#file="/home/laurie/Desktop/ICCAT/SCRS/2012/bfte/VPA/2012/K2SM/2012/Reported/low/bfte2012.d1"
utils::globalVariables(c("variable","id."))
utils::globalVariables(c("read.table"))
utils::globalVariables(c("melt"))
utils::globalVariables(c("str_trim"))
utils::globalVariables(c("maply"))
utils::globalVariables(c("mlply"))
utils::globalVariables(c("llply"))
utils::globalVariables(c("ldply"))
iU2box = function(file,na.strings="NA") {
skip.hash=function(i) {
i=i+1
while (substr(scan(file,skip=i,nlines=1,what=("character"),quiet=TRUE)[1],1,1)=="#")
i=i+1
return(i)}
skip.until.minus.1=function(i) {
i=i+1
while (scan(file,skip=i,nlines=1,what=("character"),quiet=TRUE)[1]!="-1")
i=i+1
return(i)}
# range
range=numeric(5)
names(range)=c("min","max","plusgroup","minyear","maxyear")
i = skip.hash(0)
range[c("minyear", "maxyear")] = scan(file,skip = i, nlines = 1, nmax = 2, quiet = TRUE,na.strings=na.strings)
i = skip.hash(i)
range[c("min", "max", "plusgroup")] = scan(file,skip = i, nlines = 1, nmax = 3, quiet = TRUE,na.strings=na.strings)
i = skip.hash(i+1)
NIndex = scan(file,skip=i,nlines=1,nmax=1,quiet=TRUE)
i = skip.until.minus.1(i)
i = skip.hash(i)
smry. = array("",dim=c(NIndex,8))
j = numeric(1)
for (i in i:(i+NIndex-1)) {
j=j+1
smry.[j,]=scan(file,skip=i,nlines=1,nmax=8,quiet=TRUE,na.strings=na.strings,what=as.character())
}
i=skip.hash(i)
i=skip.hash(i)
index.=array(0,dim=c(skip.until.minus.1(i)-i, 4))
for (j in i:(skip.until.minus.1(i)-1))
index.[j-i+1,]=scan(file,skip=j,nlines=1,nmax=4,quiet=T,na.strings=na.strings,quiet=TRUE)
i=skip.until.minus.1(i)+1
if ((skip.until.minus.1(i)-i-3)>0)
p.=read.table(file,skip=i,fill=T,nrows=(skip.until.minus.1(i)-i-3),colClasses="numeric",na.strings=na.strings)
else p.=NULL
smry=as.data.frame(smry.[,-1])
dimnames(smry)=list(seq(NIndex),c("pdf","units","sel","timing","minage","maxage","index"))
smry[,"pdf"]=factor(c("do not use","lognormal","normal")[as.numeric(smry[,"pdf"])+1],
levels=c("do not use","lognormal","normal"))
smry[,"units"]=factor(c("numbers","biomass")[smry[,"units"]],
levels=c("numbers","biomass"))
smry[,"minage"]=as.numeric(as.character(smry[,"minage"]))
smry[,"maxage"]=as.numeric(as.character(smry[,"maxage"]))
smry[,"sel"]=factor(c("fixed","fractional","Powers and Restrepo","Butterworth and Geromont")[smry[,"sel"]],
levels=c("fixed","fractional","Powers and Restrepo","Butterworth and Geromont"))
# TIMING (-1 = AVERAGE DURING YEAR, POSITIVE INTEGER = NUMBER OF MONTHS ELAPSED)
smry[,"timing"]=as.numeric(as.character(smry[,"timing"]))
dimnames(index.)=list(NULL,c("index","year","cpue","cv"))
index.=as.data.frame(index.)
if (!is.null(p.)){
dimnames(p.)[[2]][1:2]=c("index","year")
p.=melt(p.,id=c("index","year"))
p.=transform(p.,age=(range[1]:range[2])[as.numeric(variable)])[,c("index","year","age","value")]
names(p.)[4]=c("fraction")
p. =p.[p.$index>=1,]
p.$index =smry[p.$index, "index"]
}
index.$index=smry[index.$index,"index"]
attributes(index.)$smry=smry
index.$cv[ index.$cv <0]=NA
index.$cpue[index.$cpue<0]=NA
names(index.)[1:4]=c("name","year","index","cv")
return(index.)}
#return(list(smry=smry,index=index.,fraction=p.))}
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