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BoxPlotDataCode.R
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BoxPlotDataCode.R
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####Box Plot Data####
####Set directory####
require(dplyr)
require(matrixStats)
setwd("C:/Users/jjesse/Box/HCR_Sims")#change this accordingly
wd<-getwd()
<<<<<<< HEAD
####Catch Boxplot####
=======
####Read in Data for SSB/SSBMSY####
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
setwd(paste(wd,"/Sim_1/sim",sep=""))
sims <- list.files()
for (k in 1:length(sims)){
if (file.size(sims[k])==0){
sims[k]<-NA}
}
sims<-na.omit(sims)
catch<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
catch[k,]<-omvalGlobal[[1]]$SSB[169:190]/omvalGlobal[[1]]$SSBPROXYT2[169:190]
}
catchs<-rowMedians(catch[,1:5])
Df<-as.data.frame(catchs)
Df$catch<-catchs
Df$catchs<-NULL
Df$Time<-'Short-term'
catchm<-rowMedians(catch[,6:10])
Df2<-as.data.frame(catchm)
Df2$catch<-catchm
Df2$catchm<-NULL
Df2$Time<-'Medium-term'
Df<-full_join(Df,Df2)
catchl<-rowMedians(catch[,11:21])
Df2<-as.data.frame(catchl)
Df2$catch<-catchl
Df2$catchl<-NULL
Df2$Time<-'Long-term'
Df<-full_join(Df,Df2)
Df$Scenario<-1
<<<<<<< HEAD
for (i in 2:32){
setwd(paste(wd,"/Sim_",i,"/sim",sep=""))
sims <- list.files()
for (k in 1:length(sims)){
if (file.size(sims[k])==0){
sims[k]<-NA}
}
sims<-na.omit(sims)
catch<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
catch[k,]<-omvalGlobal[[1]]$sumCW[169:190]
}
=======
for (i in 2:32){
setwd(paste(wd,"/Sim_",i,"/sim",sep=""))
sims <- list.files()
for (k in 1:length(sims)){
if (file.size(sims[k])==0){
sims[k]<-NA}
}
sims<-na.omit(sims)
catch<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
catch[k,]<-omvalGlobal[[1]]$SSB[169:190]/omvalGlobal[[1]]$SSBPROXYT2[169:190]
}
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
catchs<-rowMedians(catch[,1:5])
Df2<-as.data.frame(catchs)
Df2$catch<-catchs
Df2$catchs<-NULL
Df2$Time<-'Short-term'
<<<<<<< HEAD
=======
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
catchm<-rowMedians(catch[,6:10])
Df3<-as.data.frame(catchm)
Df3$catch<-catchm
Df3$catchm<-NULL
Df3$Time<-'Medium-term'
<<<<<<< HEAD
Df2<-full_join(Df2,Df3)
=======
Df2<-full_join(Df3,Df2)
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
catchl<-rowMedians(catch[,11:21])
Df3<-as.data.frame(catchl)
Df3$catch<-catchl
Df3$catchl<-NULL
Df3$Time<-'Long-term'
<<<<<<< HEAD
Df2<-full_join(Df2,Df3)
Df2$Scenario<-i
Df<-full_join(Df,Df2)
}
write.csv(Df,here("Data/Catch_box.csv"))
##### estimated/true SSBMSY boxplot ####
setwd("C:/Users/jjesse/Box/HCR_Sims")#change this accordingly
wd<-getwd()
setwd(paste(wd,"/Sim_1/sim",sep=""))
sims <- list.files()
for (k in 1:length(sims)){
if (file.size(sims[k])==0){
sims[k]<-NA}
}
sims<-na.omit(sims)
Fratiot<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
Fratiot[k,]<-omvalGlobal[[1]]$SSBPROXY[169:190]/omvalGlobal[[1]]$SSBPROXYT2[169:190]
}
Fratiots<-rowMedians(Fratiot[,1:5])
Df<-as.data.frame(Fratiots)
Df$Fratiot<-Fratiots
Df$Fratiots<-NULL
Df$Time<-'Short-term'
Fratiotm<-rowMedians(Fratiot[,6:10])
Df2<-as.data.frame(Fratiotm)
Df2$Fratiot<-Fratiotm
Df2$Fratiotm<-NULL
Df2$Time<-'Medium-term'
Df<-full_join(Df,Df2)
Fratiotl<-rowMedians(Fratiot[,11:21])
Df2<-as.data.frame(Fratiotl)
Df2$Fratiot<-Fratiotl
Df2$Fratiotl<-NULL
Df2$Time<-'Long-term'
Df<-full_join(Df,Df2)
Df$Scenario<-1
for (i in 2:32){
setwd(paste(wd,"/Sim_",i,"/sim",sep=""))
sims <- list.files()
for (k in 1:length(sims)){
if (file.size(sims[k])==0){
sims[k]<-NA}
}
sims<-na.omit(sims)
Fratiot<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
Fratiot[k,]<-omvalGlobal[[1]]$SSBPROXY[169:190]/omvalGlobal[[1]]$SSBPROXYT2[169:190]
}
Fratiots<-rowMedians(Fratiot[,1:5])
Df2<-as.data.frame(Fratiots)
Df2$Fratiot<-Fratiots
Df2$Fratiots<-NULL
Df2$Time<-'Short-term'
Fratiotm<-rowMedians(Fratiot[,6:10])
Df3<-as.data.frame(Fratiotm)
Df3$Fratiot<-Fratiotm
Df3$Fratiotm<-NULL
Df3$Time<-'Medium-term'
Df2<-full_join(Df2,Df3)
Fratiotl<-rowMedians(Fratiot[,11:21])
Df3<-as.data.frame(Fratiotl)
Df3$Fratiot<-Fratiotl
Df3$Fratiotl<-NULL
Df3$Time<-'Long-term'
Df2<-full_join(Df2,Df3)
=======
Df2<-full_join(Df3,Df2)
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
Df2$Scenario<-i
Df<-full_join(Df,Df2)
}
<<<<<<< HEAD
Df<-rename(Df, SSBratiot=Fratiot)
write.csv(Df,here("Data/SSBMSY_box.csv"))
##### estimated/true FMSY boxplot #####
setwd("C:/Users/jjesse/Box/HCR_Sims")#change this accordingly
wd<-getwd()
=======
Df$SSBratio<-Df$catch
Df$catch<-NULL
data<-Df
####Read in Data for F/FMSY####
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
setwd(paste(wd,"/Sim_1/sim",sep=""))
sims <- list.files()
for (k in 1:length(sims)){
if (file.size(sims[k])==0){
sims[k]<-NA}
}
sims<-na.omit(sims)
<<<<<<< HEAD
Fratiot<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
Fratiot[k,]<-omvalGlobal[[1]]$FPROXY[169:190]/omvalGlobal[[1]]$FPROXYT2[169:190]
}
Fratiots<-rowMedians(Fratiot[,1:5])
Df<-as.data.frame(Fratiots)
Df$Fratiot<-Fratiots
Df$Fratiots<-NULL
Df$Time<-'Short-term'
Fratiotm<-rowMedians(Fratiot[,6:10])
Df2<-as.data.frame(Fratiotm)
Df2$Fratiot<-Fratiotm
Df2$Fratiotm<-NULL
Df2$Time<-'Medium-term'
Df<-full_join(Df,Df2)
Fratiotl<-rowMedians(Fratiot[,11:21])
Df2<-as.data.frame(Fratiotl)
Df2$Fratiot<-Fratiotl
Df2$Fratiotl<-NULL
=======
catch<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
catch[k,]<-omvalGlobal[[1]]$F_full[169:190]/omvalGlobal[[1]]$FPROXYT2[169:190]
}
catchs<-rowMedians(catch[,1:5])
Df<-as.data.frame(catchs)
Df$catch<-catchs
Df$catchs<-NULL
Df$Time<-'Short-term'
catchm<-rowMedians(catch[,6:10])
Df2<-as.data.frame(catchm)
Df2$catch<-catchm
Df2$catchm<-NULL
Df2$Time<-'Medium-term'
Df<-full_join(Df,Df2)
catchl<-rowMedians(catch[,11:21])
Df2<-as.data.frame(catchl)
Df2$catch<-catchl
Df2$catchl<-NULL
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
Df2$Time<-'Long-term'
Df<-full_join(Df,Df2)
Df$Scenario<-1
<<<<<<< HEAD
for (i in 2:32){
setwd(paste(wd,"/Sim_",i,"/sim",sep=""))
sims <- list.files()
=======
for (i in 2:32){
setwd(paste(wd,"/Sim_",i,"/sim",sep=""))
sims <- list.files()
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
for (k in 1:length(sims)){
if (file.size(sims[k])==0){
sims[k]<-NA}
}
sims<-na.omit(sims)
<<<<<<< HEAD
Fratiot<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
Fratiot[k,]<-omvalGlobal[[1]]$FPROXY[169:190]/omvalGlobal[[1]]$FPROXYT2[169:190]
}
Fratiots<-rowMedians(Fratiot[,1:5])
Df2<-as.data.frame(Fratiots)
Df2$Fratiot<-Fratiots
Df2$Fratiots<-NULL
Df2$Time<-'Short-term'
Fratiotm<-rowMedians(Fratiot[,6:10])
Df3<-as.data.frame(Fratiotm)
Df3$Fratiot<-Fratiotm
Df3$Fratiotm<-NULL
Df3$Time<-'Medium-term'
Df2<-full_join(Df2,Df3)
Fratiotl<-rowMedians(Fratiot[,11:21])
Df3<-as.data.frame(Fratiotl)
Df3$Fratiot<-Fratiotl
Df3$Fratiotl<-NULL
Df3$Time<-'Long-term'
Df2<-full_join(Df2,Df3)
=======
catch<-matrix(NA,nrow=length(sims),ncol=22)
for (k in 1:length(sims)){
load(sims[k])
catch[k,]<-omvalGlobal[[1]]$F_full[169:190]/omvalGlobal[[1]]$FPROXYT2[169:190]
}
catchs<-rowMedians(catch[,1:5])
Df2<-as.data.frame(catchs)
Df2$catch<-catchs
Df2$catchs<-NULL
Df2$Time<-'Short-term'
catchm<-rowMedians(catch[,6:10])
Df3<-as.data.frame(catchm)
Df3$catch<-catchm
Df3$catchm<-NULL
Df3$Time<-'Medium-term'
Df2<-full_join(Df3,Df2)
catchl<-rowMedians(catch[,11:21])
Df3<-as.data.frame(catchl)
Df3$catch<-catchl
Df3$catchl<-NULL
Df3$Time<-'Long-term'
Df2<-full_join(Df3,Df2)
>>>>>>> 4d412cce130251c513546408669031f79cdcef70
Df2$Scenario<-i
Df<-full_join(Df,Df2)
}
<<<<<<< HEAD
write.csv(Df,here("Data/FMSY_box.csv"))
##### merge code #####
boxdata<-read.csv(here("Data/Catch_box.csv"))%>%
full_join(read.csv(here("Data/SSBMSY_box.csv")))%>%
full_join(read.csv(here("Data/FMSY_box.csv")))
#bring in scenario info
scenarios<-read.csv(here("Data/scenarios.csv"))
#change rho and frequency inputs to make coding shiny easier
scenarios$Rho[scenarios$Rho==2]<-"No rho-adjustment"
scenarios$Rho[scenarios$Rho==1]<-"Rho-adjustment"
scenarios$Frequency[scenarios$Frequency==1]<-"Two year updates"
scenarios$Frequency[scenarios$Frequency==2]<-"Annual updates"
full_data<-full_join(boxdata,scenarios, by=c("Scenario"))
write.csv(full_data, here("Data/boxdata_jj.csv"))
=======
Df$Fratio<-Df$catch
Df$catch<-NULL
data<-full_join(Df,data)
>>>>>>> 4d412cce130251c513546408669031f79cdcef70