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Scripts and spreadsheets for performing single-variate Best Linear Unbiased Predictor (BLUP) to find beef cattle breeding values #KeepEPDsReal
51 commits 3 branches 4 tags 440 KiB
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Thomas A. Christensen II 88ebbb2969
Remove AOD from worksheet
2020-02-16 15:56:01 -08:00
Excel Remove AOD from worksheet 2020-02-16 15:56:01 -08:00
Julia Complete port of beefblup to Julia 2020-02-15 20:13:39 -08:00
MATLAB Fixed additive relationship matrix creation 2019-08-24 15:52:24 -07:00
.gitattributes Added git meta files to avoid corruption 2018-09-07 09:20:01 -06:00
.gitignore Add Julia stuff to gitignore 2020-02-15 20:13:37 -08:00
LICENSE.md Terminate if there are more contemporary groups than animals 2018-09-14 21:40:50 -06:00
README.md More work on README 2020-02-16 15:46:32 -08:00

README.md

[🐮]: beefblup

beefblup is a program for ranchers to calculate expected breeding values (EBVs) for their own beef cattle. It is intended to be usable by anyone without requiring any prior knowledge of computer programming or linear algebra. Why? It's part of my effort to #KeepEPDsReal

🔽 Download beefblup

Notice: beefblup for MATLAB and beefblup for Python are going away. I'm going to make changes here soon that will break the MATLAB version of beefblup, and I don't intend to update it anymore. (How many ranchers do you know that can afford MATLAB?) As for beefblup for Python, it never really got off the ground, and beefblup for Julia has superceded it.

For Users

Installation

Windows (My Platform)

  1. Press the Windows Key + X, and then press A, and select Yes
  2. Install Chocolatey using the PowerShell window that opened
  3. Close PowerShell
  4. Press the Windows Key + X, and then press A, and select Yes (Again)
  5. Type choco install Julia -y into PowerShell and press Enter
  6. Close PowerShell once Chocolatey has finished
  7. Download beefblup and unzip it to somewhere you will remember it
  8. Hold down the Shift key, and right-click in a blank space in the "Julia" folder of beefblup
  9. Click **Open PowerShell window here"
  10. Type julia install.jl into PowerShell and press Enter
  11. Close PowerShell once Julia has finished

Why do you need Chocolatey? Because it allows you to access Julia (and therefore beefblup) from the Shift+Right-click menu directly, without having to worry about cd commands or editing your %PATH%. That's good, right?

Mac

  1. Download and install Julia
  2. Open terminal.app, and run the following
curl https://github.com/MillironX/beefblup/archive/master.zip -o beefblup.zip
unzip beefblup.zip
rm beefblup.zip
  1. Quit terminal.app
  2. Open julia.app, and run the following
cd("~/beefblup/beefblup-master/Julia")
include("install.jl")
  1. Quit julia.app

I don't know if these are right, since I can't afford a Mac. If any of you super-privileged Apple snobs out there use beefblup, please add proper instructions here and submit a pull request.

Debian/Ubuntu Linux

TODO: Add instructions here. This is slightly complicated since there is no Julia package in the main repositories, and I don't use Debian distros enough to know where to find a third-party repos

Fedora Linux (The best platform)

From a new terminal, run

sudo dnf install julia -y
wget https://github.com/MillironX/beefblup/archive/master.zip -O beefblup.zip
unzip beefblup.zip
rm beefblup.zip
cd beefblup/beefblup-master/Julia
julia install.jl
exit

Other Platforms

Seriously? If you're enough of a geek to be using something else, you can figure this out on your own.

How to Use

Note: beefblup and Juno/Julia Pro currently don't get along. Although it's tempting to just open up beefblup in Juno and press the big play button, it won't work. Follow these instructions until it's fixed. If you don't know what Juno is: ignore this message.

All platforms

  1. Download the Excel template
  2. Replace the sample data in the spreadsheet with your own
  3. If you wish to add more contemporary group traits to your analysis, replace or add them to the right of the Purple section
  4. Save, and continue with your platform-specific instructions below

Windows

  1. Remember where you downloaded beefblup to when you installed it
  2. Hold down the Shift key, and right-click in a blank space in the "Julia" folder of beefblup
  3. Click **Open PowerShell window here"
  4. Type julia beefblup.jl into PowerShell and press Enter
  5. Select the spreadsheet you created in Step 4
  6. Follow the on-screen prompts
  7. #KeepEPDsReal!

Mac

  1. Open julia.app, and run the following
cd("~/beefblup/beefblup-master/Julia")
include("beefblup.jl")
  1. Select the spreadsheet you created in Step 4
  2. Follow the on-screen prompts
  3. #KeepEPDsReal!

All Linux

  1. Open a new terminal, and type
cd beefblup/beefblup-master/Julia
julia beefblup.jl
  1. Select the spreadsheet you created in Step 4
  2. Follow the on-screen prompts
  3. #KeepEPDsReal!

For Programmers

Development Roadmap

Version Feature
v0.1 Julia port of original MATLAB script
v0.2 Spreadsheet format redesign
v0.3 API rewrite (change to function calls instead of script running)
v0.4 Add GUI for all options
v0.5 Automatically calculated Age-Of-Dam, Year, and Season fixed-effects
v0.6 Repeated measurement BLUP (aka dairyblup)
v0.7 Multiple trait BLUP
v0.8 Maternal effects BLUP
v0.9 Genomic BLUP
v0.10 beefblup binaries
v1.0 Finally, RELEASE!!!

Bug Reports

For every bug report, please include at least the following:

  • Platform (Windows, Mac, Fedora, etc)
  • Julia version
  • beefblup version
  • How you are running Julia (From PowerShell, via the REPL, etc.)
  • A beefblup spreadsheet that can be used to recreate the issue
  • Description of the problem
  • Expected behavior
  • A screenshot and/or REPL printout

Feature and Pull Requests

Although I doubt there will be many contributors here,

License

Distributed under the 3-Clause BSD License