Translated poistaTyhjatPopulaatiot
This commit is contained in:
Waldir Leoncio
parent
e31dec2786
commit
7113162566
2 changed files with 16 additions and 185 deletions
186
R/indMix.R
186
R/indMix.R
|
|
@ -565,60 +565,6 @@ indMix <- function(c, npops, dispText) {
|
|||
list(logml = logml, npops = npops, partitionSummary = partitionSummary)
|
||||
)
|
||||
}
|
||||
# %--------------------------------------------------------------------------
|
||||
|
||||
|
||||
# function Z = linkage(Y, method)
|
||||
# [k, n] = size(Y);
|
||||
# m = (1+sqrt(1+8*n))/2;
|
||||
# if k ~= 1 | m ~= fix(m)
|
||||
# error('The first input has to match the output of the PDIST function in size.');
|
||||
# end
|
||||
# if nargin == 1 % set default switch to be 'co'
|
||||
# method = 'co';
|
||||
# end
|
||||
# method = lower(method(1:2)); % simplify the switch string.
|
||||
# monotonic = 1;
|
||||
# Z = zeros(m-1,3); % allocate the output matrix.
|
||||
# N = zeros(1,2*m-1);
|
||||
# N(1:m) = 1;
|
||||
# n = m; % since m is changing, we need to save m in n.
|
||||
# R = 1:n;
|
||||
# for s = 1:(n-1)
|
||||
# X = Y;
|
||||
# [v, k] = min(X);
|
||||
# i = floor(m+1/2-sqrt(m^2-m+1/4-2*(k-1)));
|
||||
# j = k - (i-1)*(m-i/2)+i;
|
||||
# Z(s,:) = [R(i) R(j) v]; % update one more row to the output matrix A
|
||||
# I1 = 1:(i-1); I2 = (i+1):(j-1); I3 = (j+1):m; % these are temp variables.
|
||||
# U = [I1 I2 I3];
|
||||
# I = [I1.*(m-(I1+1)/2)-m+i i*(m-(i+1)/2)-m+I2 i*(m-(i+1)/2)-m+I3];
|
||||
# J = [I1.*(m-(I1+1)/2)-m+j I2.*(m-(I2+1)/2)-m+j j*(m-(j+1)/2)-m+I3];
|
||||
|
||||
# switch method
|
||||
# case 'si' %single linkage
|
||||
# Y(I) = min(Y(I),Y(J));
|
||||
# case 'av' % average linkage
|
||||
# Y(I) = Y(I) + Y(J);
|
||||
# case 'co' %complete linkage
|
||||
# Y(I) = max(Y(I),Y(J));
|
||||
# case 'ce' % centroid linkage
|
||||
# K = N(R(i))+N(R(j));
|
||||
# Y(I) = (N(R(i)).*Y(I)+N(R(j)).*Y(J)-(N(R(i)).*N(R(j))*v^2)./K)./K;
|
||||
# case 'wa'
|
||||
# Y(I) = ((N(R(U))+N(R(i))).*Y(I) + (N(R(U))+N(R(j))).*Y(J) - ...
|
||||
# N(R(U))*v)./(N(R(i))+N(R(j))+N(R(U)));
|
||||
# end
|
||||
# J = [J i*(m-(i+1)/2)-m+j];
|
||||
# Y(J) = []; % no need for the cluster information about j.
|
||||
|
||||
# % update m, N, R
|
||||
# m = m-1;
|
||||
# N(n+s) = N(R(i)) + N(R(j));
|
||||
# R(i) = n+s;
|
||||
# R(j:(n-1))=R((j+1):n);
|
||||
# end
|
||||
|
||||
|
||||
# %-----------------------------------------------------------------------
|
||||
|
||||
|
|
@ -648,18 +594,6 @@ indMix <- function(c, npops, dispText) {
|
|||
# %-----------------------------------------------------------------------
|
||||
|
||||
|
||||
# function loggis = laskeLoggis(counts, sumcounts, adjprior)
|
||||
# npops = size(counts,3);
|
||||
|
||||
# logml2 = sum(sum(sum(gammaln(counts+repmat(adjprior,[1 1 npops]))))) ...
|
||||
# - npops*sum(sum(gammaln(adjprior))) - ...
|
||||
# sum(sum(gammaln(1+sumcounts)));
|
||||
# loggis = logml2;
|
||||
|
||||
|
||||
# %------------------------------------------------------------------------------------
|
||||
|
||||
|
||||
# function diffInCounts = computeDiffInCounts(rows, max_noalle, nloci, data)
|
||||
# % Muodostaa max_noalle*nloci taulukon, jossa on niiden alleelien
|
||||
# % lukum<75><6D>r<EFBFBD>t (vastaavasti kuin COUNTS:issa), jotka ovat data:n
|
||||
|
|
@ -720,110 +654,7 @@ indMix <- function(c, npops, dispText) {
|
|||
# end
|
||||
# npops = length(notEmpty);
|
||||
|
||||
|
||||
# %---------------------------------------------------------------
|
||||
|
||||
|
||||
# function dispLine;
|
||||
# disp('---------------------------------------------------');
|
||||
|
||||
# %--------------------------------------------------------------
|
||||
|
||||
# function num2 = omaRound(num)
|
||||
# % Py<50>rist<73><74> luvun num 1 desimaalin tarkkuuteen
|
||||
# num = num*10;
|
||||
# num = round(num);
|
||||
# num2 = num/10;
|
||||
|
||||
# %---------------------------------------------------------
|
||||
# function mjono = logml2String(logml)
|
||||
# % Palauttaa logml:n string-esityksen.
|
||||
|
||||
# mjono = ' ';
|
||||
# if abs(logml)<10000
|
||||
# %Ei tarvita e-muotoa
|
||||
# mjono(7) = palautaYks(abs(logml),-1);
|
||||
# mjono(6) = '.';
|
||||
# mjono(5) = palautaYks(abs(logml),0);
|
||||
# mjono(4) = palautaYks(abs(logml),1);
|
||||
# mjono(3) = palautaYks(abs(logml),2);
|
||||
# mjono(2) = palautaYks(abs(logml),3);
|
||||
# pointer = 2;
|
||||
# while mjono(pointer)=='0' & pointer<7
|
||||
# mjono(pointer) = ' ';
|
||||
# pointer=pointer+1;
|
||||
# end
|
||||
# if logml<0
|
||||
# mjono(pointer-1) = '-';
|
||||
# end
|
||||
# else
|
||||
# suurinYks = 4;
|
||||
# while abs(logml)/(10^(suurinYks+1)) >= 1
|
||||
# suurinYks = suurinYks+1;
|
||||
# end
|
||||
# if suurinYks<10
|
||||
# mjono(7) = num2str(suurinYks);
|
||||
# mjono(6) = 'e';
|
||||
# mjono(5) = palautaYks(abs(logml),suurinYks-1);
|
||||
# mjono(4) = '.';
|
||||
# mjono(3) = palautaYks(abs(logml),suurinYks);
|
||||
# if logml<0
|
||||
# mjono(2) = '-';
|
||||
# end
|
||||
# elseif suurinYks>=10
|
||||
# mjono(6:7) = num2str(suurinYks);
|
||||
# mjono(5) = 'e';
|
||||
# mjono(4) = palautaYks(abs(logml),suurinYks-1);
|
||||
# mjono(3) = '.';
|
||||
# mjono(2) = palautaYks(abs(logml),suurinYks);
|
||||
# if logml<0
|
||||
# mjono(1) = '-';
|
||||
# end
|
||||
# end
|
||||
# end
|
||||
|
||||
# function digit = palautaYks(num,yks)
|
||||
# % palauttaa luvun num 10^yks termin kertoimen
|
||||
# % string:in<69>
|
||||
# % yks t<>ytyy olla kokonaisluku, joka on
|
||||
# % v<>hint<6E><74>n -1:n suuruinen. Pienemmill<6C>
|
||||
# % luvuilla tapahtuu jokin py<70>ristysvirhe.
|
||||
|
||||
# if yks>=0
|
||||
# digit = rem(num, 10^(yks+1));
|
||||
# digit = floor(digit/(10^yks));
|
||||
# else
|
||||
# digit = num*10;
|
||||
# digit = floor(rem(digit,10));
|
||||
# end
|
||||
# digit = num2str(digit);
|
||||
|
||||
|
||||
# function mjono = kldiv2str(div)
|
||||
# mjono = ' ';
|
||||
# if abs(div)<100
|
||||
# %Ei tarvita e-muotoa
|
||||
# mjono(6) = num2str(rem(floor(div*1000),10));
|
||||
# mjono(5) = num2str(rem(floor(div*100),10));
|
||||
# mjono(4) = num2str(rem(floor(div*10),10));
|
||||
# mjono(3) = '.';
|
||||
# mjono(2) = num2str(rem(floor(div),10));
|
||||
# arvo = rem(floor(div/10),10);
|
||||
# if arvo>0
|
||||
# mjono(1) = num2str(arvo);
|
||||
# end
|
||||
|
||||
# else
|
||||
# suurinYks = floor(log10(div));
|
||||
# mjono(6) = num2str(suurinYks);
|
||||
# mjono(5) = 'e';
|
||||
# mjono(4) = palautaYks(abs(div),suurinYks-1);
|
||||
# mjono(3) = '.';
|
||||
# mjono(2) = palautaYks(abs(div),suurinYks);
|
||||
# end
|
||||
|
||||
|
||||
# %--------------------------------------------------------------------------
|
||||
|
||||
# function T = cluster_own(Z,nclust)
|
||||
# true=logical(1);
|
||||
|
|
@ -899,19 +730,4 @@ indMix <- function(c, npops, dispText) {
|
|||
# SUMCOUNTS(pop,:) = SUMCOUNTS(pop,:)+diffInSumCounts;
|
||||
# end
|
||||
# apuTaulu = sortrows(apuTaulu,2);
|
||||
# inds = apuTaulu(ninds:-1:1,1);
|
||||
|
||||
# %--------------------------------------------------------------------------
|
||||
|
||||
# function [emptyPop, pops] = findEmptyPop(npops)
|
||||
# % Palauttaa ensimm<6D>isen tyhj<68>n populaation indeksin. Jos tyhji<6A>
|
||||
# % populaatioita ei ole, palauttaa -1:n.
|
||||
|
||||
# global PARTITION;
|
||||
# pops = unique(PARTITION)';
|
||||
# if (length(pops) ==npops)
|
||||
# emptyPop = -1;
|
||||
# else
|
||||
# popDiff = diff([0 pops npops+1]);
|
||||
# emptyPop = min(find(popDiff > 1));
|
||||
# end
|
||||
# inds = apuTaulu(ninds:-1:1,1);
|
||||
15
R/poistaTyhjatPopulaatiot.R
Normal file
15
R/poistaTyhjatPopulaatiot.R
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
poistaTyhjatPopulaatiot <- function(npops) {
|
||||
# % Poistaa tyhjentyneet populaatiot COUNTS:ista ja
|
||||
# % SUMCOUNTS:ista. P<>ivitt<74><74> npops:in ja PARTITION:in.
|
||||
notEmpty <- find(any(SUMCOUNTS, 2))
|
||||
COUNTS <<- COUNTS[, , notEmpty]
|
||||
SUMCOUNTS <<- SUMCOUNTS[notEmpty, ]
|
||||
LOGDIFF <<- LOGDIFF[, notEmpty]
|
||||
|
||||
for (n in 1:length(notEmpty)) {
|
||||
apu <- find(PARTITION == notEmpty(n))
|
||||
PARTITION(apu) <<- n
|
||||
}
|
||||
npops <- length(notEmpty)
|
||||
return(npops)
|
||||
}
|
||||
Loading…
Add table
Reference in a new issue