diff --git a/Julia/beefblup.jl b/Julia/beefblup.jl index 16c0c6e..5cf891b 100644 --- a/Julia/beefblup.jl +++ b/Julia/beefblup.jl @@ -2,7 +2,7 @@ # Main script for performing single-variate BLUP to find beef cattle # breeding values # Usage: julia beefblup.jl -# (C) 2019 Thomas A. Christensen II +# (C) 2020 Thomas A. Christensen II # Licensed under BSD-3-Clause License # Import the required packages @@ -12,8 +12,8 @@ using Dates using Gtk # Display stuff -println("beefblup v 0.0.0.1") -println("(C) 2019 Thomas A. Christensen II") +println("beefblup v 0.1") +println("(C) 2020 Thomas A. Christensen II") println("https://github.com/millironx/beefblup") print("\n") diff --git a/Julia/install.jl b/Julia/install.jl index 1a3698d..2de4ccd 100644 --- a/Julia/install.jl +++ b/Julia/install.jl @@ -2,7 +2,7 @@ # Prepares the Julia environment for using beefblup by installing the requisite # packages # Usage: julia install.jl -# (C) 2019 Thomas A. Christensen II +# (C) 2020 Thomas A. Christensen II # Licensed under BSD-3-Clause License # Import the package manager diff --git a/LICENSE.md b/LICENSE.md index e50a0eb..08e6c89 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ BSD 3-Clause License -Copyright (c) 2018, Thomas A. Christensen II +Copyright (c) 2020, Thomas A. Christensen II All rights reserved. Redistribution and use in source and binary forms, with or without diff --git a/MATLAB/beefblup.m b/MATLAB/beefblup.m index 242fd29..d26f887 100644 --- a/MATLAB/beefblup.m +++ b/MATLAB/beefblup.m @@ -2,7 +2,7 @@ % Main script for performing single-variate BLUP to find beef cattle % breeding values % Usage: beefblup -% (C) 2018 Thomas A. Christensen II +% (C) 2020 Thomas A. Christensen II % Licensed under BSD-3-Clause License % Prepare the workspace for computation @@ -11,8 +11,8 @@ clc close all %% Display stuff -disp('beefblup v. 0.0.0.1') -disp('(C) 2018 Thomas A. Christensen II') +disp('beefblup v. 0.1') +disp('(C) 2020 Thomas A. Christensen II') disp('https://github.com/millironx/beefblup') disp(' ') @@ -77,7 +77,7 @@ for i=1:numanimals 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); @@ -91,7 +91,7 @@ colstodelete = 6; % Coerce each group to string format for i = 7:length(headers) - data(:,i) = cellfun(@num2str, data(:,i), 'UniformOutput', false); + data(:,i) = cellfun(@num2str, data(:,i), 'UniformOutput', false); end % Find any columns that need to be deleted @@ -100,7 +100,7 @@ for i = 7:length(headers) colname = headers{i}; disp(['Column "' colname '" does not have any unique animals and will be removed']) disp('from this analysis'); - colstodelete = [colstodelete i]; + colstodelete = [colstodelete i]; end end @@ -167,19 +167,19 @@ adjustedtraits = cell(1, sum(numgroups)-length(numgroups)); for i = 1:length(normal) % Find the traits that are present in this trait traits = uniquecell(data(:,i+5)); - + % Remove the "normal" version from the analysis normalindex = find(strcmp(traits, normal{i})); traits(normalindex) = []; - + % Iterate inside of the group for j = 1:length(traits) matchedindex = find(strcmp(data(:,i+5), traits{j})); X(matchedindex, I) = 1; - + % Add this trait to the string adjustedtraits(I - 1) = traits(j); - + % Increment the big counter I = I + 1; end @@ -217,7 +217,7 @@ for i = 1:numanimals A(j,i) = 0.5*A(j,sire(i)); A(i,j) = A(j,i); end - A(i,i) = 1; + A(i,i) = 1; else for j = 1:(i-1) A(j,i) = 0; @@ -313,7 +313,7 @@ for i = 1:length(numgroups) fprintf(fileID, '\t'); fprintf(fileID, num2str(reliability(I))); fprintf(fileID, '\n'); - + I = I + 1; end fprintf(fileID, '\n');