Rfolder/plots/age_hists.R
In jBernardADFG/ChenaSalchaSR: Chena Salcha State-Space Spawner-Recruit Analysis
#' Escapement by Age Histogram
#' @param samples (data.frame) output of clean_chains
#' @param file_path (character) file path to store output jpeg file.
#' @param width (numeric) width of the output plot (in px).
#' @param height (numeric) height of the output plot (in px).
#' @export
age_hist <- function(samples, file_path, width=500, height=1000, final_year=2025){
#
file_path=paste("Plots/age_hists/", model_specs$run_name, ".jpeg", sep="")
final_year=2025
width=500
height=1000
#
eb_samples_c <- samples[,substr(names(samples), 1, 7)=="N_1_dot" & substr(names(samples), nchar(names(samples))-1, nchar(names(samples)))=="1]"]
eb_c <- apply(eb_samples_c, MARGIN=2, quantile, probs = c(0.25, 0.75))
eb_lo_c <- as.numeric(eb_c[1,])
eb_hi_c <- as.numeric(eb_c[2,])
eb_c <- data.frame(lo = eb_lo_c, hi=eb_hi_c)
eb_samples_s <- samples[,substr(names(samples), 1, 7)=="N_1_dot" & substr(names(samples), nchar(names(samples))-1, nchar(names(samples)))=="2]"]
eb_s <- apply(eb_samples_s, MARGIN=2, quantile, probs = c(0.25, 0.75))
eb_lo_s <- as.numeric(eb_s[1,])
eb_hi_s <- as.numeric(eb_s[2,])
# file_path=paste("Plots/age_hists/", model_specs$run_name, ".jpeg", sep="")
# final_year=2030
# width=500
# height=1000
# final_year=2020
aba_samples <- samples[,substr(names(samples), 1, 3)=="N_1" &
substr(names(samples), 4, 4)!="_"]
quants <- apply(aba_samples, MARGIN=2, quantile, probs = c(0.5))
tot_years <- length(1994:2030)
n_years <- length(1994:final_year)
med_array <- array(NA, dim=c(tot_years, 2, 6))
l <- 1
for (k in 1:6){
for (j in 1:2){
for (i in 1:tot_years){
med_array[i,j,k] <- quants[l]
l <- l + 1
}
}
}
med_array <- med_array[1:n_years,,]
chena_tab <- salcha_tab <- data.frame(
year=1994:final_year,
Age_3=rep(NA, n_years),
Age_4=rep(NA, n_years),
Age_5=rep(NA, n_years),
Age_6=rep(NA, n_years),
Age_7=rep(NA, n_years),
Age_8=rep(NA, n_years)
)
for (i in 1:n_years){
for (k in 1:6){
chena_tab[i, k+1] <- med_array[i, 1, k]
salcha_tab[i, k+1] <- med_array[i, 2, k]
}
}
chena_n <- data.frame(year=rep(1994:final_year, rep(6, length(1994:final_year))),
Age=rep(1:6, length(1994:final_year)),
run=rep(NA, 6*length(1994:final_year)))
salcha_n <- data.frame(year=rep(1994:final_year, rep(6, length(1994:final_year))),
Age=rep(1:6, length(1994:final_year)),
run=rep(NA, 6*length(1994:final_year)))
k <- 1
for(i in 1:nrow(chena_tab)){
for(j in 2:ncol(chena_tab)){
chena_n[k,3] <- chena_tab[i,j]
salcha_n[k,3] <- salcha_tab[i,j]
k<- k+1
}
}
aam_samples <- samples[,substr(names(samples), 1, 1) == "p" &
substr(names(samples), 2, 2) != "h"]
quants <- apply(aam_samples, MARGIN=2, quantile, probs = c(0.5))
tot_years <- length(1986:2030)
med_array <- array(NA, dim=c(tot_years, 2, 6))
l <- 1
for (k in 1:6){
for (j in 1:2){
if (j == 1){
tot_years <- 45
}
else{
tot_years <- 43
}
for (i in 1:tot_years){
med_array[i,j,k] <- quants[l]
l <- l + 1
}
}
}
med_array <- med_array[9:length(1986:final_year),,]
chena_tab <- salcha_tab <- data.frame(
year=1994:final_year,
Age_3=rep(NA, n_years),
Age_4=rep(NA, n_years),
Age_5=rep(NA, n_years),
Age_6=rep(NA, n_years),
Age_7=rep(NA, n_years),
Age_8=rep(NA, n_years)
)
for (i in 1:n_years){
for (k in 1:6){
chena_tab[i, k+1] <- med_array[i, 1, k]
salcha_tab[i, k+1] <- med_array[i, 2, k]
}
}
chena_tab
salcha_tab
chena_norm <- apply(chena_tab[,2:ncol(chena_tab)], MARGIN=1, sum)
salcha_norm <- apply(salcha_tab[,2:ncol(salcha_tab)], MARGIN=1, sum)
for(i in 1:nrow(chena_tab)){
for(j in 2:ncol(chena_tab)){
chena_tab[i,j] <- chena_tab[i,j]/chena_norm[i]
salcha_tab[i,j] <- salcha_tab[i,j]/salcha_norm[i]
}
}
chena_p <- data.frame(year=rep(1994:final_year, rep(6, n_years)),
Age=rep(1:6, n_years),
run=rep(NA, 6*n_years))
salcha_p <- data.frame(year=rep(1994:final_year, rep(6, n_years)),
Age=rep(1:6, n_years),
run=rep(NA, 6*n_years))
k <- 1
for(i in 1:nrow(chena_tab)){
for(j in 2:ncol(chena_tab)){
chena_p[k,3] <- chena_tab[i,j]
salcha_p[k,3] <- salcha_tab[i,j]
k<- k+1
}
}
chena_n$Age <- chena_n$Age + 2
salcha_n$Age <- salcha_n$Age + 2
chena_p$Age <- chena_p$Age + 2
salcha_p$Age <- salcha_p$Age + 2
jpeg(filename = file_path, width=width, height=height, unit="px")
library(ggplot2)
p1 <- ggplot2::ggplot(chena_n, aes(x=year, y=run, fill=Age))+
geom_col()+
theme_classic()+
ggtitle("Chena River -- Total Run by Age") + ylab("Number of Chinook") +
theme(
plot.title = element_text(size=16, face="bold", hjust=0.5),
axis.title.x = element_blank(),
axis.title.y = element_text(size=14),
axis.text.x = element_text(angle=90, vjust=0.5,hjust=1),
legend.position = "none"
) +
scale_x_continuous(breaks=1994:final_year)+
geom_segment(ggplot2::aes(x=1994, y=eb_lo_c[1], yend=eb_hi_c[1], xend=1994), color="red") +
geom_segment(ggplot2::aes(x=1995, y=eb_lo_c[2], yend=eb_hi_c[2], xend=1995), color="red") +
geom_segment(ggplot2::aes(x=1996, y=eb_lo_c[3], yend=eb_hi_c[3], xend=1996), color="red") +
geom_segment(ggplot2::aes(x=1997, y=eb_lo_c[4], yend=eb_hi_c[4], xend=1997), color="red") +
geom_segment(ggplot2::aes(x=1998, y=eb_lo_c[5], yend=eb_hi_c[5], xend=1998), color="red") +
geom_segment(ggplot2::aes(x=1999, y=eb_lo_c[6], yend=eb_hi_c[6], xend=1999), color="red") +
geom_segment(ggplot2::aes(x=2000, y=eb_lo_c[7], yend=eb_hi_c[7], xend=2000), color="red") +
geom_segment(ggplot2::aes(x=2001, y=eb_lo_c[8], yend=eb_hi_c[8], xend=2001), color="red") +
geom_segment(ggplot2::aes(x=2002, y=eb_lo_c[9], yend=eb_hi_c[9], xend=2002), color="red") +
geom_segment(ggplot2::aes(x=2003, y=eb_lo_c[10], yend=eb_hi_c[10], xend=2003), color="red") +
geom_segment(ggplot2::aes(x=2004, y=eb_lo_c[11], yend=eb_hi_c[11], xend=2004), color="red") +
geom_segment(ggplot2::aes(x=2005, y=eb_lo_c[12], yend=eb_hi_c[12], xend=2005), color="red") +
geom_segment(ggplot2::aes(x=2006, y=eb_lo_c[13], yend=eb_hi_c[13], xend=2006), color="red") +
geom_segment(ggplot2::aes(x=2007, y=eb_lo_c[14], yend=eb_hi_c[14], xend=2007), color="red") +
geom_segment(ggplot2::aes(x=2008, y=eb_lo_c[15], yend=eb_hi_c[15], xend=2008), color="red") +
geom_segment(ggplot2::aes(x=2009, y=eb_lo_c[16], yend=eb_hi_c[16], xend=2009), color="red") +
geom_segment(ggplot2::aes(x=2010, y=eb_lo_c[17], yend=eb_hi_c[17], xend=2010), color="red") +
geom_segment(ggplot2::aes(x=2011, y=eb_lo_c[18], yend=eb_hi_c[18], xend=2011), color="red") +
geom_segment(ggplot2::aes(x=2012, y=eb_lo_c[19], yend=eb_hi_c[19], xend=2012), color="red") +
geom_segment(ggplot2::aes(x=2013, y=eb_lo_c[20], yend=eb_hi_c[20], xend=2013), color="red") +
geom_segment(ggplot2::aes(x=2014, y=eb_lo_c[21], yend=eb_hi_c[21], xend=2014), color="red") +
geom_segment(ggplot2::aes(x=2015, y=eb_lo_c[22], yend=eb_hi_c[22], xend=2015), color="red") +
geom_segment(ggplot2::aes(x=2016, y=eb_lo_c[23], yend=eb_hi_c[23], xend=2016), color="red") +
geom_segment(ggplot2::aes(x=2017, y=eb_lo_c[24], yend=eb_hi_c[24], xend=2017), color="red") +
geom_segment(ggplot2::aes(x=2018, y=eb_lo_c[25], yend=eb_hi_c[25], xend=2018), color="red") +
geom_segment(ggplot2::aes(x=2019, y=eb_lo_c[26], yend=eb_hi_c[26], xend=2019), color="red") +
geom_segment(ggplot2::aes(x=2020, y=eb_lo_c[27], yend=eb_hi_c[27], xend=2020), color="red") +
geom_segment(ggplot2::aes(x=2021, y=eb_lo_c[28], yend=eb_hi_c[28], xend=2021), color="red") +
geom_segment(ggplot2::aes(x=2022, y=eb_lo_c[29], yend=eb_hi_c[29], xend=2022), color="red") +
geom_segment(ggplot2::aes(x=2023, y=eb_lo_c[30], yend=eb_hi_c[30], xend=2023), color="red") +
geom_segment(ggplot2::aes(x=2024, y=eb_lo_c[31], yend=eb_hi_c[31], xend=2024), color="red") +
geom_segment(ggplot2::aes(x=2025, y=eb_lo_c[32], yend=eb_hi_c[32], xend=2025), color="red") +
geom_segment(ggplot2::aes(x=1993.75, y=eb_lo_c[1], yend=eb_lo_c[1], xend=1994.25), color="red") +
geom_segment(ggplot2::aes(x=1994.75, y=eb_lo_c[2], yend=eb_lo_c[2], xend=1995.25), color="red") +
geom_segment(ggplot2::aes(x=1995.75, y=eb_lo_c[3], yend=eb_lo_c[3], xend=1996.25), color="red") +
geom_segment(ggplot2::aes(x=1996.75, y=eb_lo_c[4], yend=eb_lo_c[4], xend=1997.25), color="red") +
geom_segment(ggplot2::aes(x=1997.75, y=eb_lo_c[5], yend=eb_lo_c[5], xend=1998.25), color="red") +
geom_segment(ggplot2::aes(x=1998.75, y=eb_lo_c[6], yend=eb_lo_c[6], xend=1999.25), color="red") +
geom_segment(ggplot2::aes(x=1999.75, y=eb_lo_c[7], yend=eb_lo_c[7], xend=2000.25), color="red") +
geom_segment(ggplot2::aes(x=2000.75, y=eb_lo_c[8], yend=eb_lo_c[8], xend=2001.25), color="red") +
geom_segment(ggplot2::aes(x=2001.75, y=eb_lo_c[9], yend=eb_lo_c[9], xend=2002.25), color="red") +
geom_segment(ggplot2::aes(x=2002.75, y=eb_lo_c[10], yend=eb_lo_c[10], xend=2003.25), color="red") +
geom_segment(ggplot2::aes(x=2003.75, y=eb_lo_c[11], yend=eb_lo_c[11], xend=2004.25), color="red") +
geom_segment(ggplot2::aes(x=2004.75, y=eb_lo_c[12], yend=eb_lo_c[12], xend=2005.25), color="red") +
geom_segment(ggplot2::aes(x=2005.75, y=eb_lo_c[13], yend=eb_lo_c[13], xend=2006.25), color="red") +
geom_segment(ggplot2::aes(x=2006.75, y=eb_lo_c[14], yend=eb_lo_c[14], xend=2007.25), color="red") +
geom_segment(ggplot2::aes(x=2007.75, y=eb_lo_c[15], yend=eb_lo_c[15], xend=2008.25), color="red") +
geom_segment(ggplot2::aes(x=2008.75, y=eb_lo_c[16], yend=eb_lo_c[16], xend=2009.25), color="red") +
geom_segment(ggplot2::aes(x=2009.75, y=eb_lo_c[17], yend=eb_lo_c[17], xend=2010.25), color="red") +
geom_segment(ggplot2::aes(x=2010.75, y=eb_lo_c[18], yend=eb_lo_c[18], xend=2011.25), color="red") +
geom_segment(ggplot2::aes(x=2011.75, y=eb_lo_c[19], yend=eb_lo_c[19], xend=2012.25), color="red") +
geom_segment(ggplot2::aes(x=2012.75, y=eb_lo_c[20], yend=eb_lo_c[20], xend=2013.25), color="red") +
geom_segment(ggplot2::aes(x=2013.75, y=eb_lo_c[21], yend=eb_lo_c[21], xend=2014.25), color="red") +
geom_segment(ggplot2::aes(x=2014.75, y=eb_lo_c[22], yend=eb_lo_c[22], xend=2015.25), color="red") +
geom_segment(ggplot2::aes(x=2015.75, y=eb_lo_c[23], yend=eb_lo_c[23], xend=2016.25), color="red") +
geom_segment(ggplot2::aes(x=2016.75, y=eb_lo_c[24], yend=eb_lo_c[24], xend=2017.25), color="red") +
geom_segment(ggplot2::aes(x=2017.75, y=eb_lo_c[25], yend=eb_lo_c[25], xend=2018.25), color="red") +
geom_segment(ggplot2::aes(x=2018.75, y=eb_lo_c[26], yend=eb_lo_c[26], xend=2019.25), color="red") +
geom_segment(ggplot2::aes(x=2019.75, y=eb_lo_c[27], yend=eb_lo_c[27], xend=2020.25), color="red") +
geom_segment(ggplot2::aes(x=2020.75, y=eb_lo_c[28], yend=eb_lo_c[28], xend=2021.25), color="red") +
geom_segment(ggplot2::aes(x=2021.75, y=eb_lo_c[29], yend=eb_lo_c[29], xend=2022.25), color="red") +
geom_segment(ggplot2::aes(x=2022.75, y=eb_lo_c[30], yend=eb_lo_c[30], xend=2023.25), color="red") +
geom_segment(ggplot2::aes(x=2023.75, y=eb_lo_c[31], yend=eb_lo_c[31], xend=2024.25), color="red") +
geom_segment(ggplot2::aes(x=2024.75, y=eb_lo_c[32], yend=eb_lo_c[32], xend=2025.25), color="red") +
geom_segment(ggplot2::aes(x=1993.75, y=eb_hi_c[1], yend=eb_hi_c[1], xend=1994.25), color="red") +
geom_segment(ggplot2::aes(x=1994.75, y=eb_hi_c[2], yend=eb_hi_c[2], xend=1995.25), color="red") +
geom_segment(ggplot2::aes(x=1995.75, y=eb_hi_c[3], yend=eb_hi_c[3], xend=1996.25), color="red") +
geom_segment(ggplot2::aes(x=1996.75, y=eb_hi_c[4], yend=eb_hi_c[4], xend=1997.25), color="red") +
geom_segment(ggplot2::aes(x=1997.75, y=eb_hi_c[5], yend=eb_hi_c[5], xend=1998.25), color="red") +
geom_segment(ggplot2::aes(x=1998.75, y=eb_hi_c[6], yend=eb_hi_c[6], xend=1999.25), color="red") +
geom_segment(ggplot2::aes(x=1999.75, y=eb_hi_c[7], yend=eb_hi_c[7], xend=2000.25), color="red") +
geom_segment(ggplot2::aes(x=2000.75, y=eb_hi_c[8], yend=eb_hi_c[8], xend=2001.25), color="red") +
geom_segment(ggplot2::aes(x=2001.75, y=eb_hi_c[9], yend=eb_hi_c[9], xend=2002.25), color="red") +
geom_segment(ggplot2::aes(x=2002.75, y=eb_hi_c[10], yend=eb_hi_c[10], xend=2003.25), color="red") +
geom_segment(ggplot2::aes(x=2003.75, y=eb_hi_c[11], yend=eb_hi_c[11], xend=2004.25), color="red") +
geom_segment(ggplot2::aes(x=2004.75, y=eb_hi_c[12], yend=eb_hi_c[12], xend=2005.25), color="red") +
geom_segment(ggplot2::aes(x=2005.75, y=eb_hi_c[13], yend=eb_hi_c[13], xend=2006.25), color="red") +
geom_segment(ggplot2::aes(x=2006.75, y=eb_hi_c[14], yend=eb_hi_c[14], xend=2007.25), color="red") +
geom_segment(ggplot2::aes(x=2007.75, y=eb_hi_c[15], yend=eb_hi_c[15], xend=2008.25), color="red") +
geom_segment(ggplot2::aes(x=2008.75, y=eb_hi_c[16], yend=eb_hi_c[16], xend=2009.25), color="red") +
geom_segment(ggplot2::aes(x=2009.75, y=eb_hi_c[17], yend=eb_hi_c[17], xend=2010.25), color="red") +
geom_segment(ggplot2::aes(x=2010.75, y=eb_hi_c[18], yend=eb_hi_c[18], xend=2011.25), color="red") +
geom_segment(ggplot2::aes(x=2011.75, y=eb_hi_c[19], yend=eb_hi_c[19], xend=2012.25), color="red") +
geom_segment(ggplot2::aes(x=2012.75, y=eb_hi_c[20], yend=eb_hi_c[20], xend=2013.25), color="red") +
geom_segment(ggplot2::aes(x=2013.75, y=eb_hi_c[21], yend=eb_hi_c[21], xend=2014.25), color="red") +
geom_segment(ggplot2::aes(x=2014.75, y=eb_hi_c[22], yend=eb_hi_c[22], xend=2015.25), color="red") +
geom_segment(ggplot2::aes(x=2015.75, y=eb_hi_c[23], yend=eb_hi_c[23], xend=2016.25), color="red") +
geom_segment(ggplot2::aes(x=2016.75, y=eb_hi_c[24], yend=eb_hi_c[24], xend=2017.25), color="red") +
geom_segment(ggplot2::aes(x=2017.75, y=eb_hi_c[25], yend=eb_hi_c[25], xend=2018.25), color="red") +
geom_segment(ggplot2::aes(x=2018.75, y=eb_hi_c[26], yend=eb_hi_c[26], xend=2019.25), color="red") +
geom_segment(ggplot2::aes(x=2019.75, y=eb_hi_c[27], yend=eb_hi_c[27], xend=2020.25), color="red") +
geom_segment(ggplot2::aes(x=2020.75, y=eb_hi_c[28], yend=eb_hi_c[28], xend=2021.25), color="red") +
geom_segment(ggplot2::aes(x=2021.75, y=eb_hi_c[29], yend=eb_hi_c[29], xend=2022.25), color="red") +
geom_segment(ggplot2::aes(x=2022.75, y=eb_hi_c[30], yend=eb_hi_c[30], xend=2023.25), color="red") +
geom_segment(ggplot2::aes(x=2023.75, y=eb_hi_c[31], yend=eb_hi_c[31], xend=2024.25), color="red") +
geom_segment(ggplot2::aes(x=2024.75, y=eb_hi_c[32], yend=eb_hi_c[32], xend=2025.25), color="red")
p2 <- ggplot2::ggplot(salcha_n, aes(x=year, y=run, fill=Age))+geom_col()+theme_classic()+
ggtitle("Salcha River -- Total Run by Age") + ylab("Number of Chinook") +
theme(
plot.title = element_text(size=16, face="bold", hjust=0.5),
axis.title.x = element_blank(),
axis.title.y = element_text(size=14),
axis.text.x = element_text(angle=90, vjust=0.5,hjust=1),
legend.position = "none"
) +
scale_x_continuous(breaks=1994:final_year)+
geom_segment(aes(x=1994, y=eb_lo_s[1], yend=eb_hi_s[1], xend=1994), color="red") +
geom_segment(aes(x=1995, y=eb_lo_s[2], yend=eb_hi_s[2], xend=1995), color="red") +
geom_segment(aes(x=1996, y=eb_lo_s[3], yend=eb_hi_s[3], xend=1996), color="red") +
geom_segment(aes(x=1997, y=eb_lo_s[4], yend=eb_hi_s[4], xend=1997), color="red") +
geom_segment(aes(x=1998, y=eb_lo_s[5], yend=eb_hi_s[5], xend=1998), color="red") +
geom_segment(aes(x=1999, y=eb_lo_s[6], yend=eb_hi_s[6], xend=1999), color="red") +
geom_segment(aes(x=2000, y=eb_lo_s[7], yend=eb_hi_s[7], xend=2000), color="red") +
geom_segment(aes(x=2001, y=eb_lo_s[8], yend=eb_hi_s[8], xend=2001), color="red") +
geom_segment(aes(x=2002, y=eb_lo_s[9], yend=eb_hi_s[9], xend=2002), color="red") +
geom_segment(aes(x=2003, y=eb_lo_s[10], yend=eb_hi_s[10], xend=2003), color="red") +
geom_segment(aes(x=2004, y=eb_lo_s[11], yend=eb_hi_s[11], xend=2004), color="red") +
geom_segment(aes(x=2005, y=eb_lo_s[12], yend=eb_hi_s[12], xend=2005), color="red") +
geom_segment(aes(x=2006, y=eb_lo_s[13], yend=eb_hi_s[13], xend=2006), color="red") +
geom_segment(aes(x=2007, y=eb_lo_s[14], yend=eb_hi_s[14], xend=2007), color="red") +
geom_segment(aes(x=2008, y=eb_lo_s[15], yend=eb_hi_s[15], xend=2008), color="red") +
geom_segment(aes(x=2009, y=eb_lo_s[16], yend=eb_hi_s[16], xend=2009), color="red") +
geom_segment(aes(x=2010, y=eb_lo_s[17], yend=eb_hi_s[17], xend=2010), color="red") +
geom_segment(aes(x=2011, y=eb_lo_s[18], yend=eb_hi_s[18], xend=2011), color="red") +
geom_segment(aes(x=2012, y=eb_lo_s[19], yend=eb_hi_s[19], xend=2012), color="red") +
geom_segment(aes(x=2013, y=eb_lo_s[20], yend=eb_hi_s[20], xend=2013), color="red") +
geom_segment(aes(x=2014, y=eb_lo_s[21], yend=eb_hi_s[21], xend=2014), color="red") +
geom_segment(aes(x=2015, y=eb_lo_s[22], yend=eb_hi_s[22], xend=2015), color="red") +
geom_segment(aes(x=2016, y=eb_lo_s[23], yend=eb_hi_s[23], xend=2016), color="red") +
geom_segment(aes(x=2017, y=eb_lo_s[24], yend=eb_hi_s[24], xend=2017), color="red") +
geom_segment(aes(x=2018, y=eb_lo_s[25], yend=eb_hi_s[25], xend=2018), color="red") +
geom_segment(aes(x=2019, y=eb_lo_s[26], yend=eb_hi_s[26], xend=2019), color="red") +
geom_segment(aes(x=2020, y=eb_lo_s[27], yend=eb_hi_s[27], xend=2020), color="red") +
geom_segment(aes(x=2021, y=eb_lo_s[28], yend=eb_hi_s[28], xend=2021), color="red") +
geom_segment(aes(x=2022, y=eb_lo_s[29], yend=eb_hi_s[29], xend=2022), color="red") +
geom_segment(aes(x=2023, y=eb_lo_s[30], yend=eb_hi_s[30], xend=2023), color="red") +
geom_segment(aes(x=2024, y=eb_lo_s[31], yend=eb_hi_s[31], xend=2024), color="red") +
geom_segment(aes(x=2025, y=eb_lo_s[32], yend=eb_hi_s[32], xend=2025), color="red") +
geom_segment(aes(x=1993.75, y=eb_lo_s[1], yend=eb_lo_s[1], xend=1994.25), color="red") +
geom_segment(aes(x=1994.75, y=eb_lo_s[2], yend=eb_lo_s[2], xend=1995.25), color="red") +
geom_segment(aes(x=1995.75, y=eb_lo_s[3], yend=eb_lo_s[3], xend=1996.25), color="red") +
geom_segment(aes(x=1996.75, y=eb_lo_s[4], yend=eb_lo_s[4], xend=1997.25), color="red") +
geom_segment(aes(x=1997.75, y=eb_lo_s[5], yend=eb_lo_s[5], xend=1998.25), color="red") +
geom_segment(aes(x=1998.75, y=eb_lo_s[6], yend=eb_lo_s[6], xend=1999.25), color="red") +
geom_segment(aes(x=1999.75, y=eb_lo_s[7], yend=eb_lo_s[7], xend=2000.25), color="red") +
geom_segment(aes(x=2000.75, y=eb_lo_s[8], yend=eb_lo_s[8], xend=2001.25), color="red") +
geom_segment(aes(x=2001.75, y=eb_lo_s[9], yend=eb_lo_s[9], xend=2002.25), color="red") +
geom_segment(aes(x=2002.75, y=eb_lo_s[10], yend=eb_lo_s[10], xend=2003.25), color="red") +
geom_segment(aes(x=2003.75, y=eb_lo_s[11], yend=eb_lo_s[11], xend=2004.25), color="red") +
geom_segment(aes(x=2004.75, y=eb_lo_s[12], yend=eb_lo_s[12], xend=2005.25), color="red") +
geom_segment(aes(x=2005.75, y=eb_lo_s[13], yend=eb_lo_s[13], xend=2006.25), color="red") +
geom_segment(aes(x=2006.75, y=eb_lo_s[14], yend=eb_lo_s[14], xend=2007.25), color="red") +
geom_segment(aes(x=2007.75, y=eb_lo_s[15], yend=eb_lo_s[15], xend=2008.25), color="red") +
geom_segment(aes(x=2008.75, y=eb_lo_s[16], yend=eb_lo_s[16], xend=2009.25), color="red") +
geom_segment(aes(x=2009.75, y=eb_lo_s[17], yend=eb_lo_s[17], xend=2010.25), color="red") +
geom_segment(aes(x=2010.75, y=eb_lo_s[18], yend=eb_lo_s[18], xend=2011.25), color="red") +
geom_segment(aes(x=2011.75, y=eb_lo_s[19], yend=eb_lo_s[19], xend=2012.25), color="red") +
geom_segment(aes(x=2012.75, y=eb_lo_s[20], yend=eb_lo_s[20], xend=2013.25), color="red") +
geom_segment(aes(x=2013.75, y=eb_lo_s[21], yend=eb_lo_s[21], xend=2014.25), color="red") +
geom_segment(aes(x=2014.75, y=eb_lo_s[22], yend=eb_lo_s[22], xend=2015.25), color="red") +
geom_segment(aes(x=2015.75, y=eb_lo_s[23], yend=eb_lo_s[23], xend=2016.25), color="red") +
geom_segment(aes(x=2016.75, y=eb_lo_s[24], yend=eb_lo_s[24], xend=2017.25), color="red") +
geom_segment(aes(x=2017.75, y=eb_lo_s[25], yend=eb_lo_s[25], xend=2018.25), color="red") +
geom_segment(aes(x=2018.75, y=eb_lo_s[26], yend=eb_lo_s[26], xend=2019.25), color="red") +
geom_segment(aes(x=2019.75, y=eb_lo_s[27], yend=eb_lo_s[27], xend=2020.25), color="red") +
geom_segment(aes(x=2020.75, y=eb_lo_s[28], yend=eb_lo_s[28], xend=2021.25), color="red") +
geom_segment(aes(x=2021.75, y=eb_lo_s[29], yend=eb_lo_s[29], xend=2022.25), color="red") +
geom_segment(aes(x=2022.75, y=eb_lo_s[30], yend=eb_lo_s[30], xend=2023.25), color="red") +
geom_segment(aes(x=2023.75, y=eb_lo_s[31], yend=eb_lo_s[31], xend=2024.25), color="red") +
geom_segment(aes(x=2024.75, y=eb_lo_s[32], yend=eb_lo_s[32], xend=2025.25), color="red") +
geom_segment(aes(x=1993.75, y=eb_hi_s[1], yend=eb_hi_s[1], xend=1994.25), color="red") +
geom_segment(aes(x=1994.75, y=eb_hi_s[2], yend=eb_hi_s[2], xend=1995.25), color="red") +
geom_segment(aes(x=1995.75, y=eb_hi_s[3], yend=eb_hi_s[3], xend=1996.25), color="red") +
geom_segment(aes(x=1996.75, y=eb_hi_s[4], yend=eb_hi_s[4], xend=1997.25), color="red") +
geom_segment(aes(x=1997.75, y=eb_hi_s[5], yend=eb_hi_s[5], xend=1998.25), color="red") +
geom_segment(aes(x=1998.75, y=eb_hi_s[6], yend=eb_hi_s[6], xend=1999.25), color="red") +
geom_segment(aes(x=1999.75, y=eb_hi_s[7], yend=eb_hi_s[7], xend=2000.25), color="red") +
geom_segment(aes(x=2000.75, y=eb_hi_s[8], yend=eb_hi_s[8], xend=2001.25), color="red") +
geom_segment(aes(x=2001.75, y=eb_hi_s[9], yend=eb_hi_s[9], xend=2002.25), color="red") +
geom_segment(aes(x=2002.75, y=eb_hi_s[10], yend=eb_hi_s[10], xend=2003.25), color="red") +
geom_segment(aes(x=2003.75, y=eb_hi_s[11], yend=eb_hi_s[11], xend=2004.25), color="red") +
geom_segment(aes(x=2004.75, y=eb_hi_s[12], yend=eb_hi_s[12], xend=2005.25), color="red") +
geom_segment(aes(x=2005.75, y=eb_hi_s[13], yend=eb_hi_s[13], xend=2006.25), color="red") +
geom_segment(aes(x=2006.75, y=eb_hi_s[14], yend=eb_hi_s[14], xend=2007.25), color="red") +
geom_segment(aes(x=2007.75, y=eb_hi_s[15], yend=eb_hi_s[15], xend=2008.25), color="red") +
geom_segment(aes(x=2008.75, y=eb_hi_s[16], yend=eb_hi_s[16], xend=2009.25), color="red") +
geom_segment(aes(x=2009.75, y=eb_hi_s[17], yend=eb_hi_s[17], xend=2010.25), color="red") +
geom_segment(aes(x=2010.75, y=eb_hi_s[18], yend=eb_hi_s[18], xend=2011.25), color="red") +
geom_segment(aes(x=2011.75, y=eb_hi_s[19], yend=eb_hi_s[19], xend=2012.25), color="red") +
geom_segment(aes(x=2012.75, y=eb_hi_s[20], yend=eb_hi_s[20], xend=2013.25), color="red") +
geom_segment(aes(x=2013.75, y=eb_hi_s[21], yend=eb_hi_s[21], xend=2014.25), color="red") +
geom_segment(aes(x=2014.75, y=eb_hi_s[22], yend=eb_hi_s[22], xend=2015.25), color="red") +
geom_segment(aes(x=2015.75, y=eb_hi_s[23], yend=eb_hi_s[23], xend=2016.25), color="red") +
geom_segment(aes(x=2016.75, y=eb_hi_s[24], yend=eb_hi_s[24], xend=2017.25), color="red") +
geom_segment(aes(x=2017.75, y=eb_hi_s[25], yend=eb_hi_s[25], xend=2018.25), color="red") +
geom_segment(aes(x=2018.75, y=eb_hi_s[26], yend=eb_hi_s[26], xend=2019.25), color="red") +
geom_segment(aes(x=2019.75, y=eb_hi_s[27], yend=eb_hi_s[27], xend=2020.25), color="red") +
geom_segment(aes(x=2020.75, y=eb_hi_s[28], yend=eb_hi_s[28], xend=2021.25), color="red") +
geom_segment(aes(x=2021.75, y=eb_hi_s[29], yend=eb_hi_s[29], xend=2022.25), color="red") +
geom_segment(aes(x=2022.75, y=eb_hi_s[30], yend=eb_hi_s[30], xend=2023.25), color="red") +
geom_segment(aes(x=2023.75, y=eb_hi_s[31], yend=eb_hi_s[31], xend=2024.25), color="red") +
geom_segment(aes(x=2024.75, y=eb_hi_s[32], yend=eb_hi_s[32], xend=2025.25), color="red")
p3 <- ggplot2::ggplot(chena_p, aes(x=year, y=run, fill=Age))+geom_col()+theme_classic()+
ggtitle("Chena River -- Age at Maturity") + ylab("Proportion") +
theme(
plot.title = element_text(size=16, face="bold", hjust=0.5),
axis.title.x = element_blank(),
axis.title.y = element_text(size=14),
axis.text.x = element_text(angle=90, vjust=0.5,hjust=1),
legend.position = "none"
) +
scale_x_continuous(breaks=1994:final_year)
p4 <- ggplot2::ggplot(salcha_p, aes(x=year, y=run, fill=Age))+geom_col()+theme_classic()+
ggtitle("Salcha River -- Age at Maturity") + ylab("Proportion") +
theme(
plot.title = element_text(size=16, face="bold", hjust=0.5),
axis.title.x = element_blank(),
axis.title.y = element_text(size=14),
axis.text.x = element_text(angle=90, vjust=0.5,hjust=1),
legend.position = "bottom",
legend.title = element_text(size=14, face="bold", vjust = 1)
) +
scale_x_continuous(breaks=1994:final_year)
suppressWarnings(print(ggpubr::ggarrange(p1, p2, p3, p4,
ncol = 1, nrow = 4, legend="right", common.legend = T)))
dev.off()
}
jBernardADFG/ChenaSalchaSR documentation built on Nov. 20, 2020, 10:37 p.m.
R Package Documentation
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#' Escapement by Age Histogram
#' @param samples (data.frame) output of clean_chains
#' @param file_path (character) file path to store output jpeg file.
#' @param width (numeric) width of the output plot (in px).
#' @param height (numeric) height of the output plot (in px).
#' @export
age_hist <- function(samples, file_path, width=500, height=1000, final_year=2025){
#
file_path=paste("Plots/age_hists/", model_specs$run_name, ".jpeg", sep="")
final_year=2025
width=500
height=1000
#
eb_samples_c <- samples[,substr(names(samples), 1, 7)=="N_1_dot" & substr(names(samples), nchar(names(samples))-1, nchar(names(samples)))=="1]"]
eb_c <- apply(eb_samples_c, MARGIN=2, quantile, probs = c(0.25, 0.75))
eb_lo_c <- as.numeric(eb_c[1,])
eb_hi_c <- as.numeric(eb_c[2,])
eb_c <- data.frame(lo = eb_lo_c, hi=eb_hi_c)
eb_samples_s <- samples[,substr(names(samples), 1, 7)=="N_1_dot" & substr(names(samples), nchar(names(samples))-1, nchar(names(samples)))=="2]"]
eb_s <- apply(eb_samples_s, MARGIN=2, quantile, probs = c(0.25, 0.75))
eb_lo_s <- as.numeric(eb_s[1,])
eb_hi_s <- as.numeric(eb_s[2,])
# file_path=paste("Plots/age_hists/", model_specs$run_name, ".jpeg", sep="")
# final_year=2030
# width=500
# height=1000
# final_year=2020
aba_samples <- samples[,substr(names(samples), 1, 3)=="N_1" &
substr(names(samples), 4, 4)!="_"]
quants <- apply(aba_samples, MARGIN=2, quantile, probs = c(0.5))
tot_years <- length(1994:2030)
n_years <- length(1994:final_year)
med_array <- array(NA, dim=c(tot_years, 2, 6))
l <- 1
for (k in 1:6){
for (j in 1:2){
for (i in 1:tot_years){
med_array[i,j,k] <- quants[l]
l <- l + 1
}
}
}
med_array <- med_array[1:n_years,,]
chena_tab <- salcha_tab <- data.frame(
year=1994:final_year,
Age_3=rep(NA, n_years),
Age_4=rep(NA, n_years),
Age_5=rep(NA, n_years),
Age_6=rep(NA, n_years),
Age_7=rep(NA, n_years),
Age_8=rep(NA, n_years)
)
for (i in 1:n_years){
for (k in 1:6){
chena_tab[i, k+1] <- med_array[i, 1, k]
salcha_tab[i, k+1] <- med_array[i, 2, k]
}
}
chena_n <- data.frame(year=rep(1994:final_year, rep(6, length(1994:final_year))),
Age=rep(1:6, length(1994:final_year)),
run=rep(NA, 6*length(1994:final_year)))
salcha_n <- data.frame(year=rep(1994:final_year, rep(6, length(1994:final_year))),
Age=rep(1:6, length(1994:final_year)),
run=rep(NA, 6*length(1994:final_year)))
k <- 1
for(i in 1:nrow(chena_tab)){
for(j in 2:ncol(chena_tab)){
chena_n[k,3] <- chena_tab[i,j]
salcha_n[k,3] <- salcha_tab[i,j]
k<- k+1
}
}
aam_samples <- samples[,substr(names(samples), 1, 1) == "p" &
substr(names(samples), 2, 2) != "h"]
quants <- apply(aam_samples, MARGIN=2, quantile, probs = c(0.5))
tot_years <- length(1986:2030)
med_array <- array(NA, dim=c(tot_years, 2, 6))
l <- 1
for (k in 1:6){
for (j in 1:2){
if (j == 1){
tot_years <- 45
}
else{
tot_years <- 43
}
for (i in 1:tot_years){
med_array[i,j,k] <- quants[l]
l <- l + 1
}
}
}
med_array <- med_array[9:length(1986:final_year),,]
chena_tab <- salcha_tab <- data.frame(
year=1994:final_year,
Age_3=rep(NA, n_years),
Age_4=rep(NA, n_years),
Age_5=rep(NA, n_years),
Age_6=rep(NA, n_years),
Age_7=rep(NA, n_years),
Age_8=rep(NA, n_years)
)
for (i in 1:n_years){
for (k in 1:6){
chena_tab[i, k+1] <- med_array[i, 1, k]
salcha_tab[i, k+1] <- med_array[i, 2, k]
}
}
chena_tab
salcha_tab
chena_norm <- apply(chena_tab[,2:ncol(chena_tab)], MARGIN=1, sum)
salcha_norm <- apply(salcha_tab[,2:ncol(salcha_tab)], MARGIN=1, sum)
for(i in 1:nrow(chena_tab)){
for(j in 2:ncol(chena_tab)){
chena_tab[i,j] <- chena_tab[i,j]/chena_norm[i]
salcha_tab[i,j] <- salcha_tab[i,j]/salcha_norm[i]
}
}
chena_p <- data.frame(year=rep(1994:final_year, rep(6, n_years)),
Age=rep(1:6, n_years),
run=rep(NA, 6*n_years))
salcha_p <- data.frame(year=rep(1994:final_year, rep(6, n_years)),
Age=rep(1:6, n_years),
run=rep(NA, 6*n_years))
k <- 1
for(i in 1:nrow(chena_tab)){
for(j in 2:ncol(chena_tab)){
chena_p[k,3] <- chena_tab[i,j]
salcha_p[k,3] <- salcha_tab[i,j]
k<- k+1
}
}
chena_n$Age <- chena_n$Age + 2
salcha_n$Age <- salcha_n$Age + 2
chena_p$Age <- chena_p$Age + 2
salcha_p$Age <- salcha_p$Age + 2
jpeg(filename = file_path, width=width, height=height, unit="px")
library(ggplot2)
p1 <- ggplot2::ggplot(chena_n, aes(x=year, y=run, fill=Age))+
geom_col()+
theme_classic()+
ggtitle("Chena River -- Total Run by Age") + ylab("Number of Chinook") +
theme(
plot.title = element_text(size=16, face="bold", hjust=0.5),
axis.title.x = element_blank(),
axis.title.y = element_text(size=14),
axis.text.x = element_text(angle=90, vjust=0.5,hjust=1),
legend.position = "none"
) +
scale_x_continuous(breaks=1994:final_year)+
geom_segment(ggplot2::aes(x=1994, y=eb_lo_c[1], yend=eb_hi_c[1], xend=1994), color="red") +
geom_segment(ggplot2::aes(x=1995, y=eb_lo_c[2], yend=eb_hi_c[2], xend=1995), color="red") +
geom_segment(ggplot2::aes(x=1996, y=eb_lo_c[3], yend=eb_hi_c[3], xend=1996), color="red") +
geom_segment(ggplot2::aes(x=1997, y=eb_lo_c[4], yend=eb_hi_c[4], xend=1997), color="red") +
geom_segment(ggplot2::aes(x=1998, y=eb_lo_c[5], yend=eb_hi_c[5], xend=1998), color="red") +
geom_segment(ggplot2::aes(x=1999, y=eb_lo_c[6], yend=eb_hi_c[6], xend=1999), color="red") +
geom_segment(ggplot2::aes(x=2000, y=eb_lo_c[7], yend=eb_hi_c[7], xend=2000), color="red") +
geom_segment(ggplot2::aes(x=2001, y=eb_lo_c[8], yend=eb_hi_c[8], xend=2001), color="red") +
geom_segment(ggplot2::aes(x=2002, y=eb_lo_c[9], yend=eb_hi_c[9], xend=2002), color="red") +
geom_segment(ggplot2::aes(x=2003, y=eb_lo_c[10], yend=eb_hi_c[10], xend=2003), color="red") +
geom_segment(ggplot2::aes(x=2004, y=eb_lo_c[11], yend=eb_hi_c[11], xend=2004), color="red") +
geom_segment(ggplot2::aes(x=2005, y=eb_lo_c[12], yend=eb_hi_c[12], xend=2005), color="red") +
geom_segment(ggplot2::aes(x=2006, y=eb_lo_c[13], yend=eb_hi_c[13], xend=2006), color="red") +
geom_segment(ggplot2::aes(x=2007, y=eb_lo_c[14], yend=eb_hi_c[14], xend=2007), color="red") +
geom_segment(ggplot2::aes(x=2008, y=eb_lo_c[15], yend=eb_hi_c[15], xend=2008), color="red") +
geom_segment(ggplot2::aes(x=2009, y=eb_lo_c[16], yend=eb_hi_c[16], xend=2009), color="red") +
geom_segment(ggplot2::aes(x=2010, y=eb_lo_c[17], yend=eb_hi_c[17], xend=2010), color="red") +
geom_segment(ggplot2::aes(x=2011, y=eb_lo_c[18], yend=eb_hi_c[18], xend=2011), color="red") +
geom_segment(ggplot2::aes(x=2012, y=eb_lo_c[19], yend=eb_hi_c[19], xend=2012), color="red") +
geom_segment(ggplot2::aes(x=2013, y=eb_lo_c[20], yend=eb_hi_c[20], xend=2013), color="red") +
geom_segment(ggplot2::aes(x=2014, y=eb_lo_c[21], yend=eb_hi_c[21], xend=2014), color="red") +
geom_segment(ggplot2::aes(x=2015, y=eb_lo_c[22], yend=eb_hi_c[22], xend=2015), color="red") +
geom_segment(ggplot2::aes(x=2016, y=eb_lo_c[23], yend=eb_hi_c[23], xend=2016), color="red") +
geom_segment(ggplot2::aes(x=2017, y=eb_lo_c[24], yend=eb_hi_c[24], xend=2017), color="red") +
geom_segment(ggplot2::aes(x=2018, y=eb_lo_c[25], yend=eb_hi_c[25], xend=2018), color="red") +
geom_segment(ggplot2::aes(x=2019, y=eb_lo_c[26], yend=eb_hi_c[26], xend=2019), color="red") +
geom_segment(ggplot2::aes(x=2020, y=eb_lo_c[27], yend=eb_hi_c[27], xend=2020), color="red") +
geom_segment(ggplot2::aes(x=2021, y=eb_lo_c[28], yend=eb_hi_c[28], xend=2021), color="red") +
geom_segment(ggplot2::aes(x=2022, y=eb_lo_c[29], yend=eb_hi_c[29], xend=2022), color="red") +
geom_segment(ggplot2::aes(x=2023, y=eb_lo_c[30], yend=eb_hi_c[30], xend=2023), color="red") +
geom_segment(ggplot2::aes(x=2024, y=eb_lo_c[31], yend=eb_hi_c[31], xend=2024), color="red") +
geom_segment(ggplot2::aes(x=2025, y=eb_lo_c[32], yend=eb_hi_c[32], xend=2025), color="red") +
geom_segment(ggplot2::aes(x=1993.75, y=eb_lo_c[1], yend=eb_lo_c[1], xend=1994.25), color="red") +
geom_segment(ggplot2::aes(x=1994.75, y=eb_lo_c[2], yend=eb_lo_c[2], xend=1995.25), color="red") +
geom_segment(ggplot2::aes(x=1995.75, y=eb_lo_c[3], yend=eb_lo_c[3], xend=1996.25), color="red") +
geom_segment(ggplot2::aes(x=1996.75, y=eb_lo_c[4], yend=eb_lo_c[4], xend=1997.25), color="red") +
geom_segment(ggplot2::aes(x=1997.75, y=eb_lo_c[5], yend=eb_lo_c[5], xend=1998.25), color="red") +
geom_segment(ggplot2::aes(x=1998.75, y=eb_lo_c[6], yend=eb_lo_c[6], xend=1999.25), color="red") +
geom_segment(ggplot2::aes(x=1999.75, y=eb_lo_c[7], yend=eb_lo_c[7], xend=2000.25), color="red") +
geom_segment(ggplot2::aes(x=2000.75, y=eb_lo_c[8], yend=eb_lo_c[8], xend=2001.25), color="red") +
geom_segment(ggplot2::aes(x=2001.75, y=eb_lo_c[9], yend=eb_lo_c[9], xend=2002.25), color="red") +
geom_segment(ggplot2::aes(x=2002.75, y=eb_lo_c[10], yend=eb_lo_c[10], xend=2003.25), color="red") +
geom_segment(ggplot2::aes(x=2003.75, y=eb_lo_c[11], yend=eb_lo_c[11], xend=2004.25), color="red") +
geom_segment(ggplot2::aes(x=2004.75, y=eb_lo_c[12], yend=eb_lo_c[12], xend=2005.25), color="red") +
geom_segment(ggplot2::aes(x=2005.75, y=eb_lo_c[13], yend=eb_lo_c[13], xend=2006.25), color="red") +
geom_segment(ggplot2::aes(x=2006.75, y=eb_lo_c[14], yend=eb_lo_c[14], xend=2007.25), color="red") +
geom_segment(ggplot2::aes(x=2007.75, y=eb_lo_c[15], yend=eb_lo_c[15], xend=2008.25), color="red") +
geom_segment(ggplot2::aes(x=2008.75, y=eb_lo_c[16], yend=eb_lo_c[16], xend=2009.25), color="red") +
geom_segment(ggplot2::aes(x=2009.75, y=eb_lo_c[17], yend=eb_lo_c[17], xend=2010.25), color="red") +
geom_segment(ggplot2::aes(x=2010.75, y=eb_lo_c[18], yend=eb_lo_c[18], xend=2011.25), color="red") +
geom_segment(ggplot2::aes(x=2011.75, y=eb_lo_c[19], yend=eb_lo_c[19], xend=2012.25), color="red") +
geom_segment(ggplot2::aes(x=2012.75, y=eb_lo_c[20], yend=eb_lo_c[20], xend=2013.25), color="red") +
geom_segment(ggplot2::aes(x=2013.75, y=eb_lo_c[21], yend=eb_lo_c[21], xend=2014.25), color="red") +
geom_segment(ggplot2::aes(x=2014.75, y=eb_lo_c[22], yend=eb_lo_c[22], xend=2015.25), color="red") +
geom_segment(ggplot2::aes(x=2015.75, y=eb_lo_c[23], yend=eb_lo_c[23], xend=2016.25), color="red") +
geom_segment(ggplot2::aes(x=2016.75, y=eb_lo_c[24], yend=eb_lo_c[24], xend=2017.25), color="red") +
geom_segment(ggplot2::aes(x=2017.75, y=eb_lo_c[25], yend=eb_lo_c[25], xend=2018.25), color="red") +
geom_segment(ggplot2::aes(x=2018.75, y=eb_lo_c[26], yend=eb_lo_c[26], xend=2019.25), color="red") +
geom_segment(ggplot2::aes(x=2019.75, y=eb_lo_c[27], yend=eb_lo_c[27], xend=2020.25), color="red") +
geom_segment(ggplot2::aes(x=2020.75, y=eb_lo_c[28], yend=eb_lo_c[28], xend=2021.25), color="red") +
geom_segment(ggplot2::aes(x=2021.75, y=eb_lo_c[29], yend=eb_lo_c[29], xend=2022.25), color="red") +
geom_segment(ggplot2::aes(x=2022.75, y=eb_lo_c[30], yend=eb_lo_c[30], xend=2023.25), color="red") +
geom_segment(ggplot2::aes(x=2023.75, y=eb_lo_c[31], yend=eb_lo_c[31], xend=2024.25), color="red") +
geom_segment(ggplot2::aes(x=2024.75, y=eb_lo_c[32], yend=eb_lo_c[32], xend=2025.25), color="red") +
geom_segment(ggplot2::aes(x=1993.75, y=eb_hi_c[1], yend=eb_hi_c[1], xend=1994.25), color="red") +
geom_segment(ggplot2::aes(x=1994.75, y=eb_hi_c[2], yend=eb_hi_c[2], xend=1995.25), color="red") +
geom_segment(ggplot2::aes(x=1995.75, y=eb_hi_c[3], yend=eb_hi_c[3], xend=1996.25), color="red") +
geom_segment(ggplot2::aes(x=1996.75, y=eb_hi_c[4], yend=eb_hi_c[4], xend=1997.25), color="red") +
geom_segment(ggplot2::aes(x=1997.75, y=eb_hi_c[5], yend=eb_hi_c[5], xend=1998.25), color="red") +
geom_segment(ggplot2::aes(x=1998.75, y=eb_hi_c[6], yend=eb_hi_c[6], xend=1999.25), color="red") +
geom_segment(ggplot2::aes(x=1999.75, y=eb_hi_c[7], yend=eb_hi_c[7], xend=2000.25), color="red") +
geom_segment(ggplot2::aes(x=2000.75, y=eb_hi_c[8], yend=eb_hi_c[8], xend=2001.25), color="red") +
geom_segment(ggplot2::aes(x=2001.75, y=eb_hi_c[9], yend=eb_hi_c[9], xend=2002.25), color="red") +
geom_segment(ggplot2::aes(x=2002.75, y=eb_hi_c[10], yend=eb_hi_c[10], xend=2003.25), color="red") +
geom_segment(ggplot2::aes(x=2003.75, y=eb_hi_c[11], yend=eb_hi_c[11], xend=2004.25), color="red") +
geom_segment(ggplot2::aes(x=2004.75, y=eb_hi_c[12], yend=eb_hi_c[12], xend=2005.25), color="red") +
geom_segment(ggplot2::aes(x=2005.75, y=eb_hi_c[13], yend=eb_hi_c[13], xend=2006.25), color="red") +
geom_segment(ggplot2::aes(x=2006.75, y=eb_hi_c[14], yend=eb_hi_c[14], xend=2007.25), color="red") +
geom_segment(ggplot2::aes(x=2007.75, y=eb_hi_c[15], yend=eb_hi_c[15], xend=2008.25), color="red") +
geom_segment(ggplot2::aes(x=2008.75, y=eb_hi_c[16], yend=eb_hi_c[16], xend=2009.25), color="red") +
geom_segment(ggplot2::aes(x=2009.75, y=eb_hi_c[17], yend=eb_hi_c[17], xend=2010.25), color="red") +
geom_segment(ggplot2::aes(x=2010.75, y=eb_hi_c[18], yend=eb_hi_c[18], xend=2011.25), color="red") +
geom_segment(ggplot2::aes(x=2011.75, y=eb_hi_c[19], yend=eb_hi_c[19], xend=2012.25), color="red") +
geom_segment(ggplot2::aes(x=2012.75, y=eb_hi_c[20], yend=eb_hi_c[20], xend=2013.25), color="red") +
geom_segment(ggplot2::aes(x=2013.75, y=eb_hi_c[21], yend=eb_hi_c[21], xend=2014.25), color="red") +
geom_segment(ggplot2::aes(x=2014.75, y=eb_hi_c[22], yend=eb_hi_c[22], xend=2015.25), color="red") +
geom_segment(ggplot2::aes(x=2015.75, y=eb_hi_c[23], yend=eb_hi_c[23], xend=2016.25), color="red") +
geom_segment(ggplot2::aes(x=2016.75, y=eb_hi_c[24], yend=eb_hi_c[24], xend=2017.25), color="red") +
geom_segment(ggplot2::aes(x=2017.75, y=eb_hi_c[25], yend=eb_hi_c[25], xend=2018.25), color="red") +
geom_segment(ggplot2::aes(x=2018.75, y=eb_hi_c[26], yend=eb_hi_c[26], xend=2019.25), color="red") +
geom_segment(ggplot2::aes(x=2019.75, y=eb_hi_c[27], yend=eb_hi_c[27], xend=2020.25), color="red") +
geom_segment(ggplot2::aes(x=2020.75, y=eb_hi_c[28], yend=eb_hi_c[28], xend=2021.25), color="red") +
geom_segment(ggplot2::aes(x=2021.75, y=eb_hi_c[29], yend=eb_hi_c[29], xend=2022.25), color="red") +
geom_segment(ggplot2::aes(x=2022.75, y=eb_hi_c[30], yend=eb_hi_c[30], xend=2023.25), color="red") +
geom_segment(ggplot2::aes(x=2023.75, y=eb_hi_c[31], yend=eb_hi_c[31], xend=2024.25), color="red") +
geom_segment(ggplot2::aes(x=2024.75, y=eb_hi_c[32], yend=eb_hi_c[32], xend=2025.25), color="red")
p2 <- ggplot2::ggplot(salcha_n, aes(x=year, y=run, fill=Age))+geom_col()+theme_classic()+
ggtitle("Salcha River -- Total Run by Age") + ylab("Number of Chinook") +
theme(
plot.title = element_text(size=16, face="bold", hjust=0.5),
axis.title.x = element_blank(),
axis.title.y = element_text(size=14),
axis.text.x = element_text(angle=90, vjust=0.5,hjust=1),
legend.position = "none"
) +
scale_x_continuous(breaks=1994:final_year)+
geom_segment(aes(x=1994, y=eb_lo_s[1], yend=eb_hi_s[1], xend=1994), color="red") +
geom_segment(aes(x=1995, y=eb_lo_s[2], yend=eb_hi_s[2], xend=1995), color="red") +
geom_segment(aes(x=1996, y=eb_lo_s[3], yend=eb_hi_s[3], xend=1996), color="red") +
geom_segment(aes(x=1997, y=eb_lo_s[4], yend=eb_hi_s[4], xend=1997), color="red") +
geom_segment(aes(x=1998, y=eb_lo_s[5], yend=eb_hi_s[5], xend=1998), color="red") +
geom_segment(aes(x=1999, y=eb_lo_s[6], yend=eb_hi_s[6], xend=1999), color="red") +
geom_segment(aes(x=2000, y=eb_lo_s[7], yend=eb_hi_s[7], xend=2000), color="red") +
geom_segment(aes(x=2001, y=eb_lo_s[8], yend=eb_hi_s[8], xend=2001), color="red") +
geom_segment(aes(x=2002, y=eb_lo_s[9], yend=eb_hi_s[9], xend=2002), color="red") +
geom_segment(aes(x=2003, y=eb_lo_s[10], yend=eb_hi_s[10], xend=2003), color="red") +
geom_segment(aes(x=2004, y=eb_lo_s[11], yend=eb_hi_s[11], xend=2004), color="red") +
geom_segment(aes(x=2005, y=eb_lo_s[12], yend=eb_hi_s[12], xend=2005), color="red") +
geom_segment(aes(x=2006, y=eb_lo_s[13], yend=eb_hi_s[13], xend=2006), color="red") +
geom_segment(aes(x=2007, y=eb_lo_s[14], yend=eb_hi_s[14], xend=2007), color="red") +
geom_segment(aes(x=2008, y=eb_lo_s[15], yend=eb_hi_s[15], xend=2008), color="red") +
geom_segment(aes(x=2009, y=eb_lo_s[16], yend=eb_hi_s[16], xend=2009), color="red") +
geom_segment(aes(x=2010, y=eb_lo_s[17], yend=eb_hi_s[17], xend=2010), color="red") +
geom_segment(aes(x=2011, y=eb_lo_s[18], yend=eb_hi_s[18], xend=2011), color="red") +
geom_segment(aes(x=2012, y=eb_lo_s[19], yend=eb_hi_s[19], xend=2012), color="red") +
geom_segment(aes(x=2013, y=eb_lo_s[20], yend=eb_hi_s[20], xend=2013), color="red") +
geom_segment(aes(x=2014, y=eb_lo_s[21], yend=eb_hi_s[21], xend=2014), color="red") +
geom_segment(aes(x=2015, y=eb_lo_s[22], yend=eb_hi_s[22], xend=2015), color="red") +
geom_segment(aes(x=2016, y=eb_lo_s[23], yend=eb_hi_s[23], xend=2016), color="red") +
geom_segment(aes(x=2017, y=eb_lo_s[24], yend=eb_hi_s[24], xend=2017), color="red") +
geom_segment(aes(x=2018, y=eb_lo_s[25], yend=eb_hi_s[25], xend=2018), color="red") +
geom_segment(aes(x=2019, y=eb_lo_s[26], yend=eb_hi_s[26], xend=2019), color="red") +
geom_segment(aes(x=2020, y=eb_lo_s[27], yend=eb_hi_s[27], xend=2020), color="red") +
geom_segment(aes(x=2021, y=eb_lo_s[28], yend=eb_hi_s[28], xend=2021), color="red") +
geom_segment(aes(x=2022, y=eb_lo_s[29], yend=eb_hi_s[29], xend=2022), color="red") +
geom_segment(aes(x=2023, y=eb_lo_s[30], yend=eb_hi_s[30], xend=2023), color="red") +
geom_segment(aes(x=2024, y=eb_lo_s[31], yend=eb_hi_s[31], xend=2024), color="red") +
geom_segment(aes(x=2025, y=eb_lo_s[32], yend=eb_hi_s[32], xend=2025), color="red") +
geom_segment(aes(x=1993.75, y=eb_lo_s[1], yend=eb_lo_s[1], xend=1994.25), color="red") +
geom_segment(aes(x=1994.75, y=eb_lo_s[2], yend=eb_lo_s[2], xend=1995.25), color="red") +
geom_segment(aes(x=1995.75, y=eb_lo_s[3], yend=eb_lo_s[3], xend=1996.25), color="red") +
geom_segment(aes(x=1996.75, y=eb_lo_s[4], yend=eb_lo_s[4], xend=1997.25), color="red") +
geom_segment(aes(x=1997.75, y=eb_lo_s[5], yend=eb_lo_s[5], xend=1998.25), color="red") +
geom_segment(aes(x=1998.75, y=eb_lo_s[6], yend=eb_lo_s[6], xend=1999.25), color="red") +
geom_segment(aes(x=1999.75, y=eb_lo_s[7], yend=eb_lo_s[7], xend=2000.25), color="red") +
geom_segment(aes(x=2000.75, y=eb_lo_s[8], yend=eb_lo_s[8], xend=2001.25), color="red") +
geom_segment(aes(x=2001.75, y=eb_lo_s[9], yend=eb_lo_s[9], xend=2002.25), color="red") +
geom_segment(aes(x=2002.75, y=eb_lo_s[10], yend=eb_lo_s[10], xend=2003.25), color="red") +
geom_segment(aes(x=2003.75, y=eb_lo_s[11], yend=eb_lo_s[11], xend=2004.25), color="red") +
geom_segment(aes(x=2004.75, y=eb_lo_s[12], yend=eb_lo_s[12], xend=2005.25), color="red") +
geom_segment(aes(x=2005.75, y=eb_lo_s[13], yend=eb_lo_s[13], xend=2006.25), color="red") +
geom_segment(aes(x=2006.75, y=eb_lo_s[14], yend=eb_lo_s[14], xend=2007.25), color="red") +
geom_segment(aes(x=2007.75, y=eb_lo_s[15], yend=eb_lo_s[15], xend=2008.25), color="red") +
geom_segment(aes(x=2008.75, y=eb_lo_s[16], yend=eb_lo_s[16], xend=2009.25), color="red") +
geom_segment(aes(x=2009.75, y=eb_lo_s[17], yend=eb_lo_s[17], xend=2010.25), color="red") +
geom_segment(aes(x=2010.75, y=eb_lo_s[18], yend=eb_lo_s[18], xend=2011.25), color="red") +
geom_segment(aes(x=2011.75, y=eb_lo_s[19], yend=eb_lo_s[19], xend=2012.25), color="red") +
geom_segment(aes(x=2012.75, y=eb_lo_s[20], yend=eb_lo_s[20], xend=2013.25), color="red") +
geom_segment(aes(x=2013.75, y=eb_lo_s[21], yend=eb_lo_s[21], xend=2014.25), color="red") +
geom_segment(aes(x=2014.75, y=eb_lo_s[22], yend=eb_lo_s[22], xend=2015.25), color="red") +
geom_segment(aes(x=2015.75, y=eb_lo_s[23], yend=eb_lo_s[23], xend=2016.25), color="red") +
geom_segment(aes(x=2016.75, y=eb_lo_s[24], yend=eb_lo_s[24], xend=2017.25), color="red") +
geom_segment(aes(x=2017.75, y=eb_lo_s[25], yend=eb_lo_s[25], xend=2018.25), color="red") +
geom_segment(aes(x=2018.75, y=eb_lo_s[26], yend=eb_lo_s[26], xend=2019.25), color="red") +
geom_segment(aes(x=2019.75, y=eb_lo_s[27], yend=eb_lo_s[27], xend=2020.25), color="red") +
geom_segment(aes(x=2020.75, y=eb_lo_s[28], yend=eb_lo_s[28], xend=2021.25), color="red") +
geom_segment(aes(x=2021.75, y=eb_lo_s[29], yend=eb_lo_s[29], xend=2022.25), color="red") +
geom_segment(aes(x=2022.75, y=eb_lo_s[30], yend=eb_lo_s[30], xend=2023.25), color="red") +
geom_segment(aes(x=2023.75, y=eb_lo_s[31], yend=eb_lo_s[31], xend=2024.25), color="red") +
geom_segment(aes(x=2024.75, y=eb_lo_s[32], yend=eb_lo_s[32], xend=2025.25), color="red") +
geom_segment(aes(x=1993.75, y=eb_hi_s[1], yend=eb_hi_s[1], xend=1994.25), color="red") +
geom_segment(aes(x=1994.75, y=eb_hi_s[2], yend=eb_hi_s[2], xend=1995.25), color="red") +
geom_segment(aes(x=1995.75, y=eb_hi_s[3], yend=eb_hi_s[3], xend=1996.25), color="red") +
geom_segment(aes(x=1996.75, y=eb_hi_s[4], yend=eb_hi_s[4], xend=1997.25), color="red") +
geom_segment(aes(x=1997.75, y=eb_hi_s[5], yend=eb_hi_s[5], xend=1998.25), color="red") +
geom_segment(aes(x=1998.75, y=eb_hi_s[6], yend=eb_hi_s[6], xend=1999.25), color="red") +
geom_segment(aes(x=1999.75, y=eb_hi_s[7], yend=eb_hi_s[7], xend=2000.25), color="red") +
geom_segment(aes(x=2000.75, y=eb_hi_s[8], yend=eb_hi_s[8], xend=2001.25), color="red") +
geom_segment(aes(x=2001.75, y=eb_hi_s[9], yend=eb_hi_s[9], xend=2002.25), color="red") +
geom_segment(aes(x=2002.75, y=eb_hi_s[10], yend=eb_hi_s[10], xend=2003.25), color="red") +
geom_segment(aes(x=2003.75, y=eb_hi_s[11], yend=eb_hi_s[11], xend=2004.25), color="red") +
geom_segment(aes(x=2004.75, y=eb_hi_s[12], yend=eb_hi_s[12], xend=2005.25), color="red") +
geom_segment(aes(x=2005.75, y=eb_hi_s[13], yend=eb_hi_s[13], xend=2006.25), color="red") +
geom_segment(aes(x=2006.75, y=eb_hi_s[14], yend=eb_hi_s[14], xend=2007.25), color="red") +
geom_segment(aes(x=2007.75, y=eb_hi_s[15], yend=eb_hi_s[15], xend=2008.25), color="red") +
geom_segment(aes(x=2008.75, y=eb_hi_s[16], yend=eb_hi_s[16], xend=2009.25), color="red") +
geom_segment(aes(x=2009.75, y=eb_hi_s[17], yend=eb_hi_s[17], xend=2010.25), color="red") +
geom_segment(aes(x=2010.75, y=eb_hi_s[18], yend=eb_hi_s[18], xend=2011.25), color="red") +
geom_segment(aes(x=2011.75, y=eb_hi_s[19], yend=eb_hi_s[19], xend=2012.25), color="red") +
geom_segment(aes(x=2012.75, y=eb_hi_s[20], yend=eb_hi_s[20], xend=2013.25), color="red") +
geom_segment(aes(x=2013.75, y=eb_hi_s[21], yend=eb_hi_s[21], xend=2014.25), color="red") +
geom_segment(aes(x=2014.75, y=eb_hi_s[22], yend=eb_hi_s[22], xend=2015.25), color="red") +
geom_segment(aes(x=2015.75, y=eb_hi_s[23], yend=eb_hi_s[23], xend=2016.25), color="red") +
geom_segment(aes(x=2016.75, y=eb_hi_s[24], yend=eb_hi_s[24], xend=2017.25), color="red") +
geom_segment(aes(x=2017.75, y=eb_hi_s[25], yend=eb_hi_s[25], xend=2018.25), color="red") +
geom_segment(aes(x=2018.75, y=eb_hi_s[26], yend=eb_hi_s[26], xend=2019.25), color="red") +
geom_segment(aes(x=2019.75, y=eb_hi_s[27], yend=eb_hi_s[27], xend=2020.25), color="red") +
geom_segment(aes(x=2020.75, y=eb_hi_s[28], yend=eb_hi_s[28], xend=2021.25), color="red") +
geom_segment(aes(x=2021.75, y=eb_hi_s[29], yend=eb_hi_s[29], xend=2022.25), color="red") +
geom_segment(aes(x=2022.75, y=eb_hi_s[30], yend=eb_hi_s[30], xend=2023.25), color="red") +
geom_segment(aes(x=2023.75, y=eb_hi_s[31], yend=eb_hi_s[31], xend=2024.25), color="red") +
geom_segment(aes(x=2024.75, y=eb_hi_s[32], yend=eb_hi_s[32], xend=2025.25), color="red")
p3 <- ggplot2::ggplot(chena_p, aes(x=year, y=run, fill=Age))+geom_col()+theme_classic()+
ggtitle("Chena River -- Age at Maturity") + ylab("Proportion") +
theme(
plot.title = element_text(size=16, face="bold", hjust=0.5),
axis.title.x = element_blank(),
axis.title.y = element_text(size=14),
axis.text.x = element_text(angle=90, vjust=0.5,hjust=1),
legend.position = "none"
) +
scale_x_continuous(breaks=1994:final_year)
p4 <- ggplot2::ggplot(salcha_p, aes(x=year, y=run, fill=Age))+geom_col()+theme_classic()+
ggtitle("Salcha River -- Age at Maturity") + ylab("Proportion") +
theme(
plot.title = element_text(size=16, face="bold", hjust=0.5),
axis.title.x = element_blank(),
axis.title.y = element_text(size=14),
axis.text.x = element_text(angle=90, vjust=0.5,hjust=1),
legend.position = "bottom",
legend.title = element_text(size=14, face="bold", vjust = 1)
) +
scale_x_continuous(breaks=1994:final_year)
suppressWarnings(print(ggpubr::ggarrange(p1, p2, p3, p4,
ncol = 1, nrow = 4, legend="right", common.legend = T)))
dev.off()
}
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