library(netZ)
datanamelist <- c('pm10688190','pm10900456','pm11283351','pm11805826','pm11805837','pm12052880','pm12150911','pm14574415','pm14660704','pm14759368','pm16093310','pm16319894','pm16429126','pm16554755','pm17200106','pm17634282')#
#
data(list=datanamelist)#
#
#Only initialise after running above.#
datalist <- list(pm10688190,pm10900456,pm11283351,pm11805826,pm11805837,pm12052880,pm12150911,pm14574415,pm14660704,pm14759368,pm16093310,pm16319894,pm16429126,pm16554755,pm17200106,pm17634282)#
#
#parrand=c(0.1,100),parexp=c(0.05,1),parpow=c(1.01,20),parlnorm=c(20,20),parstrexp=c(0.5,10)#
count <- 0#
direct <- '/Users/liam/Desktop/BMN_templates/example-output/'#
pngd <- 600#
for(net in datalist){#
	count <- count + 1#
	file <- datanamelist[count]#
	print(file)#
	outfile <- paste(direct,file,sep="")#
#
	netdeg <- degseq(net)#
	netlike <- mmi.likelihoods(net)#
	print("Likelihoods complete")#
	netakaike <- mmi.akaike(netlike,mmi=TRUE)#
	#netakaike <- mmi.akaike(netdeg$degree,degree=TRUE)#
	print("Akaike weights complete")#
#
	#out<-paste(outfile,'-freqrank.pdf',sep='')#
	out<-paste(outfile,'-freqrank.png',sep='')#
	print(out)#
	png(file=out, height=pngd,width=2*pngd,bg="white")#
	#pdf(file=out)#
	plot.freqrank(netdeg$degree,freq=TRUE)#
	dev.off()	#
#
	#out<-paste(outfile,'-modelfreqrank.pdf',sep='')#
	out<-paste(outfile,'-modelfreqrank.png',sep='')#
	print(out)#
	#pdf(file=out)#
	png(file=out, height=pngd,width=2*pngd,bg="white")#
	par(mfcol=c(1,2))#
	plot.modelfreq(net, netlike,title="")#
	plot.modelrank(net, netlike,title="")#
	par(mfcol=c(1,1))#
	dev.off()	#
#
	#out<-paste(outfile,'-modelsummary.pdf',sep='')#
	out<-paste(outfile,'-modelsummary.png',sep='')#
	print(out)#
	#pdf(file=out)#
	png(file=out, height=2*pngd,width=2*pngd,bg="white")#
	plot.modelsummary(netlike)#
	dev.off()	#
#
	#out<-paste(outfile,'-degreesequences.pdf',sep='')#
	out<-paste(outfile,'-degreesequences.png',sep='')#
	print(out)#
	#pdf(file=out)#
	png(file=out, height=2*pngd,width=3*pngd,bg="white")#
	plot.degreesequences(netlike,netakaike,netdeg)#
	dev.off()	#
	}
datanamelist <- c('pm10688190','pm10900456','pm11283351','pm11805826','pm11805837','pm12052880','pm12150911','pm14574415','pm14660704','pm14759368','pm16093310','pm16319894','pm16429126','pm16554755','pm17200106','pm17634282')#
#
data(list=datanamelist)#
#
#Only initialise after running above.#
datalist <- list(pm10688190,pm10900456,pm11283351,pm11805826,pm11805837,pm12052880,pm12150911,pm14574415,pm14660704,pm14759368,pm16093310,pm16319894,pm16429126,pm16554755,pm17200106,pm17634282)#
#
#parrand=c(0.1,100),parexp=c(0.05,1),parpow=c(1.01,20),parlnorm=c(20,20),parstrexp=c(0.5,10)#
count <- 0#
direct <- '/Users/liam/Desktop/BMN_templates/example-output/'#
pngd <- 450#
for(net in datalist){#
	count <- count + 1#
	file <- datanamelist[count]#
	print(file)#
	outfile <- paste(direct,file,sep="")#
#
	netdeg <- degseq(net)#
	netlike <- mmi.likelihoods(net)#
	print("Likelihoods complete")#
	netakaike <- mmi.akaike(netlike,mmi=TRUE)#
	#netakaike <- mmi.akaike(netdeg$degree,degree=TRUE)#
	print("Akaike weights complete")#
#
	#out<-paste(outfile,'-freqrank.pdf',sep='')#
	out<-paste(outfile,'-freqrank.png',sep='')#
	print(out)#
	png(file=out, height=pngd,width=2*pngd,bg="white")#
	#pdf(file=out)#
	plot.freqrank(netdeg$degree,freq=TRUE)#
	dev.off()	#
#
	#out<-paste(outfile,'-modelfreqrank.pdf',sep='')#
	out<-paste(outfile,'-modelfreqrank.png',sep='')#
	print(out)#
	#pdf(file=out)#
	png(file=out, height=pngd,width=2*pngd,bg="white")#
	par(mfcol=c(1,2))#
	plot.modelfreq(net, netlike,title="")#
	plot.modelrank(net, netlike,title="")#
	par(mfcol=c(1,1))#
	dev.off()	#
#
	#out<-paste(outfile,'-modelsummary.pdf',sep='')#
	out<-paste(outfile,'-modelsummary.png',sep='')#
	print(out)#
	#pdf(file=out)#
	png(file=out, height=2*pngd,width=2*pngd,bg="white")#
	plot.modelsummary(netlike)#
	dev.off()	#
#
	#out<-paste(outfile,'-degreesequences.pdf',sep='')#
	out<-paste(outfile,'-degreesequences.png',sep='')#
	print(out)#
	#pdf(file=out)#
	png(file=out, height=2*pngd,width=3*pngd,bg="white")#
	plot.degreesequences(netlike,netakaike,netdeg)#
	dev.off()	#
	}
library(netZ)
demo(Y2H)
Y2Hdeg
Y2Hlike
Y2H
length(Y2H[1,])
length(Y2H[,1])
Y2Hlike$dseq
Y2Hlike$samples
Y2Hlike$sample
Y2Hlike
