From f405cabeb211556416038aec39c46d8d0193d8af Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Mon, 9 Nov 2020 15:22:22 +0100
Subject: [PATCH] Removed commented out code

---
 R/indMix.R | 95 ------------------------------------------------------
 1 file changed, 95 deletions(-)

diff --git a/R/indMix.R b/R/indMix.R
index a070ce5..6b11bf9 100644
--- a/R/indMix.R
+++ b/R/indMix.R
@@ -565,98 +565,3 @@ indMix <- function(c, npops, dispText) {
 		list(logml = logml, npops = npops, partitionSummary = partitionSummary)
 	)
 }
-
-# %-----------------------------------------------------------------------
-
-
-# function [sumcounts, counts, logml] = ...
-#     initialPopCounts(data, npops, rows, noalle, adjprior)
-
-# nloci=size(data,2);
-# counts = zeros(max(noalle),nloci,npops);
-# sumcounts = zeros(npops,nloci);
-
-# for i=1:npops
-#     for j=1:nloci
-#         i_rivit = rows(i,1):rows(i,2);
-#         havainnotLokuksessa = find(data(i_rivit,j)>=0);
-#         sumcounts(i,j) = length(havainnotLokuksessa);
-#         for k=1:noalle(j)
-#             alleleCode = k;
-#             N_ijk = length(find(data(i_rivit,j)==alleleCode));
-#             counts(k,j,i) = N_ijk;
-#         end
-#     end
-# end
-
-# logml = laskeLoggis(counts, sumcounts, adjprior);
-
-# %-----------------------------------------------------------------------
-
-
-# function diffInCounts = computeDiffInCounts(rows, max_noalle, nloci, data)
-# % Muodostaa max_noalle*nloci taulukon, jossa on niiden alleelien
-# % lukum��r�t (vastaavasti kuin COUNTS:issa), jotka ovat data:n
-# % riveill� rows. rows pit�� olla vaakavektori.
-
-# diffInCounts = zeros(max_noalle, nloci);
-# for i=rows
-#     row = data(i,:);
-#     notEmpty = find(row>=0);
-
-#     if length(notEmpty)>0
-#         diffInCounts(row(notEmpty) + (notEmpty-1)*max_noalle) = ...
-#             diffInCounts(row(notEmpty) + (notEmpty-1)*max_noalle) + 1;
-#     end
-# end
-
-# %---------------------------------------------------------
-
-# function T = cluster_own(Z,nclust)
-# true=logical(1);
-# false=logical(0);
-# maxclust = nclust;
-# % Start of algorithm
-# m = size(Z,1)+1;
-# T = zeros(m,1);
-#    % maximum number of clusters based on inconsistency
-#    if m <= maxclust
-#       T = (1:m)';
-#    elseif maxclust==1
-#       T = ones(m,1);
-#    else
-#       clsnum = 1;
-#       for k = (m-maxclust+1):(m-1)
-#          i = Z(k,1); % left tree
-#          if i <= m % original node, no leafs
-#             T(i) = clsnum;
-#             clsnum = clsnum + 1;
-#          elseif i < (2*m-maxclust+1) % created before cutoff, search down the tree
-#             T = clusternum(Z, T, i-m, clsnum);
-#             clsnum = clsnum + 1;
-#          end
-#          i = Z(k,2); % right tree
-#          if i <= m  % original node, no leafs
-#             T(i) = clsnum;
-#             clsnum = clsnum + 1;
-#          elseif i < (2*m-maxclust+1) % created before cutoff, search down the tree
-#             T = clusternum(Z, T, i-m, clsnum);
-#             clsnum = clsnum + 1;
-#          end
-#       end
-#    end
-
-# function T = clusternum(X, T, k, c)
-# m = size(X,1)+1;
-# while(~isempty(k))
-#    % Get the children of nodes at this level
-#    children = X(k,1:2);
-#    children = children(:);
-
-#    % Assign this node number to leaf children
-#    t = (children<=m);
-#    T(children(t)) = c;
-
-#    % Move to next level
-#    k = children(~t) - m;
-# end