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Translated computePopulationLogml

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Waldir Leoncio 2020-10-19 14:07:12 +02:00
parent 88e22fe00a
commit d3c217c316
1 changed files with 0 additions and 48 deletions
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48
R/indMix.R
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@ -678,24 +678,6 @@ indMix <- function(c, npops, dispText) {
# %------------------------------------------------------------------------------------ # %------------------------------------------------------------------------------------
# function popLogml = computePopulationLogml(pops, adjprior, priorTerm)
# % Palauttaa length(pops)*1 taulukon, jossa on laskettu korikohtaiset
# % logml:t koreille, jotka on m<><6D>ritelty pops-muuttujalla.
# global COUNTS;
# global SUMCOUNTS;
# x = size(COUNTS,1);
# y = size(COUNTS,2);
# z = length(pops);
# popLogml = ...
# squeeze(sum(sum(reshape(...
# gammaln(repmat(adjprior,[1 1 length(pops)]) + COUNTS(:,:,pops)) ...
# ,[x y z]),1),2)) - sum(gammaln(1+SUMCOUNTS(pops,:)),2) - priorTerm;
# %--------------------------------------------------------------------------
# function [muutokset, diffInCounts] = ... # function [muutokset, diffInCounts] = ...
# laskeMuutokset(ind, globalRows, data, adjprior, priorTerm) # laskeMuutokset(ind, globalRows, data, adjprior, priorTerm)
# % Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik<69> olisi # % Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik<69> olisi
@ -1209,36 +1191,6 @@ indMix <- function(c, npops, dispText) {
# %-------------------------------------------------------------------------- # %--------------------------------------------------------------------------
# function [sumcounts, counts, logml] = ...
# initialCounts(partition, data, npops, rows, noalle, adjprior)
# nloci=size(data,2);
# ninds = size(rows, 1);
# koot = rows(:,1) - rows(:,2) + 1;
# maxSize = max(koot);
# counts = zeros(max(noalle),nloci,npops);
# sumcounts = zeros(npops,nloci);
# for i=1:npops
# for j=1:nloci
# havainnotLokuksessa = find(partition==i & data(:,j)>=0);
# sumcounts(i,j) = length(havainnotLokuksessa);
# for k=1:noalle(j)
# alleleCode = k;
# N_ijk = length(find(data(havainnotLokuksessa,j)==alleleCode));
# counts(k,j,i) = N_ijk;
# end
# end
# end
# %initializeGammaln(ninds, maxSize, max(noalle));
# logml = laskeLoggis(counts, sumcounts, adjprior);
# %--------------------------------------------------------------------------
# function [partitionSummary, added] = addToSummary(logml, partitionSummary, worstIndex) # function [partitionSummary, added] = addToSummary(logml, partitionSummary, worstIndex)
# % Tiedet<65><74>n, ett<74> annettu logml on isompi kuin huonoin arvo # % Tiedet<65><74>n, ett<74> annettu logml on isompi kuin huonoin arvo
# % partitionSummary taulukossa. Jos partitionSummary:ss<73> ei viel<65> ole # % partitionSummary taulukossa. Jos partitionSummary:ss<73> ei viel<65> ole