diff --git a/R/initialPopCounts.R b/R/initialPopCounts.R index 883fa80..a865243 100644 --- a/R/initialPopCounts.R +++ b/R/initialPopCounts.R @@ -1,22 +1,20 @@ initialPopCounts <- function(data, npops, rows, noalle, adjprior) { - # nloci=size(data,2) - # counts <- zeros(max(noalle),nloci,npops) - # sumcounts <- zeros(npops,nloci) - - # for (i in 1:npops) { - # for (j in 1:nloci) { - # i_rivit <- rows(i,1):rows(i,2) - # havainnotLokuksessa <- find(data(i_rivit,j)>=0) - # sumcounts(i,j) <- length(havainnotLokuksessa) - # for (k in 1:noalle(j)) { - # alleleCode <- k - # N_ijk <- length(find(data(i_rivit,j)==alleleCode)) - # counts(k,j,i) <- N_ijk - # } - # } - # } - - # logml <- laskeLoggis(counts, sumcounts, adjprior) + nloci <- size(data, 2) + counts <- zeros(max(noalle), nloci, npops) + sumcounts <- zeros(npops, nloci) + for (i in 1:npops) { + for (j in 1:nloci) { + i_rivit <- rows(i, 1):rows(i, 2) + havainnotLokuksessa <- find(data(i_rivit, j) >= 0) + sumcounts(i, j) <- length(havainnotLokuksessa) + for (k in 1:noalle[j]) { + alleleCode <- k + N_ijk <- length(find(data(i_rivit, j) == alleleCode)) + counts(k, j, i) <- N_ijk + } + } + } + logml <- laskeLoggis(counts, sumcounts, adjprior) return(sumcounts = sumcounts, counts = counts, logml = logml) }