doc <- paste0("## Figures \n")
-        utils::capture.output(cat(figures_doc), file = fs::path(subdir, "figures.qmd"), append = FALSE)
+        utils::capture.output(cat(figures_doc), file = fs::path(subdir, "09_figures.qmd"), append = FALSE)
       }
 
       # Part I
@@ -441,6 +441,7 @@ create_template <- function(
         # Date
         "date: today", "\n",
         "lang: en \n",
+        "keep-tex: true \n"
       )
 
       # Add species image on title page
@@ -569,32 +570,38 @@ create_template <- function(
       if (custom == FALSE) {
         sections <- add_child(
           c(
-            "executive_summary.qmd",
-            "introduction.qmd",
-            "data.qmd",
-            "modeling_approach.qmd",
-            "results.qmd",
-            "projections.qmd",
-            "discussion.qmd",
-            "acknowledgments.qmd",
-            "references.qmd",
-            "tables.qmd",
-            "figures.qmd",
-            "appendix.qmd"
+            "01_executive_summary.qmd",
+            "02_introduction.qmd",
+            "03_data.qmd",
+            "04a_assessment-configuration.qmd",
+            "04b_assessment-results.qmd",
+            "04c_assessment-sensitivity.qmd",
+            "04d_asessment-benchmarks.qmd",
+            "04e_assessment-projections.qmd",
+            "05_discussion.qmd",
+            "06_acknowledgments.qmd",
+            "07_references.qmd",
+            "08_tables.qmd",
+            "09_figures.qmd",
+            "10_notes.qmd",
+            "11_appendix.qmd"
           ),
           label = c(
-            "executive_summary",
-            "introduction",
-            "data",
-            "modeling_approach",
-            "results",
-            "projections",
-            "discussion",
-            "acknowlesgements",
-            "references",
-            "tables",
-            "figures",
-            "appendix"
+            "01_executive_summary",
+            "02_introduction",
+            "03_data",
+            "04a_assessment-configuration",
+            "04b_assessment-results",
+            "04c_assessment-sensitivity",
+            "04d_asessment-benchmarks",
+            "04e_assessment-projections",
+            "05_discussion",
+            "06_acknowledgments",
+            "07_references",
+            "08_tables",
+            "09_figures",
+            "10_notes",
+            "11_appendix"
           )
         )
       } else {
@@ -611,18 +618,21 @@ create_template <- function(
 
           if (is.null(custom_sections)) {
             sec_list1 <- list(
-              "executive_summary.qmd",
-              "introduction.qmd",
-              "data.qmd",
-              "modeling_approach.qmd",
-              "results.qmd",
-              "projections.qmd",
-              "discussion.qmd",
-              "acknowledgments.qmd",
-              "references.qmd",
-              "tables.qmd",
-              "figures.qmd",
-              "appendix.qmd"
+              "01_executive_summary.qmd",
+              "02_introduction.qmd",
+              "03_data.qmd",
+              "04a_assessment-configuration.qmd",
+              "04b_assessment-results.qmd",
+              "04c_assessment-sensitivity.qmd",
+              "04d_asessment-benchmarks.qmd",
+              "04e_assessment-projections.qmd",
+              "05_discussion.qmd",
+              "06_acknowledgments.qmd",
+              "07_references.qmd",
+              "08_tables.qmd",
+              "09_figures.qmd",
+              "10_notes.qmd",
+              "11_appendix.qmd"
             )
             sec_list2 <- add_section(
               new_section = new_section,
@@ -645,10 +655,10 @@ create_template <- function(
               stop("Defined customizations do not match one or all of the relative placement of a new section. Please review inputs.")
             }
             if (include_tables) {
-              sec_list1 <- c(sec_list1, "tables.qmd")
+              sec_list1 <- c(sec_list1, "08_tables.qmd")
             }
             if (include_figures) {
-              sec_list1 <- c(sec_list1, "figures.qmd")
+              sec_list1 <- c(sec_list1, "09_figures.qmd")
             }
             sec_list2 <- add_section(
               new_section = new_section,
@@ -736,32 +746,38 @@ create_template <- function(
       if (custom == FALSE) {
         sections <- add_child(
           c(
-            "executive_summary.qmd",
-            "introduction.qmd",
-            "data.qmd",
-            "modeling_approach.qmd",
-            "results.qmd",
-            "projections.qmd",
-            "discussion.qmd",
-            "acknowledgments.qmd",
-            "references.qmd",
-            "tables.qmd",
-            "figures.qmd",
-            "appendix.qmd"
+            "01_executive_summary.qmd",
+            "02_introduction.qmd",
+            "03_data.qmd",
+            "04a_assessment-configuration.qmd",
+            "04b_assessment-results.qmd",
+            "04c_assessment-sensitivity.qmd",
+            "04d_asessment-benchmarks.qmd",
+            "04e_assessment-projections.qmd",
+            "05_discussion.qmd",
+            "06_acknowledgments.qmd",
+            "07_references.qmd",
+            "08_tables.qmd",
+            "09_figures.qmd",
+            "10_notes.qmd",
+            "11_appendix.qmd"
           ),
           label = c(
-            "executive_summary",
-            "introduction",
-            "data",
-            "modeling_approach",
-            "results",
-            "projections",
-            "discussion",
-            "acknowlesgements",
-            "references",
-            "tables",
-            "figures",
-            "appendix"
+            "01_executive_summary",
+            "02_introduction",
+            "03_data",
+            "04a_assessment-configuration",
+            "04b_assessment-results",
+            "04c_assessment-sensitivity",
+            "04d_asessment-benchmarks",
+            "04e_assessment-projections",
+            "05_discussion",
+            "06_acknowledgments",
+            "07_references",
+            "08_tables",
+            "09_figures",
+            "10_notes",
+            "11_appendix"
           )
         )
       } else {
@@ -778,22 +794,25 @@ create_template <- function(
 
           if (is.null(custom_sections)) {
             sec_list1 <- list(
-              "executive_summary.qmd",
-              "introduction.qmd",
-              "data.qmd",
-              "modeling_approach.qmd",
-              "results.qmd",
-              "projections.qmd",
-              "discussion.qmd",
-              "acknowledgments.qmd",
-              "references.qmd",
-              "tables.qmd",
-              "figures.qmd",
-              "appendix.qmd"
+              "01_executive_summary.qmd",
+              "02_introduction.qmd",
+              "03_data.qmd",
+              "04a_assessment-configuration.qmd",
+              "04b_assessment-results.qmd",
+              "04c_assessment-sensitivity.qmd",
+              "04d_asessment-benchmarks.qmd",
+              "04e_assessment-projections.qmd",
+              "05_discussion.qmd",
+              "06_acknowledgments.qmd",
+              "07_references.qmd",
+              "08_tables.qmd",
+              "09_figures.qmd",
+              "10_notes.qmd",
+              "11_appendix.qmd"
             )
             sec_list2 <- add_section(
               new_section = new_section,
-              new_section = section_location,
+              section_location = section_location,
               custom_sections = sec_list1,
               subdir = subdir
             )
@@ -808,7 +827,7 @@ create_template <- function(
             # Create new sections as .qmd in folder
             sec_list2 <- add_section(
               new_section = new_section,
-              new_section = section_location,
+              section_location = section_location,
               custom_sections = sec_list1,
               subdir = subdir
             )