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main_table.r
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#' create the main safe table adapted from Ben Williams SAFE library (https://github.com/BenWilliams-NOAA/safe)
#' For now only the tier 3 has been changed to accomodate the pull from pdf data
#' @param data a specific dataframe holding results
#' @param year what is the current year
#' @param tier what tier
#' @param c1 estimated catch current year
#' @param c2 proj catch year + 1
#' @param c3 proj catch year + 2
#'
#' @export main_table
#'
main_table <- function(data, year, tier, c1, c2, c3){
flextable::flextable(data) %>%
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(year)), part = "header") %>%
flextable::compose(i = 2, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(year + 1))),
part = "header") %>%
flextable::compose(i = 2, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(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){
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 ", year,
" and estimates of ",
prettyNum(c2, big.mark = ","),
" t and ",
prettyNum(c3, big.mark = ","),
" t used in place of maximum permissible ABC for ",
year+1, " and ", year+2, "."))),
sep = "."),
fontname = "Times New Roman",
part = "all") %>%
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(year - 2)))) %>%
flextable::compose(i = 15, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(year-1)))) %>%
flextable::compose(i = 15, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(year)))) %>%
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$body$data)>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 ", year,
" and estimates of ",
prettyNum(c2, big.mark = ","),
" t and ",
prettyNum(c3, big.mark = ","),
" t used in place of maximum permissible ABC for ",
year+1, " and ", 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(year - 1)))) %>%
flextable::compose(i = 14, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(year)))) %>%
flextable::compose(i = 14, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(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(year - 1)))) %>%
flextable::compose(i = 11, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(year)))) %>%
flextable::compose(i = 11, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(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(year - 1)))) %>%
flextable::compose(i = 6, j = 3:4,
value = flextable::as_paragraph(flextable::as_chunk(as.character(year)))) %>%
flextable::compose(i = 6, j = 5,
value = flextable::as_paragraph(flextable::as_chunk(as.character(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()
}
}