TestScripts/Plots_for_paper_presentation.R
In Blevy2/READ-PDB-blevy2-MFS2: Mixed Fishery fleet dynamics simulation tool
#RUN BELOW AFTER RUNNING VAST_STRATMEAN_ERROR_COMPARISON_ALL_FORPAPER FIRST TO GET THE CORRECT VARIABLES
#YELLOWTAIL ONLY CONSTNATPOPULATION INCREASING TEMPERATURE PLOT
model_line_size = 1.5
model_point_size = 3.5
estimate_line_size = 1.25
estimate_point_size = 3
for(season_ in c(1,2)){
ssnn = ifelse(season_==1, "Spring Estimate", "Fall Estimate")
print(ggplot() +
#this way plots data by season
geom_point(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group = season, color = "Model"),size=model_point_size) +
geom_line(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group =season, color = "Model"),size=model_line_size) +
#plot VAST estimate without covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"),size=estimate_line_size)+
#
# #plot VAST estimate without covariates with WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov W Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"),size=2)+
# geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"))+
#plot VAST estimate with covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"),size=estimate_line_size)+
# #plot VAST estimate with covariates WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov w Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
#
#plot stratified calculation data with NO noise
geom_errorbar(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean No Noise"),width=.3) +
# geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean No Noise"), size=estimate_point_size)+
geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,color = "Strat Mean No Noise"),size=estimate_line_size)+
# #plot stratified calculation data with NO noise
# geom_errorbar(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean W Noise"),width=.3) +
# # geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
# geom_point(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
# geom_line(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
#
#
#facet_wrap(~ season, ncol =2) +
# labs(x="year",y="Biomass", title = paste(folder," SeV=",round(VAST_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FC=", toString(FC_spring),
# " SeSM=",round(SRS_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FeV=",round(VAST_Model_error[[s]][[folder]][["fall"]],digits=2),
# " FC=", toString(FC_fall),
# " FeSM=",round(SRS_Model_error[[s]][[folder]][["fall"]],digits=2),sep=""), color ="" )
labs(x="year",y="Biomass", title =paste("Yellowtail Flounder ",ssnn,sep=""), color ="" )+
theme(axis.text=element_text(size=12),
axis.title=element_text(size=12),
title=element_text(size=14))
)
}
#
#HADDOCK INCPOP CONTEMP ONLY CONSTNATPOPULATION INCREASING TEMPERATURE PLOT
model_line_size = 1.5
model_point_size = 3.5
estimate_line_size = 1.25
estimate_point_size = 3
season_ = 2
ggplot() +
#plot VAST estimate without covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"),size=estimate_line_size)+
#
# #plot VAST estimate without covariates with WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov W Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"),size=season_)+
# geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"))+
#plot VAST estimate with covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"),size=estimate_line_size)+
# #plot VAST estimate with covariates WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov w Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
#
#plot stratified calculation data with NO noise
geom_errorbar(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean No Noise"),width=.3) +
# geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean No Noise"), size=estimate_point_size)+
geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,color = "Strat Mean No Noise"),size=estimate_line_size)+
#this way plots data by season
geom_point(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group = season, color = "Model"),size=model_point_size) +
geom_line(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group =season, color = "Model"),size=model_line_size) +
# #plot stratified calculation data with NO noise
# geom_errorbar(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean W Noise"),width=.3) +
# # geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
# geom_point(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
# geom_line(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
#
#
#facet_wrap(~ season, ncol =2) +
# labs(x="year",y="Biomass", title = paste(paste(s," ",folder,sep=""), "\n", #new line
# paste(" V.NC.NN=",round(VAST_Model_error[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]][["spring"]],digits=2),
# " V.NC.YN=",round(VAST_Model_error[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]][["spring"]],digits=2),
# " V.YC.NN=",round(VAST_Model_error[[s]][["_WithCov_"]][["NoNoise_"]][[folder]][["spring"]],digits=2),
# " V.YC.YN=",round(VAST_Model_error[[s]][["_WithCov_"]][["WithNoise_"]][[folder]][["spring"]],digits=2),
# " SM.NN=",round(SRS_Model_error[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]][["spring"]],digits=2),
# " SM.YN=",round(SRS_Model_error[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]][["spring"]],digits=2),sep=""), "\n", #new line
# paste(" V.NC.NN=",round(VAST_Model_error[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]][["fall"]],digits=2),
# " V.NC.YN=",round(VAST_Model_error[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]][["fall"]],digits=2),
# " V.YC.NN=",round(VAST_Model_error[[s]][["_WithCov_"]][["NoNoise_"]][[folder]][["fall"]],digits=2),
# " V.YC.YN=",round(VAST_Model_error[[s]][["_WithCov_"]][["WithNoise_"]][[folder]][["fall"]],digits=2),
# " SM.NN=",round(SRS_Model_error[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]][["fall"]],digits=2),
# " SM.YN=",round(SRS_Model_error[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]][["fall"]],digits=2),sep=""),sep=""), color ="" )+
#
labs(x="year",y="Biomass", title ="Haddock Fall Estimate", color ="" )+
theme(axis.text=element_text(size=14),
axis.title=element_text(size=14),
title=element_text(size=16))
#COD DEC POP CON TEMP ALL STRATA AND DEC POP INC TEMP ALL STRATA
model_line_size = 1.5
model_point_size = 3.5
estimate_line_size = 1.25
estimate_point_size = 3
for(season_ in c(1,2)){
ssnn = ifelse(season_==1, "Spring Estimate", "Fall Estimate")
print(ggplot() +
#this way plots data by season
geom_point(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group = season, color = "Model"),size=model_point_size) +
geom_line(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group =season, color = "Model"),size=model_line_size) +
#plot VAST estimate without covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"),size=estimate_line_size)+
#
# #plot VAST estimate without covariates with WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov W Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"),size=2)+
# geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"))+
#plot VAST estimate with covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"),size=estimate_line_size)+
# #plot VAST estimate with covariates WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov w Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
#
#plot stratified calculation data with NO noise
geom_errorbar(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean No Noise"),width=.3) +
# geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean No Noise"), size=estimate_point_size)+
geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,color = "Strat Mean No Noise"),size=estimate_line_size)+
# #plot stratified calculation data with NO noise
# geom_errorbar(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean W Noise"),width=.3) +
# # geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
# geom_point(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
# geom_line(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
#
#
#facet_wrap(~ season, ncol =2) +
# labs(x="year",y="Biomass", title = paste(folder," SeV=",round(VAST_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FC=", toString(FC_spring),
# " SeSM=",round(SRS_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FeV=",round(VAST_Model_error[[s]][[folder]][["fall"]],digits=2),
# " FC=", toString(FC_fall),
# " FeSM=",round(SRS_Model_error[[s]][[folder]][["fall"]],digits=2),sep=""), color ="" )
labs(x="year",y="Biomass", title =paste("Atlantic Cod ",ssnn,sep=""), color ="" )+
theme(axis.text=element_text(size=12),
axis.title=element_text(size=12),
title=element_text(size=14))
)
}
# ESTIMATE RATIO PLOTS
#Yellowtail estimates are for the constant population, constant temperature, all strata
#COD DECPOP_CONTEMP
#Haddock are IncPop_IncTemp_all strata_
model_line_size = 1.5
model_point_size = 3.5
estimate_line_size = 1.25
estimate_point_size = 3
for(season_ in c(1,2)){
ssnn = ifelse(season_==1, "Spring", "Fall")
print(
ggplot() +
#this way plots data by season divided by itself so it equals 1
geom_point(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=log(Est_ratio), group = season, color = "True Biomass"),size=estimate_point_size) +
geom_line(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=log(Est_ratio), group =season, color = "True Biomass"),size=estimate_line_size ) +
#plot VAST estimate without covariates with NO noise
geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST No Cov No Noise"),size=model_point_size)+
geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST No Cov No Noise"),size=model_line_size)+
# #plot VAST estimate without covariates with WITH noise
# geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST No Cov W Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST No Cov W Noise"))+
#
#plot VAST estimate with covariates with NO noise
geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST w Cov No Noise"),size=model_point_size)+
geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST w Cov No Noise"),size=model_line_size)+
# #plot VAST estimate with covariates WITH noise
# geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST w Cov w Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST w Cov w Noise"))+
#
#plot stratified calculation data with NO noise
geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]][,1:5]),season==season_),aes(x=year,y=log(Est_ratio),group=season, color = "Strat Mean No Noise"),size=model_point_size)+
geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]][,1:5]),season==season_),aes(x=year,y=log(Est_ratio),group=season, color = "Strat Mean No Noise"),size=model_line_size)+
#
# #plot stratified calculation data with NO noise
# geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]][,1:5]),season==season_),aes(x=year,y=log(Est_ratio),group=season, color = "Strat Mean W Noise"),size=)+
# geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]][,1:5]),season==season_),aes(x=year,y=log(Est_ratio),group=season, color = "Strat Mean W Noise"),size=)+
#
#
#facet_wrap(~ season, ncol =1) +
# labs(x="year",y="Biomass", title = paste(folder," SeV=",round(VAST_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FC=", toString(FC_spring),
# " SeSM=",round(SRS_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FeV=",round(VAST_Model_error[[s]][[folder]][["fall"]],digits=2),
# " FC=", toString(FC_fall),
# " FeSM=",round(SRS_Model_error[[s]][[folder]][["fall"]],digits=2),sep=""), color ="" )
labs(x="year",y="log(Estimate / Model)", title = paste("Haddock Ratio Trend- ", ssnn,sep=""), color ="" )+
theme(axis.text=element_text(size=18),
axis.title=element_text(size=16),
title=element_text(size=16))
)
}
Blevy2/READ-PDB-blevy2-MFS2 documentation built on Nov. 29, 2023, 11:48 p.m.
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#RUN BELOW AFTER RUNNING VAST_STRATMEAN_ERROR_COMPARISON_ALL_FORPAPER FIRST TO GET THE CORRECT VARIABLES
#YELLOWTAIL ONLY CONSTNATPOPULATION INCREASING TEMPERATURE PLOT
model_line_size = 1.5
model_point_size = 3.5
estimate_line_size = 1.25
estimate_point_size = 3
for(season_ in c(1,2)){
ssnn = ifelse(season_==1, "Spring Estimate", "Fall Estimate")
print(ggplot() +
#this way plots data by season
geom_point(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group = season, color = "Model"),size=model_point_size) +
geom_line(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group =season, color = "Model"),size=model_line_size) +
#plot VAST estimate without covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"),size=estimate_line_size)+
#
# #plot VAST estimate without covariates with WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov W Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"),size=2)+
# geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"))+
#plot VAST estimate with covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"),size=estimate_line_size)+
# #plot VAST estimate with covariates WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov w Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
#
#plot stratified calculation data with NO noise
geom_errorbar(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean No Noise"),width=.3) +
# geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean No Noise"), size=estimate_point_size)+
geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,color = "Strat Mean No Noise"),size=estimate_line_size)+
# #plot stratified calculation data with NO noise
# geom_errorbar(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean W Noise"),width=.3) +
# # geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
# geom_point(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
# geom_line(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
#
#
#facet_wrap(~ season, ncol =2) +
# labs(x="year",y="Biomass", title = paste(folder," SeV=",round(VAST_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FC=", toString(FC_spring),
# " SeSM=",round(SRS_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FeV=",round(VAST_Model_error[[s]][[folder]][["fall"]],digits=2),
# " FC=", toString(FC_fall),
# " FeSM=",round(SRS_Model_error[[s]][[folder]][["fall"]],digits=2),sep=""), color ="" )
labs(x="year",y="Biomass", title =paste("Yellowtail Flounder ",ssnn,sep=""), color ="" )+
theme(axis.text=element_text(size=12),
axis.title=element_text(size=12),
title=element_text(size=14))
)
}
#
#HADDOCK INCPOP CONTEMP ONLY CONSTNATPOPULATION INCREASING TEMPERATURE PLOT
model_line_size = 1.5
model_point_size = 3.5
estimate_line_size = 1.25
estimate_point_size = 3
season_ = 2
ggplot() +
#plot VAST estimate without covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"),size=estimate_line_size)+
#
# #plot VAST estimate without covariates with WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov W Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"),size=season_)+
# geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"))+
#plot VAST estimate with covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"),size=estimate_line_size)+
# #plot VAST estimate with covariates WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov w Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
#
#plot stratified calculation data with NO noise
geom_errorbar(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean No Noise"),width=.3) +
# geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean No Noise"), size=estimate_point_size)+
geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,color = "Strat Mean No Noise"),size=estimate_line_size)+
#this way plots data by season
geom_point(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group = season, color = "Model"),size=model_point_size) +
geom_line(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group =season, color = "Model"),size=model_line_size) +
# #plot stratified calculation data with NO noise
# geom_errorbar(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean W Noise"),width=.3) +
# # geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
# geom_point(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
# geom_line(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
#
#
#facet_wrap(~ season, ncol =2) +
# labs(x="year",y="Biomass", title = paste(paste(s," ",folder,sep=""), "\n", #new line
# paste(" V.NC.NN=",round(VAST_Model_error[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]][["spring"]],digits=2),
# " V.NC.YN=",round(VAST_Model_error[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]][["spring"]],digits=2),
# " V.YC.NN=",round(VAST_Model_error[[s]][["_WithCov_"]][["NoNoise_"]][[folder]][["spring"]],digits=2),
# " V.YC.YN=",round(VAST_Model_error[[s]][["_WithCov_"]][["WithNoise_"]][[folder]][["spring"]],digits=2),
# " SM.NN=",round(SRS_Model_error[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]][["spring"]],digits=2),
# " SM.YN=",round(SRS_Model_error[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]][["spring"]],digits=2),sep=""), "\n", #new line
# paste(" V.NC.NN=",round(VAST_Model_error[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]][["fall"]],digits=2),
# " V.NC.YN=",round(VAST_Model_error[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]][["fall"]],digits=2),
# " V.YC.NN=",round(VAST_Model_error[[s]][["_WithCov_"]][["NoNoise_"]][[folder]][["fall"]],digits=2),
# " V.YC.YN=",round(VAST_Model_error[[s]][["_WithCov_"]][["WithNoise_"]][[folder]][["fall"]],digits=2),
# " SM.NN=",round(SRS_Model_error[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]][["fall"]],digits=2),
# " SM.YN=",round(SRS_Model_error[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]][["fall"]],digits=2),sep=""),sep=""), color ="" )+
#
labs(x="year",y="Biomass", title ="Haddock Fall Estimate", color ="" )+
theme(axis.text=element_text(size=14),
axis.title=element_text(size=14),
title=element_text(size=16))
#COD DEC POP CON TEMP ALL STRATA AND DEC POP INC TEMP ALL STRATA
model_line_size = 1.5
model_point_size = 3.5
estimate_line_size = 1.25
estimate_point_size = 3
for(season_ in c(1,2)){
ssnn = ifelse(season_==1, "Spring Estimate", "Fall Estimate")
print(ggplot() +
#this way plots data by season
geom_point(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group = season, color = "Model"),size=model_point_size) +
geom_line(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=biomass, group =season, color = "Model"),size=model_line_size) +
#plot VAST estimate without covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov No Noise"),size=estimate_line_size)+
#
# #plot VAST estimate without covariates with WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST No Cov W Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==2),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"),size=2)+
# geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==2),aes(x=Year,y=Estimate,group=season, color = "VAST No Cov W Noise"))+
#plot VAST estimate with covariates with NO noise
geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov No Noise"),width=.3) +
#geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"), size=estimate_point_size)+
geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov No Noise"),size=estimate_line_size)+
# #plot VAST estimate with covariates WITH noise
# geom_errorbar(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST w Cov w Noise"),width=.3) +
# #geom_linerange(data=subset(VAST_data[[s]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season,ymin=Estimate-(1.96*Std..Error.for.Estimate), ymax=Estimate+(1.96*Std..Error.for.Estimate), color = "VAST Estimate")) +
# geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=Estimate,group=season, color = "VAST w Cov w Noise"))+
#
#plot stratified calculation data with NO noise
geom_errorbar(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean No Noise"),width=.3) +
# geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean No Noise"), size=estimate_point_size)+
geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]]),season==season_),aes(x=year,y=mean.yr.absolute,group=season,color = "Strat Mean No Noise"),size=estimate_line_size)+
# #plot stratified calculation data with NO noise
# geom_errorbar(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Strat Mean W Noise"),width=.3) +
# # geom_linerange(data=as.data.frame(SRS_data[[s]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season,ymin=mean.yr.absolute-(1.96*sd.mean.yr.absolute), ymax=mean.yr.absolute+(1.96*sd.mean.yr.absolute), color = "Stratified Mean")) +
# geom_point(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
# geom_line(data=as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]]),aes(x=year,y=mean.yr.absolute,group=season, color = "Strat Mean W Noise"))+
#
#
#facet_wrap(~ season, ncol =2) +
# labs(x="year",y="Biomass", title = paste(folder," SeV=",round(VAST_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FC=", toString(FC_spring),
# " SeSM=",round(SRS_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FeV=",round(VAST_Model_error[[s]][[folder]][["fall"]],digits=2),
# " FC=", toString(FC_fall),
# " FeSM=",round(SRS_Model_error[[s]][[folder]][["fall"]],digits=2),sep=""), color ="" )
labs(x="year",y="Biomass", title =paste("Atlantic Cod ",ssnn,sep=""), color ="" )+
theme(axis.text=element_text(size=12),
axis.title=element_text(size=12),
title=element_text(size=14))
)
}
# ESTIMATE RATIO PLOTS
#Yellowtail estimates are for the constant population, constant temperature, all strata
#COD DECPOP_CONTEMP
#Haddock are IncPop_IncTemp_all strata_
model_line_size = 1.5
model_point_size = 3.5
estimate_line_size = 1.25
estimate_point_size = 3
for(season_ in c(1,2)){
ssnn = ifelse(season_==1, "Spring", "Fall")
print(
ggplot() +
#this way plots data by season divided by itself so it equals 1
geom_point(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=log(Est_ratio), group = season, color = "True Biomass"),size=estimate_point_size) +
geom_line(data = subset(as.data.frame(pop_by_season[[s]]),season==season_), aes(x=as.numeric(year),y=log(Est_ratio), group =season, color = "True Biomass"),size=estimate_line_size ) +
#plot VAST estimate without covariates with NO noise
geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST No Cov No Noise"),size=model_point_size)+
geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST No Cov No Noise"),size=model_line_size)+
# #plot VAST estimate without covariates with WITH noise
# geom_point(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST No Cov W Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_NoCovs_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST No Cov W Noise"))+
#
#plot VAST estimate with covariates with NO noise
geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST w Cov No Noise"),size=model_point_size)+
geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST w Cov No Noise"),size=model_line_size)+
# #plot VAST estimate with covariates WITH noise
# geom_point(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST w Cov w Noise"))+
# geom_line(data=subset(VAST_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]],season==season_),aes(x=Year,y=log(Est_ratio),group=season, color = "VAST w Cov w Noise"))+
#
#plot stratified calculation data with NO noise
geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]][,1:5]),season==season_),aes(x=year,y=log(Est_ratio),group=season, color = "Strat Mean No Noise"),size=model_point_size)+
geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["NoNoise_"]][[folder]][,1:5]),season==season_),aes(x=year,y=log(Est_ratio),group=season, color = "Strat Mean No Noise"),size=model_line_size)+
#
# #plot stratified calculation data with NO noise
# geom_point(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]][,1:5]),season==season_),aes(x=year,y=log(Est_ratio),group=season, color = "Strat Mean W Noise"),size=)+
# geom_line(data=subset(as.data.frame(SRS_data[[s]][["_WithCov_"]][["WithNoise_"]][[folder]][,1:5]),season==season_),aes(x=year,y=log(Est_ratio),group=season, color = "Strat Mean W Noise"),size=)+
#
#
#facet_wrap(~ season, ncol =1) +
# labs(x="year",y="Biomass", title = paste(folder," SeV=",round(VAST_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FC=", toString(FC_spring),
# " SeSM=",round(SRS_Model_error[[s]][[folder]][["spring"]],digits=2),
# " FeV=",round(VAST_Model_error[[s]][[folder]][["fall"]],digits=2),
# " FC=", toString(FC_fall),
# " FeSM=",round(SRS_Model_error[[s]][[folder]][["fall"]],digits=2),sep=""), color ="" )
labs(x="year",y="log(Estimate / Model)", title = paste("Haddock Ratio Trend- ", ssnn,sep=""), color ="" )+
theme(axis.text=element_text(size=18),
axis.title=element_text(size=16),
title=element_text(size=16))
)
}
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