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refactor: update names in BIOLOGY table #711

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Jul 14, 2022
Merged

refactor: update names in BIOLOGY table #711

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30 changes: 13 additions & 17 deletions R/SS_output.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2400,6 +2400,11 @@ SS_output <-
adjust1 = ifelse(custom, 2, 1),
header = TRUE, type.convert = TRUE
)
# updated BIOLOGY table names based on change July 2022 change
# https://github.com/nmfs-stock-synthesis/stock-synthesis/issues/348
biology <- df.rename(biology,
oldnames = c("Low", "Mean_Size", "Wt_len_F", "Mat_len", "Spawn", "Wt_len_M", "Fecundity"),
newnames = c("Len_lo", "Len_mean", "Wt_F", "Mat", "Mat*Fec", "Wt_M", "Fec"))

# determine fecundity type
FecType <- 0
Expand Down Expand Up @@ -2437,7 +2442,7 @@ SS_output <-
FecPar2name <- pl[FecGrep5[1]]
}
if (is.na(lbinspop[1])) {
lbinspop <- biology[["Low"]][biology[["GP"]] == 1]
lbinspop <- biology[["Len_lo"]][biology[["GP"]] == 1]
}

# warning for 3.30 models with multiple growth patterns that have
Expand All @@ -2456,29 +2461,20 @@ SS_output <-
# fix for extra header associated with extra column header
# for single sex models that got fixed in 3.30.16
if (nsexes == 1 &&
is.na(biology[["Fecundity"]][1]) &&
"Wt_len_M" %in% names(biology)) {
is.na(biology[["Fec"]][1]) &&
"Wt_M" %in% names(biology)) {
# copy Wt_len_M to Fecundity
biology[["Fecundity"]] <- biology[["Wt_len_M"]]
biology[["Fec"]] <- biology[["Wt_M"]]
# remove Wt_len_M
biology <- biology[, !names(biology) %in% "Wt_len_M"]
biology <- biology[, !names(biology) %in% "Wt_M"]
}

# test to figure out if fecundity is proportional to spawning biomass

# first get weight-at-length column (Wt_len_F for 2-sex models,
# Wt_len for 1-sex models starting with 3.30.16)
if ("Wt_len" %in% names(biology)) {
Wt_len_F <- biology[["Wt_len"]]
} else {
Wt_len_F <- biology[["Wt_len_F"]]
}

# check for any mismatch between weight-at-length and fecundity
returndat[["SpawnOutputUnits"]] <-
ifelse(!is.null(biology[["Fecundity"]][1]) &&
!is.na(biology[["Fecundity"]][1]) &&
any(Wt_len_F != biology[["Fecundity"]]),
ifelse(!is.null(biology[["Fec"]][1]) &&
!is.na(biology[["Fec"]][1]) &&
any(biology[["Wt_F"]] != biology[["Fec"]]),
"numbers", "biomass"
)
}
Expand Down
2 changes: 1 addition & 1 deletion R/SSbiologytables.R
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Expand Up @@ -64,7 +64,7 @@ SSbiologytables <- function(replist = NULL, printfolder = "tables", dir = "defau

# Table
# Age: Ave Len - Ave Wgt - % mature (by sex)
# "Mat*Fecund" is = biology[["Fecundity"]] %*% alk (mat = 1, fecundity = fecundity_l * ALK)
# "Mat*Fecund" is = biology[["Fec"]] %*% alk (mat = 1, fecundity = fecundity_l * ALK)
bio <- data.frame(
Age = biology[biology[["Sex"]] == 1, "Age_Beg"],
Ave_Length_f = print(biology[biology[["Sex"]] == 1, "Len_Beg"], digits = 1),
Expand Down
63 changes: 28 additions & 35 deletions R/SSplotBiology.R
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Original file line number Diff line number Diff line change
Expand Up @@ -298,19 +298,12 @@ SSplotBiology <-
## FecundAtAge <- ageselex[ageselex[["factor"]]=="Fecund", names(ageselex)%in%0:accuage]
## WtAtAge <- ageselex[ageselex[["factor"]]=="bodywt", names(ageselex)%in%0:accuage]

# column name for weight-at-length
# (Wt_len for 1-sex models starting with 3.30.16)
Wt_len_colname <- "Wt_len_F"
if ("Wt_len" %in% names(biology)) {
Wt_len_colname <- "Wt_len"
}

# determine fecundity type
# define labels and x-variable
if (FecType == 1) {
fec_ylab <- "Eggs per kg"
fec_xlab <- labels[8]
FecX <- biology[[Wt_len_colname]]
FecX <- biology[["Wt_F"]]
FecY <- FecPar1 + FecPar2 * FecX
}
if (labels[11] != "Default fecundity label") fec_ylab <- labels[11]
Expand Down Expand Up @@ -366,19 +359,19 @@ SSplotBiology <-
## This needs to be a function of sex since it can be called
## either once for a single sex model or twice to produce plots for
## each one.
x <- biology[["Mean_Size"]]
x <- biology[["Len_mean"]]
if (!wtatage_switch) { # if empirical weight-at-age is not used
if (!add) {
ymax <- max(biology[[Wt_len_colname]])
if (nsexes > 1) ymax <- max(ymax, biology[["Wt_len_M"]])
ymax <- max(biology[["Wt_F"]])
if (nsexes > 1) ymax <- max(ymax, biology[["Wt_M"]])
plot(x, x,
ylim = c(0, 1.1 * ymax), xlab = labels[1], ylab = labels[4], type = "n",
las = 1, yaxs = "i"
)
}
lines(x, biology[[Wt_len_colname]], type = "o", col = colvec[1])
lines(x, biology[["Wt_F"]], type = "o", col = colvec[1])
if (nsexes > 1) {
lines(x, biology[["Wt_len_M"]], type = "o", col = colvec[2])
lines(x, biology[["Wt_M"]], type = "o", col = colvec[2])
if (!add) {
legend(legendloc,
bty = "n", c("Females", "Males"),
Expand All @@ -403,16 +396,16 @@ SSplotBiology <-

maturity_plot <- function() { # maturity
if (!wtatage_switch) { # if empirical weight-at-age is not used
x <- biology[["Mean_Size"]]
if (min(biology[["Mat_len"]]) < 1) { # if length based
x <- biology[["Len_mean"]]
if (min(biology[["Mat"]]) < 1) { # if length based
if (!add) {
plot(x, biology[["Mat_len"]],
plot(x, biology[["Mat"]],
xlab = labels[1], ylab = labels[3],
las = 1, yaxs = "i", ylim = c(0, max(biology[["Mat_len"]])),
las = 1, yaxs = "i", ylim = c(0, max(biology[["Mat"]])),
type = "o", col = colvec[1]
)
}
if (add) lines(x, biology[["Mat_len"]], type = "o", col = colvec[1])
if (add) lines(x, biology[["Mat"]], type = "o", col = colvec[1])
} else { # else is age based
if (!add) {
plot(growdatF[["Age_Beg"]], growdatF[["Age_Mat"]],
Expand Down Expand Up @@ -535,32 +528,32 @@ SSplotBiology <-
points(FecX, FecY, col = colvec[2], pch = 19)
}
}
fecundityOK <- all(!is.na(biology[["Fecundity"]]))
fecundityOK <- all(!is.na(biology[["Fec"]]))
fec_weight_fn <- function() { # fecundity at weight from BIOLOGY section
ymax <- 1.1 * max(biology[["Fecundity"]])
ymax <- 1.1 * max(biology[["Fec"]])
if (!add) {
plot(biology[[Wt_len_colname]], biology[["Fecundity"]],
plot(biology[["Wt_F"]], biology[["Fec"]],
xlab = labels[8], ylab = labels[10],
las = 1, yaxs = "i", ylim = c(0, ymax), col = colvec[1], type = "o"
)
} else {
points(biology[["Mean_Size"]], biology[["Fecundity"]], col = colvec[1], type = "o")
points(biology[["Len_mean"]], biology[["Fec"]], col = colvec[1], type = "o")
}
}
fec_len_fn <- function() { # fecundity at length from BIOLOGY section
ymax <- 1.1 * max(biology[["Fecundity"]])
ymax <- 1.1 * max(biology[["Fec"]])
if (!add) {
plot(biology[["Mean_Size"]], biology[["Fecundity"]],
plot(biology[["Len_mean"]], biology[["Fec"]],
xlab = labels[9], ylab = labels[10],
las = 1, yaxs = "i", ylim = c(0, 1.1 * ymax), col = colvec[1], type = "o", yaxs = "i"
)
} else {
points(biology[["Mean_Size"]], biology[["Fecundity"]], col = colvec[1], type = "o")
points(biology[["Len_mean"]], biology[["Fec"]], col = colvec[1], type = "o")
}
}
spawn_output_len_fn <- function() { # spawning output at length
x <- biology[["Mean_Size"]]
y <- biology[["Spawn"]]
x <- biology[["Len_mean"]]
y <- biology[["Mat*Fec"]]
ymax <- 1.1 * max(y)
if (!add) {
plot(x, y,
Expand All @@ -585,7 +578,7 @@ SSplotBiology <-
}
}

ymax <- max(biology[["Mean_Size"]])
ymax <- max(biology[["Len_mean"]])
x <- growdatF[["Age_Beg"]]

main <- "Ending year expected growth (with 95% intervals)"
Expand Down Expand Up @@ -757,7 +750,7 @@ SSplotBiology <-
lab2 <- "Wt_Beg"
lab2long <- "Mean weight"
lab1max <- 1
lab2max <- max(c(biology[[Wt_len_colname]], biology[["Wt_len_M"]]), na.rm = TRUE)
lab2max <- max(c(biology[["Wt_F"]], biology[["Wt_M"]]), na.rm = TRUE)
lab1_axis_vec <- c(0, 0.5, 1)
}
# calculate scaling factor between CVs and SDs to share each panel
Expand Down Expand Up @@ -799,12 +792,12 @@ SSplotBiology <-
}
if (option == 2) {
# if plotting maturity and fecundity, then get this panel from length-based data
lines(biology[[Wt_len_colname]] * lab2_to_lab1_scale, biology[["Mean_Size"]],
lines(biology[["Wt_F"]] * lab2_to_lab1_scale, biology[["Len_mean"]],
col = colvec[col_index1], lwd = 3
)
lines(biology[["Mat_len"]], biology[["Mean_Size"]], col = colvec[col_index1], lty = "12")
lines(biology[["Mat"]], biology[["Len_mean"]], col = colvec[col_index1], lty = "12")
if (nsexes > 1) {
lines(biology[["Wt_len_M"]] * lab2_to_lab1_scale, biology[["Mean_Size"]],
lines(biology[["Wt_M"]] * lab2_to_lab1_scale, biology[["Len_mean"]],
col = colvec[2], lwd = 3, lty = 2
)
}
Expand Down Expand Up @@ -956,7 +949,7 @@ SSplotBiology <-
L_at_AmaxM <- Growth_Parameters[["L_a_A2"]][2]
LinfF <- Growth_Parameters[["Linf"]][1]
LinfM <- Growth_Parameters[["Linf"]][2]
ymax <- max(biology[["Mean_Size"]])
ymax <- max(biology[["Len_mean"]])
plot(0,
type = "n",
xlim = c(0, 1 + max(growdatF[["Age_Beg"]])),
Expand Down Expand Up @@ -1256,7 +1249,7 @@ SSplotBiology <-
}


x <- biology[["Mean_Size"]]
x <- biology[["Len_mean"]]
## NOTE: weight plots are now a special case since they are broken down
## by whether the model is 1-sex or 2-sex. In the latter two separate
## plots need to be made.
Expand Down Expand Up @@ -1320,7 +1313,7 @@ SSplotBiology <-
}
if (6 %in% subplots) {
file <- "bio6_maturity.png"
caption <- paste("Maturity at", ifelse(min(biology[["Mat_len"]]) < 1, "length", "age"))
caption <- paste("Maturity at", ifelse(min(biology[["Mat"]]) < 1, "length", "age"))
if (wtatage_switch) {
caption <- "Spawning output at age (maturity x fecundity)"
}
Expand Down