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#' Format a decision table | ||
#' | ||
#' Format a decision table for its inclusion in a document. | ||
#' | ||
#' @param ... Each element provided in the call to this function that is not | ||
#' assigned to a particular input argument should be a vector of file paths | ||
#' to the models you want to read for a given column of your decision table. | ||
#' For example, if a single column has results from three models and | ||
#' if your decision table has a low and high state of nature, then | ||
#' there should be two vectors passed via `...` and each vector would contain | ||
#' paths to three different models. | ||
#' The order of the vectors will be the column order from left to right. | ||
#' The order of the models within a vector will be the row order. | ||
#' @param years A vector of years you want catches for. | ||
#' @template format | ||
#' @param caption A character string that | ||
#' will be passed to the `caption` parameter of [kableExtra::kbl]. | ||
#' The default value is `NULL`. | ||
#' @param label A character string without underscores that | ||
#' will be passed to the `label` parameter of [kableExtra::kbl]. | ||
#' The default value is `NULL`. | ||
#' @param digits A vector of digits for catch, spawning output, and fraction, | ||
#' unfished. It gets passed to `r4ss::SS_decision_table_stuff()`. | ||
#' @export | ||
#' @author Kelli F. Johnson, Ian G. Taylor, Chantel R. Wetzel | ||
#' @examples | ||
#' table_decision( | ||
#' list(mod.low.A, mod.base.A, mod.high.A), | ||
#' list(mod.low.B, mod.base.B, mod.high.B), | ||
#' list(mod.low.C, mod.base.C, mod.high.C) | ||
#' ) | ||
table_decision <- function( | ||
..., | ||
years = 2023:2034, | ||
format = c("latex", "html"), | ||
caption = formals(kableExtra::kbl)$caption, | ||
label = formals(kableExtra::kbl)$label, | ||
digits = c(0, 2, 3)) { | ||
mods <- list(...) | ||
# make sure that the format input is good | ||
# chooses first option by default | ||
format <- match.arg(format) | ||
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# hardwired to prevent users from adding too-long inputs | ||
rowgroup <- c("A", "B", "C") | ||
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# process output | ||
results <- purrr::modify_depth( | ||
mods, | ||
.depth = 2, | ||
.f = r4ss::SS_decision_table_stuff, | ||
yrs = years, digits = digits | ||
) %>% | ||
purrr::modify_depth(1, dplyr::bind_cols) %>% | ||
dplyr::bind_rows(.id = "Mgmt") %>% | ||
dplyr::mutate( | ||
Mgmt = rowgroup[as.numeric(Mgmt)], | ||
# Catch = pmax(na.rm = TRUE, !!!rlang::syms(grep(value = TRUE, "catch", names(.)))) | ||
) %>% | ||
dplyr::rename(Year = "yr...1") %>% | ||
dplyr::select_if(!grepl("yr\\.+", colnames(.))) # %>% | ||
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# get the catch columns and warn if they aren't all equal | ||
# (simpler than trying to automatically italicize values associated | ||
# with mismatched catch which had issues for lingcod) | ||
catch_cols <- results %>% dplyr::select(dplyr::starts_with("catch")) | ||
if (max(abs(apply(catch_cols, 1, sd))) > 0.01) { | ||
warning("Catch differs among columns, perhaps due to a crashed model without enough biomass.") | ||
} | ||
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# clean up column names and remove extra catch columns | ||
# first rename the first catch column | ||
results <- results %>% | ||
dplyr::rename(Catch = "catch...2") %>% | ||
dplyr::select(-dplyr::starts_with("catch", ignore.case = FALSE)) | ||
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# remove repeated lables in Mgmt column | ||
results <- results %>% | ||
dplyr::mutate(Mgmt = ifelse(duplicated(Mgmt), "", Mgmt)) | ||
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# # add horizontal lines between groups (only works in latex) | ||
# # only works if Mgmt column has single value at the top of each group | ||
# results <- results %>% | ||
# kableExtra::row_spec(row = which(results$Mgmt != "")[-1] - 1, | ||
# hline_after = TRUE) | ||
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# add color to the depletion column | ||
results <- results %>% | ||
dplyr::mutate_at( | ||
.vars = dplyr::vars(grep(value = TRUE, "^dep", colnames(.))), | ||
~ kableExtra::cell_spec( | ||
format = format, | ||
x = ., | ||
color = "white", | ||
background = kableExtra::spec_color( | ||
., | ||
begin = 0, end = 1, | ||
option = "D", | ||
scale_from = c(0, 1), | ||
direction = -1 | ||
) | ||
) | ||
) | ||
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# add column names | ||
rownames(results) <- NULL | ||
colnames(results) <- c( | ||
"Mgmt", "Year", "Catch", "Low Spawn", "Low Frac", | ||
"Base Spawn", "Base Frac", "High Spawn", "High Frac" | ||
) | ||
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results %>% | ||
kableExtra::kbl( | ||
format = format, | ||
escape = FALSE, | ||
booktabs = TRUE, | ||
linesep = rep(c(rep("", length(years) - 1), "\\addlinespace"), 2), | ||
align = c("l", "l", "r", rep(c("r", "r"), 3)), | ||
caption = caption, | ||
label = label | ||
) %>% | ||
kableExtra::column_spec(c(1), bold = TRUE) %>% # first column bold | ||
# kableExtra::column_spec(c(1, 3, 3+2*3, border_right = TRUE) %>% # vertical lines (not really needed) | ||
kableExtra::column_spec(3, | ||
color = "white", # white text | ||
background = kableExtra::spec_color(results[["Catch"]], # background coloring for catch columns | ||
begin = 0.3, | ||
end = 0.7, | ||
option = "E", | ||
direction = -1 | ||
) | ||
) %>% | ||
kableExtra::column_spec(4:NCOL(results), width = "3.5em") %>% | ||
kableExtra::kable_classic(full_width = FALSE) | ||
} |
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if (FALSE) { | ||
SSexecutivesummary(mod.34.10, forecast_ofl = c(3763, 3563)) | ||
save_loc <- file.path(mod.34.10$inputs$dir, "tex_tables") | ||
dir.create(save_loc) | ||
sa4ss::es_table_tex( | ||
dir = mod.34.10$inputs$dir, | ||
save_loc = save_loc | ||
) | ||
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sa4ss::es_table_tex( | ||
# dir = mod.34.10$inputs$dir, | ||
dir = "models/2023.a034.010_fixed_forecast_catch/tables/", | ||
csv_name = "table_label_projection_modified.csv", | ||
digits = 0, | ||
save_loc = save_loc | ||
) | ||
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# Row-group names for first column; kableExtra::linebreak allows for hard returns | ||
rowgroupnames <- kableExtra::linebreak( | ||
x = c( | ||
# "Recent\n avg.\n catch", | ||
# "ACL\n$P^*$=0.40", | ||
"ACL $P^*$=0.45" | ||
), | ||
align = "l" | ||
) | ||
} # end if (FALSE) to help with sourcing the commands below | ||
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### make decision table | ||
#devtools::load_all(); | ||
caption <- "Decision table with 10-year projections. 'Mgmt' refers to the three management scenarios (A) the default harvest control rule $P^* = 0.45$, (B) [TODO: fill in something here], and (C) [TODO: fill in something here]. In each case the 2023 and 2024 catches are fixed at the ACLs which have been set for that year with estimated fleet allocation provided by the GMT. The alternative states of nature ('Low', 'Base', and 'High') are provided in the columns, with Spawning Output ('Spawn', in trillions of eggs) and Fraction of unfished ('Frac') provided for each state. The colors of catch and fraction unfished are relative with lighter colors representing lower values." | ||
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tab <- table_decision( | ||
caption = caption, | ||
label = "es-decision", | ||
list(mod.34.10, mod.34.10, mod.34.10), | ||
list(mod.34.10, mod.34.10, mod.34.10), | ||
list(mod.34.10, mod.34.10, mod.34.10) | ||
) | ||
writeLines(tab, "documents/tex_tables/decision_table.tex") | ||
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# kableExtra::save_kable(file = "documents/tex_tables/decision_table.tex") | ||
|
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\begin{table} | ||
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\caption{\label{tab:es-decision}Decision table with 10-year projections. 'Mgmt' refers to the three management scenarios (A) the default harvest control rule $P^* = 0.45$, (B) [TODO: fill in something here], and (C) [TODO: fill in something here]. In each case the 2023 and 2024 catches are fixed at the ACLs which have been set for that year with estimated fleet allocation provided by the GMT. The alternative states of nature ('Low', 'Base', and 'High') are provided in the columns, with Spawning Output ('Spawn', in trillions of eggs) and Fraction of unfished ('Frac') provided for each state. The colors of catch and fraction unfished are relative with lighter colors representing lower values.} | ||
\centering | ||
\begin{tabular}[t]{>{}ll>{}r>{\raggedleft\arraybackslash}p{3.5em}>{\raggedleft\arraybackslash}p{3.5em}>{\raggedleft\arraybackslash}p{3.5em}>{\raggedleft\arraybackslash}p{3.5em}>{\raggedleft\arraybackslash}p{3.5em}>{\raggedleft\arraybackslash}p{3.5em}} | ||
\toprule | ||
Mgmt & Year & Catch & Low Spawn & Low Frac & Base Spawn & Base Frac & High Spawn & High Frac\\ | ||
\midrule | ||
\textbf{A} & 2023 & \cellcolor[HTML]{4E576C}{\textcolor{white}{3485}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}}\\ | ||
\textbf{} & 2024 & \cellcolor[HTML]{5D616E}{\textcolor{white}{3285}} & 6.70 & \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}} & 6.70 & \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}} & 6.70 & \vphantom{2} \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}}\\ | ||
\textbf{} & 2025 & \cellcolor[HTML]{A89E75}{\textcolor{white}{2277}} & 5.85 & \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}} & 5.85 & \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}} & 5.85 & \vphantom{2} \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}}\\ | ||
\textbf{} & 2026 & \cellcolor[HTML]{AFA473}{\textcolor{white}{2196}} & 5.59 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.59 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.59 & \vphantom{2} \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}}\\ | ||
\textbf{} & 2027 & \cellcolor[HTML]{B0A473}{\textcolor{white}{2186}} & 5.52 & \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}} & 5.52 & \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}} & 5.52 & \vphantom{2} \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}}\\ | ||
\textbf{} & 2028 & \cellcolor[HTML]{ACA174}{\textcolor{white}{2229}} & 5.58 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.58 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.58 & \vphantom{2} \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}}\\ | ||
\textbf{} & 2029 & \cellcolor[HTML]{A79D75}{\textcolor{white}{2288}} & 5.72 & \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}} & 5.72 & \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}} & 5.72 & \vphantom{2} \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}}\\ | ||
\textbf{} & 2030 & \cellcolor[HTML]{A29A76}{\textcolor{white}{2342}} & 5.88 & \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}} & 5.88 & \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}} & 5.88 & \vphantom{2} \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}}\\ | ||
\textbf{} & 2031 & \cellcolor[HTML]{9F9777}{\textcolor{white}{2385}} & 6.03 & \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}} & 6.03 & \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}} & 6.03 & \vphantom{2} \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}}\\ | ||
\textbf{} & 2032 & \cellcolor[HTML]{9C9677}{\textcolor{white}{2417}} & 6.17 & \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}} & 6.17 & \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}} & 6.17 & \vphantom{2} \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}}\\ | ||
\textbf{} & 2033 & \cellcolor[HTML]{9A9377}{\textcolor{white}{2444}} & 6.28 & \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}} & 6.28 & \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}} & 6.28 & \vphantom{2} \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}}\\ | ||
\textbf{} & 2034 & \cellcolor[HTML]{999278}{\textcolor{white}{2462}} & 6.38 & \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}} & 6.38 & \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}} & 6.38 & \vphantom{2} \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}}\\ | ||
\addlinespace | ||
\textbf{B} & 2023 & \cellcolor[HTML]{4E576C}{\textcolor{white}{3485}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}}\\ | ||
\textbf{} & 2024 & \cellcolor[HTML]{5D616E}{\textcolor{white}{3285}} & 6.70 & \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}} & 6.70 & \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}} & 6.70 & \vphantom{1} \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}}\\ | ||
\textbf{} & 2025 & \cellcolor[HTML]{A89E75}{\textcolor{white}{2277}} & 5.85 & \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}} & 5.85 & \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}} & 5.85 & \vphantom{1} \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}}\\ | ||
\textbf{} & 2026 & \cellcolor[HTML]{AFA473}{\textcolor{white}{2196}} & 5.59 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.59 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.59 & \vphantom{1} \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}}\\ | ||
\textbf{} & 2027 & \cellcolor[HTML]{B0A473}{\textcolor{white}{2186}} & 5.52 & \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}} & 5.52 & \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}} & 5.52 & \vphantom{1} \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}}\\ | ||
\textbf{} & 2028 & \cellcolor[HTML]{ACA174}{\textcolor{white}{2229}} & 5.58 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.58 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.58 & \vphantom{1} \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}}\\ | ||
\textbf{} & 2029 & \cellcolor[HTML]{A79D75}{\textcolor{white}{2288}} & 5.72 & \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}} & 5.72 & \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}} & 5.72 & \vphantom{1} \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}}\\ | ||
\textbf{} & 2030 & \cellcolor[HTML]{A29A76}{\textcolor{white}{2342}} & 5.88 & \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}} & 5.88 & \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}} & 5.88 & \vphantom{1} \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}}\\ | ||
\textbf{} & 2031 & \cellcolor[HTML]{9F9777}{\textcolor{white}{2385}} & 6.03 & \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}} & 6.03 & \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}} & 6.03 & \vphantom{1} \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}}\\ | ||
\textbf{} & 2032 & \cellcolor[HTML]{9C9677}{\textcolor{white}{2417}} & 6.17 & \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}} & 6.17 & \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}} & 6.17 & \vphantom{1} \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}}\\ | ||
\textbf{} & 2033 & \cellcolor[HTML]{9A9377}{\textcolor{white}{2444}} & 6.28 & \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}} & 6.28 & \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}} & 6.28 & \vphantom{1} \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}}\\ | ||
\textbf{} & 2034 & \cellcolor[HTML]{999278}{\textcolor{white}{2462}} & 6.38 & \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}} & 6.38 & \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}} & 6.38 & \vphantom{1} \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}}\\ | ||
\addlinespace | ||
\textbf{C} & 2023 & \cellcolor[HTML]{4E576C}{\textcolor{white}{3485}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}} & 7.69 & \cellcolor[HTML]{34B679}{\textcolor{white}{0.336}}\\ | ||
\textbf{} & 2024 & \cellcolor[HTML]{5D616E}{\textcolor{white}{3285}} & 6.70 & \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}} & 6.70 & \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}} & 6.70 & \cellcolor[HTML]{48C16E}{\textcolor{white}{0.292}}\\ | ||
\textbf{} & 2025 & \cellcolor[HTML]{A89E75}{\textcolor{white}{2277}} & 5.85 & \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}} & 5.85 & \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}} & 5.85 & \cellcolor[HTML]{5AC864}{\textcolor{white}{0.255}}\\ | ||
\textbf{} & 2026 & \cellcolor[HTML]{AFA473}{\textcolor{white}{2196}} & 5.59 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.59 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.59 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}}\\ | ||
\textbf{} & 2027 & \cellcolor[HTML]{B0A473}{\textcolor{white}{2186}} & 5.52 & \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}} & 5.52 & \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}} & 5.52 & \cellcolor[HTML]{63CB5F}{\textcolor{white}{0.241}}\\ | ||
\textbf{} & 2028 & \cellcolor[HTML]{ACA174}{\textcolor{white}{2229}} & 5.58 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.58 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}} & 5.58 & \cellcolor[HTML]{60CA60}{\textcolor{white}{0.244}}\\ | ||
\textbf{} & 2029 & \cellcolor[HTML]{A79D75}{\textcolor{white}{2288}} & 5.72 & \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}} & 5.72 & \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}} & 5.72 & \cellcolor[HTML]{5CC863}{\textcolor{white}{0.25}}\\ | ||
\textbf{} & 2030 & \cellcolor[HTML]{A29A76}{\textcolor{white}{2342}} & 5.88 & \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}} & 5.88 & \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}} & 5.88 & \cellcolor[HTML]{58C765}{\textcolor{white}{0.257}}\\ | ||
\textbf{} & 2031 & \cellcolor[HTML]{9F9777}{\textcolor{white}{2385}} & 6.03 & \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}} & 6.03 & \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}} & 6.03 & \cellcolor[HTML]{56C667}{\textcolor{white}{0.263}}\\ | ||
\textbf{} & 2032 & \cellcolor[HTML]{9C9677}{\textcolor{white}{2417}} & 6.17 & \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}} & 6.17 & \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}} & 6.17 & \cellcolor[HTML]{52C569}{\textcolor{white}{0.269}}\\ | ||
\textbf{} & 2033 & \cellcolor[HTML]{9A9377}{\textcolor{white}{2444}} & 6.28 & \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}} & 6.28 & \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}} & 6.28 & \cellcolor[HTML]{50C46A}{\textcolor{white}{0.274}}\\ | ||
\textbf{} & 2034 & \cellcolor[HTML]{999278}{\textcolor{white}{2462}} & 6.38 & \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}} & 6.38 & \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}} & 6.38 & \cellcolor[HTML]{4EC36B}{\textcolor{white}{0.279}}\\ | ||
\bottomrule | ||
\end{tabular} | ||
\end{table} |