Update SAFE template table structure from flextable to asar

README.md

@@ -83,7 +83,7 @@ asar::create_template(
   species = "Petrale sole",
   spp_latin = "Eopsetta jordani",
   year = 2023,
-  author = c("Ian G. Taylor"="NWFSC", "Vladlena Gertseva"="NWFSC", "Nick Tolimieri"="NWFSC"),
+  authors = c("Ian G. Taylor"="NWFSC", "Vladlena Gertseva"="NWFSC", "Nick Tolimieri"="NWFSC"),
   include_affiliation = TRUE,
   simple_affiliation = FALSE,
   param_names = c("nf","sf"),

inst/templates/safe/01c_plan-team.qmd

@@ -5,29 +5,33 @@
 ```{r}
 #| eval: false
 #| echo: false
+# install.packages("devtools")
+# devtools::install_github("BenWilliams-NOAA/safe")
+
+year <- format(Sys.time(), "%Y")
+
 ptdata <- safe::ptdata
 
-flextable::font(
-  flextable::footnote(flextable::flextable(ptdata),
-    j = 3, part = "header", ref_symbols = "1",
-    value = flextable::as_paragraph("Total biomass (age 4+) estimates from age-structured model.")
-  ),
-  fontname = "Times New Roman",
-  part = "all"
-) %>%
-  flextable::footnote(
-    i = 2, j = 7, part = "body", ref_symbols = "2",
-    value = flextable::as_paragraph(
-      flextable::as_chunk(paste0(paste0("Current as of ", date, " . Source: NMFS Alaska Regional Office Catch Accounting System
-via the AKFIN database (http://www.akfin.org).")))
-    )
-  ) %>%
-  flextable::set_formatter(Year = function(x) sprintf("%s", x)) %>%
-  flextable::merge_at(i = 1:4, j = 1) %>%
-  flextable::hrule(rule = "exact") %>%
-  flextable::hline_top(part = "all") %>%
-  flextable::hline_bottom() %>%
-  flextable::fix_border_issues()
+ptdata |>
+  gt::gt() |>
+  gt::tab_footnote(
+    footnote = "Total biomass (age 4+) estimates from age-structured model.",
+    locations = gt::cells_column_labels(columns = Biomass)
+  ) |>
+  gt::tab_footnote(
+    footnote = paste0("Current as of ", year, ". Source: NMFS Alaska Regional Office Catch Accounting System
+via the AKFIN database (http://www.akfin.org)."),
+    locations = cells_column_labels(columns = Catch)
+  ) |>
+  gt::fmt_integer(columns = Year, sep_mark = "") |>
+  gt::fmt_integer(columns = Biomass:Catch, sep_mark = ",")  |>
+  gt::tab_options(
+    column_labels.font.weight = "bold",
+    table_body.hlines.style = "none"
+  ) |>
+  gt::sub_missing(
+    missing_text = ""
+  )
 ```
 
 {{< pagebreak >}} 
@@ -37,51 +41,43 @@ via the AKFIN database (http://www.akfin.org).")))
 #| echo: false
 ptdata2 <- safe::ptdata2
 
-flextable::font(
-  flextable::footnote(flextable::flextable(ptdata2[-1, ]),
-    j = 6, part = "header", ref_symbols = "2",
-    value = flextable::as_paragraph(flextable::as_chunk(
-      paste0(paste0(
-        "Current as of ", date,
-        " . Source: NMFS Alaska Regional Office Catch Accounting System
-via the AKFIN database (http://www.akfin.org)."
-      ))
-    ))
-  ),
-  fontname = "Times New Roman",
-  part = "all"
-) %>%
-  flextable::add_header(values = ptdata2[1, ]) %>%
-  flextable::border_remove() %>%
-  flextable::merge_at(j = 1) %>%
-  flextable::compose(
-    i = 1, j = 3:6,
-    value = flextable::as_paragraph(as.character(year - 1)),
-    part = "header"
-  ) %>%
-  flextable::compose(
-    i = 1, j = 7:8,
-    value = flextable::as_paragraph(as.character(year)),
-    part = "header"
-  ) %>%
-  flextable::compose(
-    i = 1, j = 9:10,
-    value = flextable::as_paragraph(as.character(year + 1)),
-    part = "header"
-  ) %>%
-  flextable::merge_at(i = 1, j = 3:6, part = "header") %>%
-  flextable::merge_at(i = 1, j = 7:8, part = "header") %>%
-  flextable::merge_at(i = 1, j = 9:10, part = "header") %>%
-  flextable::align(i = 1, part = "header", align = "center") %>%
-  flextable::compose(
-    i = 2, j = 7:10,
-    value = flextable::as_paragraph(rep(c("ABC", "OFL"), 2)),
-    part = "header"
-  ) %>%
-  flextable::hline_top(part = "body") %>%
-  flextable::hline_top(part = "header") %>%
-  flextable::vline(j = c(2, 6, 8)) %>%
-  flextable::hline_bottom(part = "body") %>%
-  flextable::fix_border_issues(part = "all") %>%
-  flextable::set_table_properties(width = .5, layout = "autofit")
+year <- format(Sys.time(), "%Y")
+date <- Sys.Date()
+
+yr_prev  <- ptdata2[1, 3]  # "2021"
+yr_curr  <- ptdata2[1, 7]  # "2022"
+yr_next  <- ptdata2[1, 9]  # "2023"
+
+ptdata2[-1, ] |>
+  gt::gt() |>
+  gt::tab_options(
+    column_labels.font.weight = "bold",
+    table_body.hlines.style = "none"
+  ) |>
+    gt::cols_label(
+      OFL   = paste(yr_prev, "OFL"),
+      ABC   = paste(yr_prev, "ABC"),
+      TAC   = paste(yr_prev, "TAC"),
+      Catch = paste(yr_prev, "Catch"),
+      OFL.1 = paste(yr_curr, "ABC"),
+      ABC.1 = paste(yr_curr, "OFL"),
+      OFL.2 = paste(yr_next, "ABC"),
+      ABC.2 = paste(yr_next, "OFL")
+  ) |>
+  gt::tab_footnote(
+    footnote = paste0("Current as of ", date, ". Source: NMFS Alaska Regional Office Catch Accounting System via the AKFIN database (http://www.akfin.org)."),
+    locations = cells_column_labels(columns = 6)
+  ) |>
+  gt::fmt_integer() |>
+  gt::cols_align(align = "center", columns = 3:10) |>
+  gt::cols_align(align = "left", columns = 1:2) |>
+  gt::sub_missing(
+    missing_text = ""
+  ) |>
+  gt::tab_style(
+    style = cell_borders(sides = "right", color = "mediumgrey", weight = px(2)),
+    locations = list(
+      cells_body(columns = c(6, 8)),
+      cells_column_labels(columns = c(6, 8))
+    )  )
 ```

inst/templates/safe/05_data.qmd

@@ -32,15 +32,12 @@ data.frame(
     "1991-1997, 2003, 2007, 2009, 2011, 2013, 2015, 2017, 2019"
   )
 ) |>
-  flextable::flextable() |>
-  flextable::width(j = ~Source, width = 1) |>
-  flextable::width(j = ~Data, width = 1.5) |>
-  flextable::width(j = ~Years, width = 4) |>
-  flextable::merge_v(j = 1) |>
-  flextable::font(fontname = "Times", part = "all") |>
-  flextable::fontsize(size = 10) |>
-  flextable::theme_vanilla() |>
-  flextable::fix_border_issues()
+  gt::gt() |>
+  gt::cols_width(
+    Source ~ px(100),
+    Data ~ px(150),
+    Years ~ px(400)
+  )
 ```
 
 ## Fishery

vignettes/accessibility_guide.Rmd

@@ -185,6 +185,8 @@ recruitment_alt_text <- new_alt_text
 
 3.  As stated earlier, if you see text that looks like a placeholder (e.g., "The x axis, showing the year, spans from B.start.year to B.end.year..."), that means that there was at least one instance where our tool failed to extract a specific value from the model results and substitute it into the placeholder. Please make sure that your alt text and captions contain the expected values before moving forward with your report. Check out the inst/resources/captions_alt_text_template.csv file in the `stockplotr` package to view the template with placeholders. The same package's `write_captions()` function shows how values are extracted from the model results and substituted into the placeholders.
 
+4. If you add a special character (e.g., percentage sign (%) or dollar sign ($); see [full list on this wiki page](https://en.wikibooks.org/wiki/LaTeX/Special_Characters#Other_symbols)), please add two backslashes before the character to avoid issues compiling your report later on (specifically, the conversion from Quarto to LaTeX via Pandoc, and then compilation of the LaTeX report after running `add_accessibility()` or `add_alttext()`). For example, "The 95% CI" would be written as "The 95\\\\% CI".
+
 ### More resources
 
 Looking for more resources for writing alt text? Check out the [NOAA Library's website for creating accessible documents](https://library.noaa.gov/Section508/CreatingDocs).