1 | PlotIndex_Fn(PlotName = "Index.png", DirName, TmbData, Sdreport, Year_Set, strata.limits, ...)
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PlotName |
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DirName |
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TmbData |
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Sdreport |
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Year_Set |
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strata.limits |
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... |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (PlotName = "Index.png", DirName, TmbData, Sdreport,
Year_Set, strata.limits, ...)
{
png(file = paste0(DirName, "/", PlotName), width = 4, height = 4,
res = 200, units = "in")
par(mar = c(3, 3, 2, 0), mgp = c(2, 0.5, 0), tck = -0.02,
yaxs = "i", ...)
log_Index = array(summary(Sdreport)[which(rownames(summary(Sdreport)) ==
"ln_Index_tl"), ], dim = c(unlist(TmbData[c("n_t", "n_l")]),
2), dimnames = list(NULL, NULL, c("Estimate", "Std. Error")))
Index = array(summary(Sdreport)[which(rownames(summary(Sdreport)) ==
"Index_tl"), ], dim = c(unlist(TmbData[c("n_t", "n_l")]),
2), dimnames = list(NULL, NULL, c("Estimate", "Std. Error")))
plot(1, type = "n", xlim = range(Year_Set), ylim = 1.05 *
c(0, max(exp(log_Index[, , "Estimate"] + 1 * log_Index[,
, "Std. Error"]))), xlab = "Year", ylab = "Abundance")
for (l in 1:dim(Index)[2]) {
lines(y = Index[, l, "Estimate"], x = Year_Set + seq(-0.1,
0.1, length = dim(Index)[2])[l], type = "b", col = rainbow(TmbData[["n_l"]])[l])
for (t in 1:dim(Index)[1]) {
lines(x = rep(Year_Set[t], 2) + seq(-0.1, 0.1, length = dim(Index)[2])[l],
y = exp(log_Index[t, l, "Estimate"] + c(-1, 1) *
log_Index[t, l, "Std. Error"]), col = rainbow(TmbData[["n_l"]])[l])
}
}
Names = strata.limits[, "STRATA"]
Table = data.frame(Year = Year_Set, Unit = 1, Fleet = rep(Names,
each = dim(Index)[1]), Estimate = as.vector(Index[, ,
"Estimate"]), SD = as.vector(log_Index[, , "Std. Error"]))
write.csv(Table, file = paste0(DirName, "/Table_for_SS3.csv"),
row.names = FALSE)
dev.off()
Return = Table
return(Return)
}
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