#'
#'
get.index.mat<- function(x, cv, neff, first.year, nyears, catch.ages, survey.ages) {
n.ages = length(catch.ages)
last.yr <- first.year+nyears - 1
tmp.yrs <- as.numeric(rownames(x))
all.years = first.year-1 + 1:nyears
years.use.ind = which(tmp.yrs %in% all.years)
#if (tmp.yrs[length(tmp.yrs)]>last.yr) tmp.yrs <- tmp.yrs[-which(tmp.yrs>last.yr)]
tmp.ages <- as.numeric(colnames(x))
tmp.ages = catch.ages
survey.ages.index = which(catch.ages %in% survey.ages)
i.mat <- matrix(0, nyears, (n.ages + 4))
i.mat[,1] <- all.years
rownames(x) <- c()
colnames(x) <- c()
x[is.na(x)] <- 0
print(dim(x))
print(dim(i.mat))
print(survey.ages.index)
print(tmp.yrs)
print(sum(all.years %in% tmp.yrs))
print(all.years)
print(x)
tmp.ind.total <- apply(x[years.use.ind,], 1, sum)
i.mat.ind = which(all.years %in% tmp.yrs[years.use.ind])
i.mat[i.mat.ind,2:3] <- cbind(tmp.ind.total, rep(cv, length(years.use.ind)))
i.mat[i.mat.ind, (3+survey.ages.index)] <- x[years.use.ind,]
i.mat[i.mat.ind, (n.ages+4)] <- rep(neff, length(years.use.ind))
return(i.mat)
}
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