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SuppMat.Rmd
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SuppMat.Rmd
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---
title: "Appendix: Tail associations in ecological variables and their impact on extinction risk"
author: "Shyamolina Ghosh, Lawrence W. Sheppard, Daniel C. Reuman"
date: ""
fontsize: 12pt
geometry: "left=1in,right=1in,top=1in,bottom=1in"
output:
pdf_document:
number_sections: yes
keep_tex: yes
fig_caption: yes
includes:
in_header: head_suppmat.sty
mainfont: Times New Roman
tables: True
link-citations: True
urlcolor : blue
indent : True
csl: ecosphere.csl
bibliography: Ref_extrisk.bib
---
\pagenumbering{roman}
\tableofcontents
\listoffigures
\pagebreak
\pagenumbering{arabic}
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
seed<-101
library(abind)
source("mtime.R")
```
```{r get_srho_common, echo=F, results="hide", cache=T, cache.extra=list(seed,mtime("ExtremeTailDep.R"))}
set.seed(seed)
library(copula)
source("./ExtremeTailDep.R")
np<-1000000
srho_common<-0.875 #7/8
xtc_r<-retd(n=np,d=2,rl=1,mn=0,sdev=1) # copula with extreme right tail
saveRDS(srho_common,"./Results/srho_common.RDS")
# flip xtc_r to get xtc_l
#xtc_l<-1-xtc_r
# make marginals uniform
xtc_r<-pnorm(xtc_r)
xtc_l<-1-xtc_r
# for clayton : left tail dep.
copC<-claytonCopula(3)
parC<-iRho(copC,rho=srho_common)
# first generate Clayton copula
cc<-claytonCopula(par=parC,dim=2)
mtc_l<-rCopula(np,cc)
# flip Clayton copula
mtc_r<-1-mtc_l
# calculate rho with sampling variation
scor_el<-cor(xtc_l,xtc_l,method = "spearman")
scor_el<-scor_el[1,2]
scor_er<-cor(xtc_r,xtc_r,method = "spearman")
scor_er<- scor_er[1,2]
scor_ml<-cor(mtc_l,mtc_l,method = "spearman")
scor_ml<- scor_ml[1,2]
scor_mr<-cor(mtc_r,mtc_r,method ="spearman")
scor_mr<- scor_mr[1,2]
```
```{r plot_intro_fig, echo=F, results="hide"}
#--------- Plot for intro + methods ------------------------------------
# for plotting purpose I just showed only first 500 points
pdf("./Results/introfig_copula.pdf", height=3, width=12)
op<-par(mfrow=c(1,4),mar=c(6,6,2,2),mgp=c(3,1,0))
# extreme left tail
plot(xtc_l[1:500,1],xtc_l[1:500,2],col=rgb(0,0,0,0.1),pch=19,xlab="u",ylab="v",cex.lab=2.5,cex.axis=2)
#legend(x="topleft",legend="A",bty="n",cex=2.5)
text(x=0.1,y=0.9,"A",cex=2.5)
text(x=0.8,y=0.1,round(scor_el,4),cex=2)
# moderate left tail
plot(mtc_l[1:500,1],mtc_l[1:500,2],col=rgb(0,0,0,0.1),pch=19,xlab="u",ylab="v",cex.lab=2.5,cex.axis=2)
text(x=0.1,y=0.9,"B",cex=2.5)
text(x=0.8,y=0.1,round(scor_ml,4),cex=2)
# moderate right tail
plot(mtc_r[1:500,1],mtc_r[1:500,2],col=rgb(0,0,0,0.1),pch=19,xlab="u",ylab="v",cex.lab=2.5,cex.axis=2)
text(x=0.1,y=0.9,"C",cex=2.5)
text(x=0.8,y=0.1,round(scor_mr,4),cex=2)
# extreme right tail
plot(xtc_r[1:500,1],xtc_r[1:500,2],col=rgb(0,0,0,0.1),pch=19,xlab="u",ylab="v",cex.lab=2.5,cex.axis=2)
text(x=0.1,y=0.9,"D",cex=2.5)
text(x=0.8,y=0.1,round(scor_er,4),cex=2)
par(op)
dev.off()
#========== Schematic fig for partial spearman correlation ==============
pdf("./Results/PartialSpearmanFig.pdf", width=6, height=6)
op<-par(mar=c(6,6,2,2),mgp=c(3,1,0))
plot(mtc_r[1:150,1],mtc_r[1:150,2],type='p',pch=19,col=rgb(0,0,0,0.15),cex=1.5,
cex.axis=2,cex.lab=2.5,xlab="x",ylab="y")
lines(c(0,0.3),c(0.3,0),type='l')
lines(c(0,0.6),c(0.6,0),type='l')
lines(c(0,1.4),c(1.4,0),type='l')
lines(c(0,1.7),c(1.7,0),type='l')
par(op)
dev.off()
```
```{r sim_linear_mtd, echo=F, cache=T, cache.extra=list(seed,srho_common,mtime("ext_risk_cop_age_str.R"))}
# extinction risk with moderate tail dep. for single patch linear age structure model
set.seed(seed)
source("ext_risk_cop_age_str.R")
numsims<-10000
numsteps<-25
p0<-c(5,10)
ext_thrs<-2
gshape<-2
gscale<-1
bshape1<-3
bshape2<-2
par_dist<-c(gshape,gscale,bshape1,bshape2)
omg<-Inf
srho<-srho_common # Spearman's rho
# for clayton
copC<-claytonCopula(3)
parC<-iRho(copC,rho=srho)
par<-parC
fam<-3
cop<-BiCopSim(N=(numsteps*numsims), family = fam, par = par)
tempo<-paste("./Results/age_str_results/",BiCopName(family=fam),"_par_",par,"_scor_",srho,"_linear",sep="")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
C_age<-sim_age_str(p0=p0,ext_thrs = ext_thrs,cop=cop,par_dist = par_dist,omg=omg,
numsims = numsims,numsteps = numsteps,ploton=T,resloc=resloc)
saveRDS(C_age,paste(resloc,BiCopName(family = fam),"_sim_age_str.RDS",sep=""))
#---------------------------------------------------------------------------------
# Now for survival clayton : should be the same parameter as of clayton if Spearman's rho is the same
fam<-13
par<-parC
cop<-BiCopSim(N=(numsteps*numsims), family = fam, par = par)
tempo<-paste("./Results/age_str_results/",BiCopName(family=fam),"_par_",par,"_scor_",srho,"_linear",sep="")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
SC_age<-sim_age_str(p0=p0,ext_thrs = ext_thrs,cop=cop,par_dist = par_dist,omg=omg,
numsims = numsims,numsteps = numsteps,ploton=T,resloc=resloc)
saveRDS(SC_age,paste(resloc,BiCopName(family = fam),"_sim_age_str.RDS",sep=""))
```
```{r fig_agestr_mtd_linear, echo=F,results="hide"}
xL<-C_age$extdf
xR<-SC_age$extdf
t<-c(0:(nrow(xL)-1))
pdf(paste("./Results/age_str_results/extrisk_age_str_C_SC_linear.pdf",sep=""),height=5,width=5)
op<-par(mar=c(5,4,1.5,1.5),mgp=c(2,0.7,0))
plot(0,-1,ylim=c(0,1),xlim=range(t),ylab="Extinction risk",xlab="time",cex.lab=2,cex.axis=1.5)
x<-xL
polygon(c(rev(t), t), c(rev(x$CI0.975), x$CI0.025), col = rgb(1,0,0,0.3), border = NA)
lines(t,x$erA,col="red",type="l")
x<-xR
polygon(c(rev(t), t), c(rev(x$CI0.975), x$CI0.025), col = rgb(0,0,1,0.3), border = NA)
lines(t,x$erA,col="blue",type="l")
legend(x=-2,y=1.05, c("moderate LT","moderate RT",
#expression(paste(Omega,"%->%", infinity))
expression(symbol('\127') *symbol('\256')* symbol('\245'))
),
lty=c(1,1, NA),
col=c('red', 'blue', NA), horiz=F, bty='n', cex=1.5, x.intersp = 0.2
#, seg.len = 1
)
par(op)
dev.off()
```
```{r sim_nonlinear_mtd, echo=F, cache=T, cache.extra=list(seed,srho_common,mtime("ext_risk_cop_age_str.R"))}
# extinction risk with moderate tail dep. for single patch non-linear age structure model
set.seed(seed)
source("ext_risk_cop_age_str.R")
numsims<-10000
numsteps<-25
p0<-c(5,10)
ext_thrs<-2
gshape<-2
gscale<-1
bshape1<-3
bshape2<-2
par_dist<-c(gshape,gscale,bshape1,bshape2)
omg<-100
srho<-srho_common # Spearman's rho
# for clayton
copC<-claytonCopula(3)
parC<-iRho(copC,rho=srho)
par<-parC
fam<-3
cop<-BiCopSim(N=(numsteps*numsims), family = fam, par = par)
tempo<-paste("./Results/age_str_results/",BiCopName(family=fam),"_par_",par,"_scor_",srho,"_nonlinear",sep="")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
C_age<-sim_age_str(p0=p0,ext_thrs = ext_thrs,cop=cop,par_dist = par_dist,omg=omg,
numsims = numsims,numsteps = numsteps,ploton=T,resloc=resloc)
saveRDS(C_age,paste(resloc,BiCopName(family = fam),"_sim_age_str.RDS",sep=""))
#---------------------------------------------------------------------------------
# Now for survival clayton : should be the same parameter as of clayton if Spearman's rho is the same
fam<-13
par<-parC
cop<-BiCopSim(N=(numsteps*numsims), family = fam, par = par)
tempo<-paste("./Results/age_str_results/",BiCopName(family=fam),"_par_",par,"_scor_",srho,"_linear",sep="")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
SC_age<-sim_age_str(p0=p0,ext_thrs = ext_thrs,cop=cop,par_dist = par_dist,omg=omg,
numsims = numsims,numsteps = numsteps,ploton=T,resloc=resloc)
saveRDS(SC_age,paste(resloc,BiCopName(family = fam),"_sim_age_str.RDS",sep=""))
```
```{r fig_agestr_mtd_nonlinear, echo=F,results="hide"}
xL<-C_age$extdf
xR<-SC_age$extdf
t<-c(0:(nrow(xL)-1))
pdf(paste("./Results/age_str_results/extrisk_age_str_C_SC_nonlinear_omg_",omg,".pdf",sep=""),height=5,width=5)
op<-par(mar=c(5,4,1.5,1.5),mgp=c(2,0.7,0))
plot(0,-1,ylim=c(0,1),xlim=range(t),ylab="Extinction risk",xlab="time",cex.lab=2,cex.axis=1.5)
x<-xL
polygon(c(rev(t), t), c(rev(x$CI0.975), x$CI0.025), col = rgb(1,0,0,0.3), border = NA)
lines(t,x$erA,col="red",type="l")
x<-xR
polygon(c(rev(t), t), c(rev(x$CI0.975), x$CI0.025), col = rgb(0,0,1,0.3), border = NA)
lines(t,x$erA,col="blue",type="l")
legend(x=-2,y=1.05, c("moderate LT","moderate RT", as.expression(bquote(Omega==.(omg)))), lty=c(1,1,NA),
col=c('red', 'blue',NA), horiz=F, bty='n', cex=1.5, x.intersp = 0.2
#, seg.len = 1
)
par(op)
dev.off()
```
```{r sim_agestr_with_extremetail_linear, echo=F, results="hide", cache=T, cache.extra=list(seed,mtime("ext_risk_cop_age_str.R"),mtime("ExtremeTailDep.R"))}
# extinction risk with extreme tail dep. for single patch linear age structure model
set.seed(seed)
source("ext_risk_cop_age_str.R")
source("ExtremeTailDep.R")
numsims<-10000
numsteps<-25
p0<-c(5,10)
ext_thrs<-2
gshape<-2
gscale<-1
bshape1<-3
bshape2<-2
par_dist<-c(gshape,gscale,bshape1,bshape2)
omg<-Inf
# For extreme right tail dep.
mr<-retd(n = (numsteps*numsims),d = 2,rl =1,mn=0,sdev=1)
cop<-pnorm(mr) # to make normal to uniformly distributed
tempo<-paste("./Results/age_str_results/extreme_right_taildep_linear")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
pdf(paste(resloc,"extreme_right_tail_cop.pdf",sep=""),height = 5,width=5)
plot(cop[,1],cop[,2])
dev.off()
las_exR<-sim_age_str(p0=p0,ext_thrs = ext_thrs,cop=cop,par_dist = par_dist,omg=omg,
numsims = numsims,numsteps = numsteps,ploton=T,resloc=resloc)
saveRDS(las_exR,paste(resloc,"sim_age_str_extreme_right_taildep.RDS",sep=""))
# For extreme left tail dep.
ml<-retd(n = (numsteps*numsims),d = 2,rl =-1,mn=0,sdev=1)
cop<-pnorm(ml) # to make normal to uniformly distributed
tempo<-paste("./Results/age_str_results/extreme_left_taildep_linear")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
pdf(paste(resloc,"extreme_left_tail_cop.pdf",sep=""),height = 5,width=5)
plot(cop[,1],cop[,2])
dev.off()
las_exL<-sim_age_str(p0=p0,ext_thrs = ext_thrs,cop=cop,par_dist = par_dist,omg=omg,
numsims = numsims,numsteps = numsteps,ploton=T,resloc=resloc)
saveRDS(las_exL,paste(resloc,"sim_age_str_extreme_left_taildep.RDS",sep=""))
```
```{r fig_agestr_with_extremetail_linear, echo=F,results="hide"}
xL<-las_exL$extdf
xR<-las_exR$extdf
t<-c(0:(nrow(xL)-1))
pdf(paste("./Results/age_str_results/extrisk_age_str_extremetail_linear.pdf",sep=""),height=5,width=5)
op<-par(mar=c(5,4,1.5,1.5),mgp=c(2,0.7,0))
plot(0,-1,ylim=c(0,1),xlim=range(t),ylab="Extinction risk",xlab="time",cex.lab=2,cex.axis=1.5)
x<-xL
polygon(c(rev(t), t), c(rev(x$CI0.975), x$CI0.025), col = rgb(1,0,0,0.3), border = NA)
lines(t,x$erA,col="red",type="l")
x<-xR
polygon(c(rev(t), t), c(rev(x$CI0.975), x$CI0.025), col = rgb(0,0,1,0.3), border = NA)
lines(t,x$erA,col="blue",type="l")
legend(x=-2,y=1.05, c("extreme LT","extreme RT", expression(symbol('\127') *symbol('\256')* symbol('\245'))),
lty=c(1,1, NA),
col=c('red', 'blue', NA), horiz=F, bty='n', cex=1.5, x.intersp = 0.2
#, seg.len = 1
)
par(op)
dev.off()
```
```{r sim_agestr_with_extremetail_nonlinear, echo=F, results="hide", cache=T, cache.extra=list(seed,mtime("ext_risk_cop_age_str.R"),mtime("ExtremeTailDep.R"))}
# extinction risk with extreme tail dep. for single patch non-linear age structure model
set.seed(seed)
source("ext_risk_cop_age_str.R")
source("ExtremeTailDep.R")
numsims<-10000
numsteps<-25
p0<-c(5,10)
ext_thrs<-2
gshape<-2
gscale<-1
bshape1<-3
bshape2<-2
par_dist<-c(gshape,gscale,bshape1,bshape2)
omg<-100
# For extreme right tail dep.
mr<-retd(n = (numsteps*numsims),d = 2,rl =1,mn=0,sdev=1)
cop<-pnorm(mr) # to make normal to uniformly distributed
tempo<-paste("./Results/age_str_results/extreme_right_taildep_nonlinear")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
pdf(paste(resloc,"extreme_right_tail_cop_omg_",omg,".pdf",sep=""),height = 5,width=5)
plot(cop[,1],cop[,2])
dev.off()
nlas_exR<-sim_age_str(p0=p0,ext_thrs = ext_thrs,cop=cop,par_dist = par_dist,omg=omg,
numsims = numsims,numsteps = numsteps,ploton=T,resloc=resloc)
saveRDS(nlas_exR,paste(resloc,"sim_age_str_extreme_right_taildep.RDS",sep=""))
# For extreme left tail dep.
ml<-retd(n = (numsteps*numsims),d = 2,rl =-1,mn=0,sdev=1)
cop<-pnorm(ml) # to make normal to uniformly distributed
tempo<-paste("./Results/age_str_results/extreme_left_taildep_nonlinear")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
pdf(paste(resloc,"extreme_right_tail_cop_omg_",omg,".pdf",sep=""),height = 5,width=5)
plot(cop[,1],cop[,2])
dev.off()
nlas_exL<-sim_age_str(p0=p0,ext_thrs = ext_thrs,cop=cop,par_dist = par_dist,omg=omg,
numsims = numsims,numsteps = numsteps,ploton=T,resloc=resloc)
saveRDS(nlas_exL,paste(resloc,"sim_age_str_extreme_left_taildep.RDS",sep=""))
```
```{r fig_agestr_with_extremetail_nonlinear, echo=F,results="hide"}
xL<-nlas_exL$extdf
xR<-nlas_exR$extdf
t<-c(0:(nrow(xL)-1))
pdf(paste("./Results/age_str_results/extrisk_age_str_extremetail_nonlinear_omg_",omg,".pdf",sep=""),height=5,width=5)
op<-par(mar=c(5,4,1.5,1.5),mgp=c(2,0.7,0))
plot(0,-1,ylim=c(0,1),xlim=range(t),ylab="Extinction risk",xlab="time",cex.lab=2,cex.axis=1.5)
x<-xL
polygon(c(rev(t), t), c(rev(x$CI0.975), x$CI0.025), col = rgb(1,0,0,0.3), border = NA)
lines(t,x$erA,col="red",type="l")
x<-xR
polygon(c(rev(t), t), c(rev(x$CI0.975), x$CI0.025), col = rgb(0,0,1,0.3), border = NA)
lines(t,x$erA,col="blue",type="l")
legend(x=-2,y=1.05, c("extreme LT","extreme RT", as.expression(bquote(Omega==.(omg)))), lty=c(1,1,NA),
col=c('red', 'blue',NA), horiz=F, bty='n', cex=1.5, x.intersp = 0.2
#, seg.len = 1
)
par(op)
dev.off()
```
```{r sim_ricker_scl_1, echo=F, cache=T, cache.extra=list(seed,srho_common,mtime("mydispersal.R"),mtime("ExtremeTailDep.R"))}
set.seed(seed)
source("mydispersal.R")
rc_ricker<-1 # transition from under to overcompensatory dynamics
r_bf_ricker<-2 # bifurcation parameter stable to unstable eqm
rng1<-runif(10000,min=0,max=r_bf_ricker)
qr1<-quantile(rng1,probs=c(.025,.975))
q1<-abs(unname(qr1[1])-rc_ricker)
q2<-abs(unname(qr1[2])-rc_ricker)
qs<-c(q1,q2)
iqmin<-which.min(qs)
iqmax<-which.max(qs)
fromr<-range(qr1)[iqmin]
tor<-range(qr1)[iqmax]
if(fromr>tor){
byr<--qs[iqmin]/4
}else{
byr<-qs[iqmin]/4
}
rlist<-sort(seq(from=fromr,to=tor, by = byr))
xx<-diff(rlist)
vxx<-var(xx)
if(vxx>1e-10){
warning("Not equal spacing in rlist : Ricker model !!!",immediate.=T,call.=T)
}
numsims<-10000
numsteps<-25
numlocs<-5
K<-50
scl<-1
srho<-srho_common
ext_thrs<-K/10
model<-"ricker"
tempo<-paste("./Results/",model,"_scl_",scl,sep="")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
#initiate a dataframe to store ext risk at dispersal d=0 for all r
ricker_extrisk_d0<-data.frame(rlist,NA*numeric(length(rlist)),NA*numeric(length(rlist)),
NA*numeric(length(rlist)),NA*numeric(length(rlist)))
colnames(ricker_extrisk_d0)<-c("r","risk_xleft_d0","risk_xright_d0","risk_mleft_d0","risk_mright_d0")
res_ricker_local<-c()
for(i in c(1:length(rlist))){
r<- rlist[i]
params<-c(r,K)
ss<-varying_d(numsims=numsims,numsteps=numsteps,numlocs=numlocs,p0=K,params=params,ext_thrs=ext_thrs,
scl=scl,srho=srho,model=model,disp_everywhere=F,plotteron = F,resloc=resloc, getacf=F)
temp_mat<-cbind(ss$d_seq,ss$risk_xleft,ss$risk_xright,ss$risk_mleft,ss$risk_mright)
res_ricker_local<-abind(res_ricker_local,temp_mat,along = 3)
ricker_extrisk_d0$risk_xleft_d0[i]<-ss$risk_xleft[1]
ricker_extrisk_d0$risk_xright_d0[i]<-ss$risk_xright[1]
ricker_extrisk_d0$risk_mleft_d0[i]<-ss$risk_mleft[1]
ricker_extrisk_d0$risk_mright_d0[i]<-ss$risk_mright[1]
}
anm<-paste("r_",rlist,sep="")
cnm<-c("d","risk_xleft","risk_xright","risk_mleft","risk_mright")
dimnames(res_ricker_local)<-list(NULL,cnm,anm)
saveRDS(ricker_extrisk_d0,paste(resloc,"ricker_extrisk_d0.RDS",sep=""))
saveRDS(res_ricker_local,paste(resloc,"res_ricker_local.RDS",sep=""))
# For global dispersion
res_ricker_global<-c()
for(r in rlist){
#cat("r=",r,"\n")
params<-c(r,K)
ss<-varying_d(numsims=numsims,numsteps=numsteps,numlocs=numlocs,p0=K,params=params,ext_thrs=ext_thrs,
scl=scl,srho=srho,model=model,disp_everywhere=T,plotteron = F,resloc=resloc, getacf=F)
temp_mat<-cbind(ss$d_seq,ss$risk_xleft,ss$risk_xright,ss$risk_mleft,ss$risk_mright)
res_ricker_global<-abind(res_ricker_global,temp_mat,along = 3)
}
anm<-paste("r_",rlist,sep="")
cnm<-c("d","risk_xleft","risk_xright","risk_mleft","risk_mright")
dimnames(res_ricker_global)<-list(NULL,cnm,anm)
saveRDS(res_ricker_global,paste(resloc,"res_ricker_global.RDS",sep=""))
```
```{r fig_ricker_scl_1, echo=F, results="hide",cache=T, cache.extra=list(seed,res_ricker_local,res_ricker_global)}
pdf("./Results/common_legend_extreme_noise.pdf",height=1,width=12)
op<-par(fig = c(0, 1, 0, 1), oma = c(0, 0, 0, 0), mar = c(0, 0, 0, 0))
plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
legend("center", c("noise: extreme LTdep.","noise: extreme RTdep."), lty=c(1,1), pch=c(1,1),
col=c('red', 'blue'),x.intersp = 0.2,
cex = 2.5, xpd = TRUE, horiz = T, inset = c(0,0),
bty = "n")
par(op)
dev.off()
pdf("./Results/common_legend_moderate_noise.pdf",height=1,width=12)
op<-par(fig = c(0, 1, 0, 1), oma = c(0, 0, 0, 0), mar = c(0, 0, 0, 0))
plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
legend("center", c("noise: moderate LTdep.","noise: moderate RTdep."), lty=c(1,1), pch=c(1,1),
col=c('red', 'blue'),x.intersp = 0.2,
cex = 2.5, xpd = TRUE, horiz = T, inset = c(0,0),
bty = "n")
par(op)
dev.off()
pdf("./Results/common_legend_extreme_and_moderate_noise.pdf",height=1,width=12)
op<-par(fig = c(0, 1, 0, 1), oma = c(0, 0, 0, 0), mar = c(0, 0, 0, 0))
plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
legend("center", c("extreme LT,","moderate LT,", "moderate RT,","extreme RT"), lty=c(1,1), pch=c(1,1,1,1),
col=c('red', 'orange','skyblue','blue'),x.intersp = 0.1,
cex = 2.2, xpd = TRUE, horiz = T, inset = c(0,0),
bty = "n")
par(op)
dev.off()
#-------------------------------------- plot for extreme tail dep. noise ---------------------------------------
pdf(paste(resloc,"ricker_ext_risk_local_disp_extremenoise.pdf",sep=""),height=9,width=9)
#op<-par(mfrow=c(3,3),mar=c(5.2,4.2,1.2,6.2))
op<-par(mfrow=c(3,3),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_ricker_local)[3]){
#s<-res_ricker_local[,,i]
ss<-res_ricker_local[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_xleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_xright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
pdf(paste(resloc,"ricker_ext_risk_global_disp_extremenoise.pdf",sep=""),height=9,width=9)
op<-par(mfrow=c(3,3),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_ricker_global)[3]){
#ss<-res_ricker_global
ss<-res_ricker_global[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_xleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_xright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
#-------------------------------------- plot for moderate tail dep. noise --------------------------------------
pdf(paste(resloc,"ricker_ext_risk_local_disp_moderatenoise.pdf",sep=""),height=9,width=9)
op<-par(mfrow=c(3,3),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_ricker_local)[3]){
#s<-res_ricker_local[,,i]
ss<-res_ricker_local[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_mleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_mright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
pdf(paste(resloc,"ricker_ext_risk_global_disp_moderatenoise.pdf",sep=""),height=9,width=9)
op<-par(mfrow=c(3,3),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_ricker_global)[3]){
#ss<-res_ricker_global
ss<-res_ricker_global[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_mleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_mright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
#----------------------- plot for extreme and moderate tail dep. noise ---------------------------------------
pdf(paste(resloc,"ricker_ext_risk_local_disp_extreme_and_moderate_noise.pdf",sep=""),height=9,width=9)
#op<-par(mfrow=c(3,3),mar=c(5.2,4.2,1.2,6.2))
op<-par(mfrow=c(3,3),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_ricker_local)[3]){
#s<-res_ricker_local[,,i]
ss<-res_ricker_local[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_xleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_mleft,type="b",col="orange")
lines(ss$d,ss$risk_mright,type="b",col="skyblue")
lines(ss$d,ss$risk_xright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
pdf(paste(resloc,"ricker_ext_risk_global_disp_extreme_and_moderate_noise.pdf",sep=""),height=9,width=9)
op<-par(mfrow=c(3,3),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_ricker_global)[3]){
#ss<-res_ricker_global
ss<-res_ricker_global[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_xleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_mleft,type="b",col="orange")
lines(ss$d,ss$risk_mright,type="b",col="skyblue")
lines(ss$d,ss$risk_xright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
```
```{r fig_ricker_extrisk_d0_scl_1, echo=F,results="hide"}
set.seed(seed)
ricker_extrisk_d0<-readRDS(paste(resloc,"ricker_extrisk_d0.RDS",sep=""))
numsims<-10000
ricker_extrisk_d0$CI0.025xleft<-qbinom(p=0.025,size=numsims,prob=ricker_extrisk_d0$risk_xleft_d0)/numsims
ricker_extrisk_d0$CI0.975xleft<-qbinom(p=0.975,size=numsims,prob=ricker_extrisk_d0$risk_xleft_d0)/numsims
ricker_extrisk_d0$CI0.025xright<-qbinom(p=0.025,size=numsims,prob=ricker_extrisk_d0$risk_xright_d0)/numsims
ricker_extrisk_d0$CI0.975xright<-qbinom(p=0.975,size=numsims,prob=ricker_extrisk_d0$risk_xright_d0)/numsims
ricker_extrisk_d0$CI0.025mleft<-qbinom(p=0.025,size=numsims,prob=ricker_extrisk_d0$risk_mleft_d0)/numsims
ricker_extrisk_d0$CI0.975mleft<-qbinom(p=0.975,size=numsims,prob=ricker_extrisk_d0$risk_mleft_d0)/numsims
ricker_extrisk_d0$CI0.025mright<-qbinom(p=0.025,size=numsims,prob=ricker_extrisk_d0$risk_mright_d0)/numsims
ricker_extrisk_d0$CI0.975mright<-qbinom(p=0.975,size=numsims,prob=ricker_extrisk_d0$risk_mright_d0)/numsims
#-------------------------------------- plot for extreme tail dep. noise ---------------------------------------
pdf(paste(resloc,"ricker_extrisk_d0_extremenoise.pdf",sep=""),height=5,width=5)
op<-par(mar=c(5,4,1.5,1.5),mgp=c(2,0.7,0))
plot(ricker_extrisk_d0$r,ricker_extrisk_d0$risk_xleft_d0,col="red",type="b",
ylim=c(0,1),xlim = range(ricker_extrisk_d0$r),xlab="r",ylab="Extinction risk",cex.lab=2,cex.axis=1.5,pch=1)
arrows(x0=ricker_extrisk_d0$r,y0=ricker_extrisk_d0$CI0.025xleft,x1=ricker_extrisk_d0$r,y1=ricker_extrisk_d0$CI0.975xleft,
angle=90,length=0.1,col="red",code=3)
abline(v=rc_ricker,lty="dotted",col="black") #rc=1
lines(ricker_extrisk_d0$r,ricker_extrisk_d0$risk_xright_d0,col="blue",type="b",ylim=c(0,1),pch=1)
arrows(x0=ricker_extrisk_d0$r,y0=ricker_extrisk_d0$CI0.025xright,x1=ricker_extrisk_d0$r,
y1=ricker_extrisk_d0$CI0.975xright,angle=90,length=0.1,col="blue",code=3)
legend("topleft", legend=c("Ricker"), horiz=F, bty='n',cex=1.8)
mtext(paste0("K = ",K),side = 3, line=-16, adj=0.95, cex=1.8, col="black")
legend("bottomright",legend=bquote(sigma==.(scl)), horiz=F,bty='n',cex=1.8)
#legend("bottomright", legend=c("Ricker",paste0("K = ",K)), horiz=F, bty='n',cex=1.8)
par(op)
dev.off()
#-------------------------------------- plot for moderate tail dep. noise ---------------------------------------
pdf(paste(resloc,"ricker_extrisk_d0_moderatenoise.pdf",sep=""),height=5,width=5)
op<-par(mar=c(5,4,1.5,1.5),mgp=c(2,0.7,0))
plot(ricker_extrisk_d0$r,ricker_extrisk_d0$risk_mleft_d0,col="red",type="b",
ylim=c(0,1),xlim = range(ricker_extrisk_d0$r),xlab="r",ylab="Extinction risk",cex.lab=2,cex.axis=1.5,pch=1)
arrows(x0=ricker_extrisk_d0$r,y0=ricker_extrisk_d0$CI0.025mleft,x1=ricker_extrisk_d0$r,
y1=ricker_extrisk_d0$CI0.975mleft,angle=90,length=0.1,col="red",code=3)
abline(v=rc_ricker,lty="dotted",col="black") #rc=1
lines(ricker_extrisk_d0$r,ricker_extrisk_d0$risk_mright_d0,col="blue",type="b",ylim=c(0,1),pch=1)
arrows(x0=ricker_extrisk_d0$r,y0=ricker_extrisk_d0$CI0.025mright,
x1=ricker_extrisk_d0$r,y1=ricker_extrisk_d0$CI0.975mright,angle=90,length=0.1,col="blue",code=3)
legend("topleft", legend=c("Ricker"), horiz=F, bty='n',cex=1.8)
mtext(paste0("K = ",K),side = 3, line=-16, adj=0.95, cex=1.8, col="black")
legend("bottomright",legend=bquote(sigma==.(scl)), horiz=F,bty='n',cex=1.8)
#legend("bottomright", legend=c("Ricker",paste0("K = ",K)), horiz=F, bty='n',cex=1.8)
par(op)
dev.off()
#-------------------- plot for extreme and moderate tail dep. noise ---------------------------------------
pdf(paste(resloc,"ricker_extrisk_d0_extreme_and_moderate_noise.pdf",sep=""),height=5,width=5)
op<-par(mar=c(5,4,1.5,1.5),mgp=c(2,0.7,0))
plot(ricker_extrisk_d0$r,ricker_extrisk_d0$risk_xleft_d0,col="red",type="b",
ylim=c(0,1),xlim = range(ricker_extrisk_d0$r),xlab="r",ylab="Extinction risk",cex.lab=2,cex.axis=1.5,pch=1)
arrows(x0=ricker_extrisk_d0$r,y0=ricker_extrisk_d0$CI0.025xleft,x1=ricker_extrisk_d0$r,y1=ricker_extrisk_d0$CI0.975xleft,
angle=90,length=0.1,col="red",code=3)
abline(v=rc_ricker,lty="dotted",col="black") #rc=1
lines(ricker_extrisk_d0$r,ricker_extrisk_d0$risk_mleft_d0,col="orange",type="b",ylim=c(0,1),pch=1)
arrows(x0=ricker_extrisk_d0$r,y0=ricker_extrisk_d0$CI0.025mleft,
x1=ricker_extrisk_d0$r,y1=ricker_extrisk_d0$CI0.975mleft,angle=90,length=0.1,col="orange",code=3)
lines(ricker_extrisk_d0$r,ricker_extrisk_d0$risk_mright_d0,col="skyblue",type="b",ylim=c(0,1),pch=1)
arrows(x0=ricker_extrisk_d0$r,y0=ricker_extrisk_d0$CI0.025mright,
x1=ricker_extrisk_d0$r,y1=ricker_extrisk_d0$CI0.975mright,angle=90,length=0.1,col="skyblue",code=3)
lines(ricker_extrisk_d0$r,ricker_extrisk_d0$risk_xright_d0,col="blue",type="b",ylim=c(0,1),pch=1)
arrows(x0=ricker_extrisk_d0$r,y0=ricker_extrisk_d0$CI0.025xright,
x1=ricker_extrisk_d0$r,y1=ricker_extrisk_d0$CI0.975xright,angle=90,length=0.1,col="blue",code=3)
legend("topleft", legend=c("Ricker"), horiz=F, bty='n',cex=1.8)
mtext(paste0("K = ",K),side = 3, line=-16, adj=0.95, cex=1.8, col="black")
legend("bottomright",legend=bquote(sigma==.(scl)), horiz=F,bty='n',cex=1.8)
par(op)
dev.off()
```
```{r sim_hassell_scl_1, echo=F, cache=T, cache.extra=list(seed,srho_common,mtime("mydispersal.R"),mtime("ExtremeTailDep.R"))}
set.seed(seed)
source("mydispersal.R")
model<-"hassell"
numsims<-10000
numsteps<-25
numlocs<-5
a<-0.5
b<-100
scl<-1
srho<-srho_common
tempo<-paste("./Results/",model,"_scl_",scl,sep="")
if (!dir.exists(tempo)){
dir.create(tempo)
}
resloc<-paste(tempo,"/",sep="")
rc_hassell<-((b/(b-1)))^b # transition from under to overcompensatory dynamics
r_bf_hassell<- ((b/(b-2)))^b # bifurcation parameter stable to unstable eqm
rng1<-runif(10000,min=1,max=r_bf_hassell) # r must be > 1
qr1<-quantile(rng1,probs=c(.025,.975))
q1<-abs(unname(qr1[1])-rc_hassell)
q2<-abs(unname(qr1[2])-rc_hassell)
qs<-c(q1,q2)
iqmin<-which.min(qs)
iqmax<-which.max(qs)
fromr<-range(qr1)[iqmin]
tor<-range(qr1)[iqmax]
if(fromr>tor){
byr<--qs[iqmin]/4
}else{
byr<-qs[iqmin]/4
}
rlist<-sort(seq(from=fromr,to=tor, by = byr))
xx<-diff(rlist)
vxx<-var(xx)
if(vxx>1e-10){
warning("Not equal spacing in rlist : Hassell model !!!",immediate.=T,call.=T)
}
hassell_extrisk_d0<-data.frame(rlist,NA*numeric(length(rlist)),NA*numeric(length(rlist)),
NA*numeric(length(rlist)),NA*numeric(length(rlist))) #initiate a dataframe to store
# ext risk at dispersal d=0 for all r
colnames(hassell_extrisk_d0)<-c("r","risk_xleft_d0","risk_xright_d0","risk_mleft_d0","risk_mright_d0")
res_hassell_local<-c()
for(i in c(1:length(rlist))){
r<- rlist[i]
K_e<-((r^(1/b))-1)/a
ext_thrs<-K_e/10
params<-c(r,a,b)
ss<-varying_d(numsims=numsims,numsteps=numsteps,numlocs=numlocs,p0=K_e,params=params,ext_thrs=ext_thrs,
scl=scl,srho=srho,model=model,disp_everywhere=F,plotteron = F,resloc=resloc, getacf=F)
temp_mat<-cbind(ss$d_seq,ss$risk_xleft,ss$risk_xright,ss$risk_mleft,ss$risk_mright)
res_hassell_local<-abind(res_hassell_local,temp_mat,along = 3)
hassell_extrisk_d0$risk_xleft_d0[i]<-ss$risk_xleft[1]
hassell_extrisk_d0$risk_xright_d0[i]<-ss$risk_xright[1]
hassell_extrisk_d0$risk_mleft_d0[i]<-ss$risk_mleft[1]
hassell_extrisk_d0$risk_mright_d0[i]<-ss$risk_mright[1]
}
anm<-paste("r_",rlist,sep="")
cnm<-c("d","risk_xleft","risk_xright","risk_mleft","risk_mright")
dimnames(res_hassell_local)<-list(NULL,cnm,anm)
saveRDS(hassell_extrisk_d0,paste(resloc,"hassell_extrisk_d0.RDS",sep=""))
saveRDS(res_hassell_local,paste(resloc,"res_hassell_local.RDS",sep=""))
# For global dispersion
res_hassell_global<-c()
for(r in rlist){
#cat("r=",r,"\n")
K_e<-((r^(1/b))-1)/a
ext_thrs<-K_e/10
params<-c(r,a,b)
ss<-varying_d(numsims=numsims,numsteps=numsteps,numlocs=numlocs,p0=K_e,params=params,ext_thrs=ext_thrs,
scl=scl,srho=srho,model=model,disp_everywhere=T,plotteron = F,resloc=resloc, getacf=F)
temp_mat<-cbind(ss$d_seq,ss$risk_xleft,ss$risk_xright,ss$risk_mleft,ss$risk_mright)
res_hassell_global<-abind(res_hassell_global,temp_mat,along = 3)
}
anm<-paste("r_",rlist,sep="")
cnm<-c("d","risk_xleft","risk_xright","risk_mleft","risk_mright")
dimnames(res_hassell_global)<-list(NULL,cnm,anm)
saveRDS(res_hassell_global,paste(resloc,"res_hassell_global.RDS",sep=""))
```
```{r fig_hassell_scl_1, echo=F, results="hide",cache=T, cache.extra=list(seed,res_hassell_local,res_hassell_global)}
#-------------------------------------- plot for extreme tail dep. noise ---------------------------------------
pdf(paste(resloc,"hassell_ext_risk_local_disp_extremenoise.pdf",sep=""),height=12,width=12)
op<-par(mfrow=c(4,4),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_hassell_local)[3]){
ss<-res_hassell_local[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_xleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_xright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
pdf(paste(resloc,"hassell_ext_risk_global_disp_extremenoise.pdf",sep=""),height=12,width=12)
op<-par(mfrow=c(4,4),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_hassell_global)[3]){
ss<-res_hassell_global[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_xleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_xright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
#-------------------------------------- plot for moderate tail dep. noise ---------------------------------------
pdf(paste(resloc,"hassell_ext_risk_local_disp_moderatenoise.pdf",sep=""),height=12,width=12)
op<-par(mfrow=c(4,4),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_hassell_local)[3]){
ss<-res_hassell_local[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_mleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_mright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
pdf(paste(resloc,"hassell_ext_risk_global_disp_moderatenoise.pdf",sep=""),height=12,width=12)
op<-par(mfrow=c(4,4),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_hassell_global)[3]){
ss<-res_hassell_global[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_mleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_mright,type="b",col="blue")
#legend("bottomleft", c("noise : left","noise : right"), lty=c(1,1), pch=c(1,1),
# col=c('red', 'blue'), horiz=T, bty='n', cex=1.2)
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
#----------------------- plot for extreme and moderate tail dep. noise --------------------------------------
pdf(paste(resloc,"hassell_ext_risk_local_disp_extreme_and_moderate_noise.pdf",sep=""),height=12,width=12)
op<-par(mfrow=c(4,4),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_hassell_local)[3]){
ss<-res_hassell_local[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_xleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_mleft,type="b",col="orange")
lines(ss$d,ss$risk_mright,type="b",col="skyblue")
lines(ss$d,ss$risk_xright,type="b",col="blue")
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
pdf(paste(resloc,"hassell_ext_risk_global_disp_extreme_and_moderate_noise.pdf",sep=""),height=12,width=12)
op<-par(mfrow=c(4,4),mar=c(5,4,1.5,1.5),mgp=c(2,0.5,0))
for(i in 1:dim(res_hassell_global)[3]){
ss<-res_hassell_global[,,i][1:6,] # plot for d in range (0 to 0.5)
ss<-as.data.frame(ss)
plot(ss$d,ss$risk_xleft,xlim=range(ss$d),ylim=c(0,1),type="b",col="red",
#panel.first = grid(),
xlab="d",ylab="Extinction risk",cex.lab=2,cex.axis=1.5)
lines(ss$d,ss$risk_mleft,type="b",col="orange")
lines(ss$d,ss$risk_mright,type="b",col="skyblue")
lines(ss$d,ss$risk_xright,type="b",col="blue")
mtext(paste0("r = ", round(rlist[i],5)),cex=1.2)
}
par(op)
dev.off()
```
```{r fig_hassell_extrisk_d0_scl_1, echo=F,results="hide"}
set.seed(seed)
numsims<-10000
hassell_extrisk_d0<-readRDS(paste(resloc,"hassell_extrisk_d0.RDS",sep=""))
hassell_extrisk_d0$CI0.025xleft<-qbinom(p=0.025,size=numsims,prob=hassell_extrisk_d0$risk_xleft_d0)/numsims
hassell_extrisk_d0$CI0.975xleft<-qbinom(p=0.975,size=numsims,prob=hassell_extrisk_d0$risk_xleft_d0)/numsims
hassell_extrisk_d0$CI0.025xright<-qbinom(p=0.025,size=numsims,prob=hassell_extrisk_d0$risk_xright_d0)/numsims
hassell_extrisk_d0$CI0.975xright<-qbinom(p=0.975,size=numsims,prob=hassell_extrisk_d0$risk_xright_d0)/numsims