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Fixed additive relationship matrix creation

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Thomas A. Christensen II 2019-08-24 15:52:24 -07:00
parent 0ba6bae677
commit f54fd46fda
2 changed files with 44 additions and 57 deletions
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91
MATLAB/beefblup.m
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@ -61,13 +61,29 @@ data = sortrows(data,2);
strings = [1 3 4];
data(:,strings) = cellfun(@num2str, data(:,strings), 'UniformOutput', false);
% Create a lookup lambda function to find the animal represented by a
% certain id
animal2row = @(id) find(strcmp(data(:,1), id));
row2animal = @(rownum) [data{rownum,1}];
ids = [data{:,1}];
% Define fields to hold id values for animals and their parents
ids = char(data{:,1});
damids = char(data{:,3});
sireids = char(data{:,4});
numanimals = length(data(:,1));
% Define fields to hold the index values for animals and their parents
dam = zeros(numanimals,1);
sire = zeros(numanimals,1);
% Find all row numbers where an animal was a parent
for i=1:numanimals
% Find all animals that this animal birthed
dammatch = ismember(damids, ids(i,:), 'rows');
damindexes = find(dammatch == 1);
dam(damindexes) = i;
% Find all animals that this animal sired
sirematch = ismember(sireids, ids(i,:), 'rows');
sireindexes = find(sirematch == 1);
sire(sireindexes) = i;
end
% Store column numbers that need to be deleted
% Column 6 contains an intermediate Excel calculation and always needs to
% be deleted
@ -181,53 +197,34 @@ disp('Creating the additive relationship matrix...')
% Create an empty matrix for the additive relationship matrix
A = zeros(numanimals, numanimals);
% Create lambdas to find sire and dam of each animal
id2dam = @(id) [data{animal2row(num2str(id)), 3}];
id2sire = @(id) [data{animal2row(num2str(id)), 4}];
row2dam = @(rownum) [data{rownum, 3}];
row2sire = @(rownum) [data{rownum, 4}];
rowofdam = @(id) animal2row(id2dam(id));
rowofsire = @(id) animal2row(id2sire(id));
row2rowofdam = @(rownum) rowofdam(row2animal(rownum));
row2rowofsire = @(rownum) rowofsire(row2animal(rownum));
% Create the additive relationship matrix by the FORTRAN method presented
% by Henderson
for i = 1:numanimals
id = row2animal(i);
if isempty(row2rowofsire(i)) && isempty(row2rowofdam(i))
if dam(i) ~= 0 && sire(i) ~= 0
for j = 1:(i-1)
A(j,i) = 0;
A(j,i) = 0.5*(A(j,sire(i))+A(j,dam(i)));
A(i,j) = A(j,i);
end
A(i,i) = 1;
continue
end
if isempty(row2rowofsire(i)) && not(isempty(row2dam(i)))
for j = 1:(i-1)
A(j,i) = A(j,row2rowofdam(i));
A(i,j) = A(j,row2rowofdam(i));
end
A(i,i) = 1;
continue
end
if isempty(row2rowofdam(i)) && not(isempty(row2rowofsire(i)))
for j=1:(i-1)
A(j,i) = A(j,row2rowofsire(i));
A(i,j) = A(j,row2rowofsire(i));
end
A(i,i) = 1;
continue
end
for j=1:(i-1)
A(j,i) = 0.5.*(A(j,row2rowofsire(i)) + A(j,row2rowofdam(i)));
A(i,j) = 0.5.*(A(j,row2rowofsire(i)) + A(j,row2rowofdam(i)));
end
A(i,i) = 1 + 0.5.*A(row2rowofsire(i), row2rowofdam(i));
continue
A(i,i) = 1 + 0.5*A(sire(i),dam(i));
elseif dam(i) ~= 0 && sire(i) == 0
for j = 1:(i-1)
A(j,i) = 0.5*A(j,dam(i));
A(i,j) = A(j,i);
end
A(i,i) = 1;
elseif dam(i) == 0 && sire(i) ~=0
for j = 1:(i-1)
A(j,i) = 0.5*A(j,sire(i));
A(i,j) = A(j,i);
end
A(i,i) = 1;
else
for j = 1:(i-1)
A(j,i) = 0;
A(i,j) = 0;
end
A(i,i) = 1;
end
end
disp('Creating the additive relationship matrix... Done!')

10
MATLAB/uniquenan.m
View file

@ -1,10 +0,0 @@
% uniquenan
% Serves the same purpose as UNIQUE, but ensures any NaN fields are not
% counted
function y = uniquenan(x)
y = unique(x);
if any(isnan(y))
y(isnan(y)) = [];
y(end + 1) = NaN;
end
end