# RAPFish - Rapid Assessment of Fishery Sustaintability

# # for local execution in R

#produces Rapfish Scores plots, radar plots, and writes the results to csv files
#
# 2012-04-15 Divya Varkey Created from Ken's main function for final execution
# of all subsidiary Rapfish functions in
rapfish_function.r

source("rapfish_functions.R")

#to be obtained from site

num_fish=12
anchor_files=c('anchors4.csv','anchors5.csv','anchors6.csv','anchors7.csv',
'anchors8.csv','anchors9.csv','anchors10.csv','anchors11.csv','anchors12.csv')
filenames=c('HG_Ecology.csv','HG_Economics.csv','HG_Ethical.csv',
'HG_Institutional.csv','HG_Social.csv','HG_Technology.csv')
nfield=length(filenames)

print("Starting...")

discipline.names =strsplit(filenames, ".csv")

sustainability=matrix(data=0,nrow=num_fish,ncol=nfield)

n_radar=round(num_fish/10,0)
p1_radar=seq(1,n_radar*10,by=10)
p2_radar=p1_radar
p2_radar[1:(n_radar-1)]=p1_radar[2:n_radar]-1
p2_radar[n_radar]=num_fish

# ----MAIN--------------------------------------------------

for(i in 1:nfield) {
fisheries.all = loaddata(filenames[i])
n_att=ncol(fisheries.all)
anchors=loaddata(anchor_files[n_att-3])
n_an=nrow(anchors)

colnames(anchors)<-colnames(fisheries.all)
fisheries.dat=fisheries.all[1:num_fish,]
fisheries.raw=rbind(anchors,fisheries.dat)
fisheries.scaled = mdscale(fisheries.raw)

f_images=paste(discipline.names,".jpg",sep="")
jpeg(filename=f_images[i],width=20,height=16,units="cm",res=500)

Res=ifelse(nfield>30,
RAPplot1(fisheries.scaled,num_fish,n_an),
RAPplot2(fisheries.scaled,num_fish,n_an))

mtext(side=3, line=1, discipline.names[i],adj=0)

dev.off()
resfiles=paste("Results_",discipline.names,".csv",sep="")
write.csv(fisheries.scaled[(n_an+1):nrow(fisheries.scaled),],resfiles[i])

sustainability[,i]= fisheries.scaled[(n_an+1):nrow(fisheries.scaled),1]
}
rownames(sustainability)<-rownames(fisheries.dat)
colnames(sustainability)<-discipline.names

#Radar plots
for(i in 1:n_radar) {
f_images=paste("Radar_",seq(1,n_radar),".jpg",sep="")
jpeg(filename=f_images[i],width=20,height=16,units="cm",res=500)
radarplot(sustainability[p1_radar[i]:p2_radar[i],])
dev.off()
}

print("Complete.")