Improved docs

R/admix1.R

@@ -350,54 +350,4 @@ admix1 <- function(tietue) {
 #             save([pathname filename], 'tietue', '-v7.3'); # added by Lu Cheng, 08.06.2012
 #         end
 #     end
-}
-
-
-# function [npops] = poistaLiianPienet(npops, rowsFromInd, alaraja)
-# % Muokkaa tulokset muotoon, jossa outlier yksilöt on
-# % poistettu. Tarkalleen ottaen poistaa ne populaatiot,
-# % joissa on vähemmän kuin 'alaraja':n verran yksilöit?
-
-# global PARTITION;
-# global COUNTS;
-# global SUMCOUNTS;
-
-# popSize=zeros(1,npops);
-# for i=1:npops
-#     popSize(i)=length(find(PARTITION==i));
-# end
-# miniPops = find(popSize<alaraja);
-
-# if length(miniPops)==0
-#     return;
-# end
-
-# outliers = [];
-# for pop = miniPops
-#     inds = find(PARTITION==pop);
-#     disp('Removed individuals: ');
-#     disp(num2str(inds));
-#     outliers = [outliers; inds];
-# end
-
-# ninds = length(PARTITION);
-# PARTITION(outliers) = 0;
-# korit = unique(PARTITION(find(PARTITION>0)));
-# for n=1:length(korit)
-#     kori = korit(n);
-#     yksilot = find(PARTITION==kori);
-#     PARTITION(yksilot) = n;
-# end
-# COUNTS(:,:,miniPops) = [];
-# SUMCOUNTS(miniPops,:) = [];
-
-# npops = npops-length(miniPops);
-
-# %------------------------------------------------------------------------
-
-# function clearGlobalVars
-
-# global COUNTS; COUNTS = [];
-# global SUMCOUNTS; SUMCOUNTS = [];
-# global PARTITION; PARTITION = [];
-# global POP_LOGML; POP_LOGML = [];
+}

man/computeAllFreqs2.Rd

@@ -4,7 +4,7 @@
 \alias{computeAllFreqs2}
 \title{Compute all freqs - version 2}
 \usage{
-computeAllFreqs2(noalle, COUNTS = matrix(NA, 0, 0), SUMCOUNTS = sum(COUNTS))
+computeAllFreqs2(noalle, COUNTS = matrix(NA, 0, 0), SUMCOUNTS = NA)
 }
 \arguments{
 \item{noalle}{noalle}

man/repmat.Rd

@@ -9,7 +9,8 @@ repmat(mx, n)
 \arguments{
 \item{mx}{matrix}
 
-\item{n}{either a scalar with the number of replications in both rows and columns or a 2-length vector with individual repetitions.}
+\item{n}{either a scalar with the number of replications in both rows and
+columns or a <= 3-length vector with individual repetitions.}
 }
 \value{
 matrix replicated over `ncol(mx) * n` columns and `nrow(mx) * n` rows