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feat: Started making risk table based on AFSC's SAFE main table
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@sbreitbart-NOAA @Schiano-NOAA
sbreitbart-NOAA authored and Schiano-NOAA committed Feb 24, 2025
1 parent 56ab69a commit 174a160
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297 changes: 297 additions & 0 deletions R/afsc_risk_table.R
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# AFSC SAFE Risk Table

#' Creates risk table. This table was adapted from a table
#' created by Ben Williams, a NOAA Research Fisheries Biologist,
#' as part of the AFSC SAFE reporting tool:
#' https://github.com/BenWilliams-NOAA/safe/blob/main/R/main_table.R
#'
#' @inheritParams plot_recruitment
#' @param tier Tier
#' @param c1 Estimated catch for the current year
#' @param c2 Projected catch year + 1
#' @param c3 Projected catch year + 2
#'
#' @export risk_table
#'
risk_table <- function(dat, end_year, tier, c1, c2, c3){

# for cells in dat with numeric values, format the numbers
# with built-in comma function
for (column in names(dat)) {
if (is.numeric(dat[[column]])) {
dat[[column]] <- sapply(dat[[column]], comma)
}
}

# Extract values
# spawning & total biomass
biomasses <- dat |>
dplyr::filter(
label %in% c("spawning_biomass", "projected_spawning_biomass",
"biomass", "projected_biomass"),
module_name %in% c("DERIVED_QUANTITIES", "t.series", "proj.t.series")
) |>
dplyr::mutate(
estimate = as.numeric(estimate),
year = as.numeric(year)) |>
dplyr::select(estimate, year, module_name, label)

# sb (spawning biomass) for end year
sb_end_yr <- biomasses |>
dplyr::filter(year == end_year,
label == "spawning_biomass") |>
dplyr::select(estimate) |>
as.numeric()

# sb for end year + 1
sb_proj1 <- biomasses |>
dplyr::filter(year == end_year + 1,
label == "projected_spawning_biomass") |>
dplyr::select(estimate) |>
as.numeric()

# sb for end year + 2
sb_proj2 <- biomasses |>
dplyr::filter(year == end_year + 2,
label == "projected_spawning_biomass") |>
dplyr::select(estimate) |>
as.numeric()


# total biomass for end year
b_end_yr <- biomasses |>
dplyr::filter(year == end_year,
label == "biomass") |>
dplyr::select(estimate) |>
as.numeric()

# total biomass for end year + 1
b_proj1 <- biomasses |>
dplyr::filter(year == end_year + 1,
label == "projected_biomass") |>
dplyr::select(estimate) |>
as.numeric()

# total biomass for end year + 2
b_proj2 <- biomasses |>
dplyr::filter(year == end_year + 2,
label == "projected_biomass") |>
dplyr::select(estimate) |>
as.numeric()

# TO DO: calculate female spawning biomass here
# (FSB = SB x proportion female, at age)?

flextable::flextable(dat) |>
flextable::font(fontname = "Times New Roman", part = "all") |>
flextable::fontsize(size = 11, part = "all") |>
flextable::add_header_row(value = c( "", "a", "b"), colwidths = c(1,2,2)) |>
flextable::compose(i=2, j=1,
value = flextable::as_paragraph( "Quantity/Status"),
part = "header") |>
flextable::compose(i = 1, j = 2:3,
value = flextable::as_paragraph( "As estimated or " , flextable::as_i("specified last"), " year for:"),
part = "header") |>
flextable::compose(i = 1, j = 4:5,
value = flextable::as_paragraph( "As estimated or " , flextable::as_i("recommended this"), " year for:"),
part = "header") |>
flextable::compose(i = 2, j = 2,
value = flextable::as_paragraph(as.character(end_year)), part = "header") |>
flextable::compose(i = 2, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year + 1))),
part = "header") |>
flextable::compose(i = 2, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year + 2))),
part = "header") |>
flextable::align(align = "center", part = "header") |>
flextable::align(j=2:5, align = "center") |>
flextable::align(j = 1, part = "header", align="left") |>
flextable::bold(i = 2, j = 1, part = "header") |>
flextable::width(j = 1, width = 2.5) |>
flextable::width(j = 2:5, width = 0.65) |>
flextable::bg(j = 2, bg = "#f7f7f7", part = "all") |>
flextable::bg(j = 3, bg = "#f7f7f7", part = "all") |>
flextable::border_remove() |>
flextable::hline_top(part = "header") |>
flextable::hline_top() |>
flextable::vline_right(part = "body") |>
flextable::vline_right(part = "header") |>
flextable::vline_left(part = "body") |>
flextable::vline_left(part = "header") -> tbl



if(tier == 3){
tier = "3a"
flextable::font(
flextable::footnote(tbl, i=2, j=4:5, part = "header", ref_symbols = "*",
value = flextable::as_paragraph(
flextable::as_chunk(paste0("Projections are based on an estimated catch of ",
prettyNum(c1, big.mark = ","), " t for ", end_year,
" and estimates of ",
prettyNum(c2, big.mark = ","),
" t and ",
prettyNum(c3, big.mark = ","),
" t used in place of maximum permissible ABC for ",
end_year+1, " and ", end_year+2, "."))),
sep = "."),
fontname = "Times New Roman",
part = "all") |>
flextable::compose(i = 2, j = 2:5,
value = flextable::as_paragraph(tier)) |>
flextable::compose(i = 5, j = 1,
value = flextable::as_paragraph("B", flextable::as_sub("100%"))) |>
flextable::compose(i = 6, j = 1,
value = flextable::as_paragraph("B", flextable::as_sub("40%"))) |>
flextable::compose(i = 7, j = 1,
value = flextable::as_paragraph("B", flextable::as_sub("35%"))) |>
flextable::compose(i = 8, j = 1,
value = flextable::as_paragraph("F", flextable::as_sub("OFL"))) |>
flextable::compose(i = 9, j = 1,
value = flextable::as_paragraph(flextable::as_i("max"),"F", flextable::as_sub("ABC"))) |>
flextable::compose(i = 10, j = 1,
value = flextable::as_paragraph("F", flextable::as_sub("ABC"))) |>
flextable::compose(i = 12, j = 1,
value = flextable::as_paragraph(flextable::as_i("max"),"ABC (t)")) |>
flextable::compose(i = 14, j = 1,
value = flextable::as_paragraph("")) |>
flextable::compose(i = 14, j = 2:3,
value = flextable::as_paragraph( "As determined " , flextable::as_i("last"), " year for:")) |>
flextable::compose(i = 14, j = 4:5,
value = flextable::as_paragraph( "As determined " , flextable::as_i("this"), " year for:")) |>
flextable::compose(i = 15, j = 2,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year - 1)))) |>
flextable::compose(i = 15, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year)))) |>
flextable::compose(i = 15, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year + 1)))) |>
flextable::compose(i=16, j=c(2,4),
value = flextable::as_paragraph("No")) |>
flextable::compose(i=16, j=c(3,5),
value = flextable::as_paragraph("n/a")) |>
flextable::compose(i=17:18, j=c(3,5),
value = flextable::as_paragraph("No")) |>
flextable::compose(i=17:18, j=c(2,4),
value = flextable::as_paragraph("n/a")) |>
flextable::colformat_double(i = c(3:7, 11:13), j = 2:5,
big.mark=",", digits = 0, na_str = "N/A") |>
flextable::merge_h(i=14, part = "body") |>
flextable::bold(i = 15, j = 1) |>
flextable::bold(i = c(11,13), j = 4) |>
flextable::hline(i=13) |>
flextable::hline(i=15) |>
flextable::hline(i=18) |>
flextable::fix_border_issues()

} else if(tier==1){

if(nrow(tbl$body$dat)>17){
stop("this is not a tier 1 input, \nmaybe you have a tier 3 stock...")
}

tier = "1a"

tbl |>
flextable::footnote(i=2, j=4:5, part = "header", ref_symbols = "*",
value = flextable::as_paragraph(as_chunk(paste0("Projections are based on an estimated catch of ",
prettyNum(c1, big.mark = ","), " t for ", end_year,
" and estimates of ",
prettyNum(c2, big.mark = ","),
" t and ",
prettyNum(c3, big.mark = ","),
" t used in place of maximum permissible ABC for ",
end_year+1, " and ", end_year+2, "."))),
sep = ".") |>
flextable::compose(i = 2, j = 2:5, value = flextable::as_paragraph(tier), part = "body") |>
flextable::compose(i = 4, j = 1, value = flextable::as_paragraph("F", flextable::as_sub("OFL")), part = "body") |>
flextable::compose(i = 5, j = 1, value = flextable::as_paragraph(flextable::as_i("max"),"F", flextable::as_sub("ABC")), part = "body") |>
flextable::compose(i = 6, j = 1, value = flextable::as_paragraph("F", flextable::as_sub("ABC")), part = "body") |>
flextable::compose(i = 7, j = 1, value = flextable::as_paragraph(flextable::as_i("max"),"ABC (t)"), part = "body") |>
flextable::compose(i = 13, j = 1, value = flextable::as_paragraph("")) |>
flextable::compose(i = 13, j = 2:3,
value = flextable::as_paragraph( "As determined " , flextable::as_i("last"), " year for:")) |>
flextable::compose(i = 13, j = 4:5,
value = flextable::as_paragraph( "As determined " , flextable::as_i("this"), " year for:")) |>
flextable::compose(i = 14, j = 2,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year - 1)))) |>
flextable::compose(i = 14, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year)))) |>
flextable::compose(i = 14, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year + 1)))) |>
flextable::compose(i=15, j=c(2,4), value = flextable::as_paragraph("No")) |>
flextable::compose(i=15, j=c(3,5), value = flextable::as_paragraph("n/a")) |>
flextable::compose(i=16:17, j=c(3,5), value = flextable::as_paragraph("No")) |>
flextable::compose(i=16:17, j=c(2,4), value = flextable::as_paragraph("n/a")) |>
flextable::colformat_double(i = c(3:7, 10:12), j = 2:5, big.mark=",", digits = 0, na_str = "N/A") |>
flextable::merge_h(i=13, part = "body") |>
flextable::align(align = "center", part = "header") |>
flextable::align(j=2:5, align = "center", part = "body") |>
flextable::align(j = 1, part = "header", align="left") |>
flextable::bold(i = 2, j = 1, part = "header") |>
flextable::bold(i = 15, j = 1) |>
flextable::hline(i=12) |>
flextable::hline(i=14) |>
flextable::hline(i=17) |>
flextable::fix_border_issues()
} else if(tier == 5){

tier = "5"

tbl |>
flextable::compose(i = 2, j = 2:5, value = flextable::as_paragraph(tier), part = "body") |>
flextable::compose(i = 4, j = 1, value = flextable::as_paragraph("F", flextable::as_sub("OFL")), part = "body") |>
flextable::compose(i = 5, j = 1, value = flextable::as_paragraph(flextable::as_i("max"),"F", flextable::as_sub("ABC")), part = "body") |>
flextable::compose(i = 6, j = 1, value = flextable::as_paragraph("F", flextable::as_sub("ABC")), part = "body") |>
flextable::compose(i = 8, j = 1, value = flextable::as_paragraph(flextable::as_i("max"),"ABC (t)"), part = "body") |>
flextable::compose(i = 10, j = 1, value = flextable::as_paragraph("")) |>
flextable::compose(i = 10, j = 2:3,
value = flextable::as_paragraph( "As determined " , flextable::as_i("last"), " year for:")) |>
flextable::compose(i = 10, j = 4:5,
value = flextable::as_paragraph( "As determined " , flextable::as_i("this"), " year for:")) |>
flextable::compose(i = 11, j = 2,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year - 1)))) |>
flextable::compose(i = 11, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year)))) |>
flextable::compose(i = 11, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year + 1)))) |>
flextable::compose(i=12, j=c(2,4), value = flextable::as_paragraph("No")) |>
flextable::compose(i=12, j=c(3,5), value = flextable::as_paragraph("n/a")) |>
flextable::colformat_double(i = c(3,7:9), j = 2:5, big.mark=",", digits = 0, na_str = "N/A") |>
flextable::merge_h(i=10, part = "body") |>
flextable::align(align = "center", part = "header") |>
flextable::align(j=2:5, align = "center", part = "body") |>
flextable::align(j = 1, part = "header", align="left") |>
flextable::hline(i=9) |>
flextable::hline(i=11) |>
flextable::hline(i=12) |>
flextable::fix_border_issues()
} else {
tier = "6"

tbl |>
flextable::compose(i = 1, j = 2:5, value = flextable::as_paragraph(as.character(tier)), part = "body") |>
flextable::compose(i = 3, j = 1, value = flextable::as_paragraph(flextable::as_i("max"),"ABC (t)"), part = "body") |>
flextable::compose(i = 5, j = 1, value = flextable::as_paragraph("")) |>
flextable::compose(i = 5, j = 2:3,
value = flextable::as_paragraph( "As determined " , flextable::as_i("last"), " year for:")) |>
flextable::compose(i = 5, j = 4:5,
value = flextable::as_paragraph( "As determined " , flextable::as_i("this"), " year for:")) |>
flextable::compose(i = 6, j = 2,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year - 1)))) |>
flextable::compose(i = 6, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year)))) |>
flextable::compose(i = 6, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(end_year + 1)))) |>
flextable::compose(i=7, j=c(2,4), value = flextable::as_paragraph("No")) |>
flextable::compose(i=7, j=c(3,5), value = flextable::as_paragraph("n/a")) |>
flextable::colformat_double(i = c(2:4), j = 2:5, big.mark=",", digits = 0, na_str = "N/A") |>
flextable::merge_h(i=5, part = "body") |>
flextable::align(align = "center", part = "header") |>
flextable::align(j=2:5, align = "center", part = "body") |>
flextable::align(j = 1, part = "header", align="left") |>
flextable::hline(i=4) |>
flextable::hline(i=6) |>
flextable::hline(i=7) |>
flextable::fix_border_issues()
}
}
14 changes: 0 additions & 14 deletions R/comma.R
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