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Rapfish Execution.r

This document contains code for running the RAPFish model, which produces sustainability scores and plots for fisheries across multiple disciplines. It loads fisheries data and anchor points for each discipline, scales the data, generates jpeg plots and csv output files for each discipline, and produces radar plots of the sustainability scores for groups of fisheries. The code executes the core RAPFish functions to analyze fishery sustainability across ecological, economic, ethical, institutional, social, and technological dimensions.

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Cecilia Fauziah
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63 views2 pages

Rapfish Execution.r

This document contains code for running the RAPFish model, which produces sustainability scores and plots for fisheries across multiple disciplines. It loads fisheries data and anchor points for each discipline, scales the data, generates jpeg plots and csv output files for each discipline, and produces radar plots of the sustainability scores for groups of fisheries. The code executes the core RAPFish functions to analyze fishery sustainability across ecological, economic, ethical, institutional, social, and technological dimensions.

Uploaded by

Cecilia Fauziah
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as TXT, PDF, TXT or read online on Scribd
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# 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.")

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