#' plotF
#' \code{plotF} plots vector of F_std from SS3 report file, with optional overlay of multiple models
#' @param SPRseries csv
#' @param saveplot logical. should plots be saved
#' @param plotloc folder to save plots; if NA, will save in location of cpue_results
#' @export
plotF <- function(SPRseries,
saveplot = T,
mods = NA,
plotloc = NA,
pdfrows = 4,
pdfcols = 2) {
# if(saveplot)jpeg( paste0(plotloc, "F_Trajectory.jpg"), width = 8, height = 5, unit = 'in', res = 1020)
if (is.na(plotloc)) {
if (!exists(paste0(getwd(), "/plots/"))) {
dir.create(paste0(getwd(), "/plots/"))
}
plotloc <- paste0(getwd(), "/plots/")
}
if (sum(is.na(mods)) == 0) {
SPRseries0 <-
SPRseries[SPRseries$MOD %in% mods, ]
} else{
SPRseries0 <- SPRseries
}
if(length(unique(SPRseries0$MOD)) <= 5){
SPRseries0 %>% ggplot(., aes(x = Year, y = F_std, col = MOD)) +
theme_bw() +
theme(
panel.grid = element_blank(),
panel.border = element_blank(),
axis.text = element_text(size = rel(1)),
axis.title = element_text(size = rel(1)),
legend.position = c(0.9, 0.80),
legend.background = element_rect(fill = NA, colour = NA),
legend.key = element_blank(),
legend.text = element_text(size = rel(1)),
legend.title = element_blank()
) +
scale_color_manual(values = rep(brewer.pal(9, name = 'Greys'), length(unique(SPRseries0$MOD)))) +
ylab("F_Std") +
xlab("Year") +
geom_line(lwd = 1.1)
} else if(length(unique(SPRseries0$MOD))> 5){
SPRseries0 %>% ggplot(., aes(x = Year, y = F_std, col = MOD)) +
theme_bw() +
theme(
panel.grid = element_blank(),
panel.border = element_blank(),
axis.text = element_text(size = rel(1)),
axis.title = element_text(size = rel(1)),
legend.position = 'none'
) +
scale_color_manual(values = rep(brewer.pal(9, name = 'Greys'), length(unique(SPRseries0$MOD)))) +
ylab("F_Std") +
xlab("Year") +
geom_line(lwd = 1.1)
}
if (saveplot == T) {
ggplot2::ggsave(
paste0(plotloc, "/F_Trajectory.jpeg"),
plot = last_plot(),
path = NULL,
scale = 1,
width = 7,
height = 5,
units = "in",
dpi = 1020,
limitsize = TRUE
)
ggplot2::ggsave(
paste0(plotloc, "/F_Trajectory.pdf"),
plot = last_plot(),
path = NULL,
scale = 1,
width = 7,
height = 5,
units = "in",
dpi = 1020,
limitsize = TRUE
)
}
cat('saved plot with model(s)',
mods,
" to ",
paste0(plotloc, "F_Trajectory.jpg"),
"\n")
cat("set plotloc or change working dir if needed", "\n")
}
# RootFile = "G:/MAKO/mako_sim/"
# SPRseries <-read.csv(paste0(RootFile,"/results/SPRseries.csv")) %>%
# plyr::rename(c('Yr' = 'Year', 'F.Z.M' = 'F_std'))
# plotF(
# SPRseries,
# saveplot = T,
# mods = NA,
# plotloc = paste0(RootFile,"/plots/"),
# pdfrows = 1,
# pdfcols = 1
# )
## not run
# SPRseries <- read.csv("G:\\MAKO\\mako_sim\\presentation\\results\\SPRseries.csv")
# plotF(
# SPRseries,
# saveplot = T,
# mods = NA,
# plotloc = NA,
# pdfrows = 4,
# pdfcols = 2
# )
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