Update SAFE template table structure from flextable to asar as per #428

Author: sbreitbart-NOAA

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