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Cleaned up code

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Corentin Choisy
2024-05-30 16:50:38 +02:00
parent 6086d74551
commit fd0d2de43f
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##############################################################################
#----------------------------------------------------------------------------#
################################# POWER PLOTS ################################
#----------------------------------------------------------------------------#
##############################################################################
## Plot 1 - baseline scenarios vs theoretical power
par(mfrow=c(1,2))
# theoretical
plot.dat <- res.dat[res.dat$scenario %in% sapply(c('A','B','C','D','E'),function(x) paste0(1:4,x)),]
plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),rep(unique(plot.dat[plot.dat$scenario.type=="A",]$theoretical.power),3),
xlab='N',ylab='Theoretical power',
xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a')
axis(1,c(100,200,300))
axis(2,seq(0,1,0.1))
lines(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$theoretical.power),col='#c6d18d',lty=4)
lines(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$theoretical.power),col='#c0c23b',lty=4)
lines(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$theoretical.power),col='#da77c7',lty=4)
lines(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$theoretical.power),col='#a12471',lty=4)
lines(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$theoretical.power),col='#b5a180',lty=4)
lines(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$theoretical.power),col='#9b6541',lty=4)
lines(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$theoretical.power),col='#30a466',lty=4)
lines(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$theoretical.power),col='#1a342b',lty=4)
points(unique(plot.dat[plot.dat$scenario %in% c("1A",'1A'),]$N),
rep(unique(plot.dat[plot.dat$scenario %in% c("1A",'1A'),]$theoretical.power),3),col='#03a18a',pch=17)
points(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$theoretical.power),col='#c6d18d',pch=17)
points(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$theoretical.power),col='#c0c23b',pch=17)
points(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$theoretical.power),col='#da77c7',pch=17)
points(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$theoretical.power),col='#a12471',pch=17)
points(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$theoretical.power),col='#b5a180',pch=17)
points(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$theoretical.power),col='#9b6541',pch=17)
points(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$theoretical.power),col='#30a466',pch=17)
points(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$theoretical.power),col='#1a342b',pch=17)
legend("topleft",lty=rep(4,5),col=c("#03a18a","#c0c23b","#a12471","#9b6541","#1a342b"),
pch=rep(17,5),
legend=c("Scenario A",
"Scenario 1-2 / B-D",
"Scenario 3-4 / B-D",
"Scenario 1-2 / C-E",
"Scenario 3-4 / C-E"),cex=0.7)
# real
plot.dat <- res.dat[res.dat$scenario %in% sapply(c('A','B','C','D','E'),function(x) paste0(1:4,x)),]
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario.type=="A" & plot.dat$N==x,]$h0.rejected.p))
plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
xlab='N',ylab='Proportion of null hypothesis rejection',
xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a')
axis(1,c(100,200,300))
axis(2,seq(0,1,0.1))
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("1B","1D") & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
mean.A,col='#c6d18d',lty=4)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("2B","2D") & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
mean.A,col='#c0c23b',lty=4)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("3B","3D") & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
mean.A,col='#da77c7',lty=4)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("4B","4D") & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
mean.A,col='#a12471',lty=4)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("1C","1E") & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
mean.A,col='#b5a180',lty=4)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("2C","2E") & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
mean.A,col='#9b6541',lty=4)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("3C","3E") & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
mean.A,col='#30a466',lty=4)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("4C","4E") & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
mean.A,col='#1a342b',lty=4)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario.type=="A" & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,pch=17,col='#03a18a')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("1B","1D") & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
mean.A,col='#c6d18d',pch=17)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("2B","2D") & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
mean.A,col='#c0c23b',pch=17)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("3B","3D") & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
mean.A,col='#da77c7',pch=17)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("4B","4D") & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
mean.A,col='#a12471',pch=17)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("1C","1E") & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
mean.A,col='#b5a180',pch=17)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("2C","2E") & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
mean.A,col='#9b6541',pch=17)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("3C","3E") & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
mean.A,col='#30a466',pch=17)
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("4C","4E") & plot.dat$N==x,]$h0.rejected.p))
points(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
mean.A,col='#1a342b',pch=17)
legend("topleft",lty=rep(4,5),col=c("#03a18a","#c0c23b","#a12471","#9b6541","#1a342b"),
pch=rep(17,5),
legend=c("Scenario A",
"Scenario 1-2 / B-D",
"Scenario 3-4 / B-D",
"Scenario 1-2 / C-E",
"Scenario 3-4 / C-E"),cex=0.7)
##############################################################################
#----------------------------------------------------------------------------#
################################# ALPHA PLOTS ################################
#----------------------------------------------------------------------------#
##############################################################################
par(mfrow=c(1,1))
#### Scenarios with J=4 / M=2
# A / H=0
plot.dat <- res.dat
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1A" & plot.dat$N==x,]$h0.rejected.p))
plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
xlab='N',ylab='Proportion of null hypothesis rejection',
xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a',main='Scenarios where H0 is TRUE')
axis(1,c(100,200,300))
axis(2,seq(0,1,0.1))
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#03a18a')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5A" & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#a12471')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7A" & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#9b6541')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9A" & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#1a342b')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11A" & plot.dat$N==x,]$h0.rejected.p))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#c0c23b')
##############################################################################
#----------------------------------------------------------------------------#
################################# BIAS PLOTS #################################
#----------------------------------------------------------------------------#
##############################################################################
par(mfrow=c(1,1))
#### Scenarios with J=4 / M=2
# A / H=0
plot.dat <- res.dat
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1A" & plot.dat$N==x,]$bias))
plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
xlab='N',ylab='Bias',
xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(-1,1),lty=4,col='#03a18a',main='Scenarios where H0 is TRUE')
axis(1,c(100,200,300))
axis(2,seq(0,1,0.1))
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#03a18a')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5A" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#a12471')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7A" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#9b6541')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9A" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#1a342b')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11A" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#c0c23b')
par(mfrow=c(1,1))
#### Scenarios with J=4 / M=2
# B/ H=0
plot.dat <- res.dat
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1B" & plot.dat$N==x,]$bias))
plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
xlab='N',ylab='Bias',
xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(-1,1),lty=4,col='#03a18a',main='Scenarios where H0 is TRUE')
axis(1,c(100,200,300))
axis(2,seq(0,1,0.1))
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#03a18a')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5B" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#a12471')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7B" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#9b6541')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9B" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#1a342b')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11B" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='#c0c23b')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5C" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='red')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='red')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7C" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='blue')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='blue')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9C" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='purple')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='purple')
mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11C" & plot.dat$N==x,]$bias))
lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='orange')
points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
pch=17,col='orange')