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# beefblup
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# [:cow:]: beefblup
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:cow: :cow: :cow:
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beefblup is an easy-to-use program for ranchers to calculate expected breeding
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values (EBVs) for their own beef cattle. Why? It's part of my effort to
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**\#KeepEPDsReal**
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#### \#KeepEPDsReal
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> **Notice:** beefblup for MATLAB and beefblup for Python are going away. I'm
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> going to make changes here soon that will break the MATLAB version of
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> beefblup, and I don't intend to update it anymore. (How many ranchers do you
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> know that can afford MATLAB?) As for beefblup for Python, it never really got
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> off the ground, and beefblup for Julia has superceded it.
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MATLAB and Python scripts and Excel spreadsheets that can be used in conjunction to find breeding values for beef cattle.
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## For Users
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### Installation
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#### Windows (My Platform)
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1. Press the **Windows Key** + **X**, and then press **A**, and select **Yes**
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2. [Install Chocolatey](https://chocolatey.org/install) using the PowerShell
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window that opened
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3. Close PowerShell
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4. Press the **Windows Key** + **X**, and then press **A**, and select **Yes**
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(Again)
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5. Type `choco install Julia -y` into PowerShell and press **Enter**
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6. Close PowerShell once Chocolatey has finished
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7. Download and unzip beefblup to somewhere you will remember it
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8. Hold down the **Shift** key, and **right-click** in a blank space in the
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"Julia" folder of beefblup
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9. Click **Open PowerShell window here"
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10. Type `julia install.jl` into PowerShell and press **Enter**
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11. Close PowerShell once Julia has finished
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Why do you need Chocolatey? Because it allows you to access Julia (and therefore
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beefblup) from the **Shift**+**Right-click** menu directly, without having to
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worry about `cd` commands or editing your `%PATH%`. That's good, right?
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#### Mac
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I don't know. I can't afford one. If any of you super-privileged Apple snobs
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out there run beefblup, please add proper instructions here and submit a pull
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request.
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#### Debian/Ubuntu Linux
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TODO: Add instructions here. This is slightly complicated since there is no
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Julia package in the main repositories, and I don't use Debian distros enough to
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know where to find a third-party repos
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#### Fedora Linux
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TODO: Add instructions here. I have this info, but it's on the work computer.
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## How to Use
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1. Download the [Excel template](https://github.com/MillironX/beefblup/raw/master/Excel/Master%20BLUP%20Worksheet.xlsx)
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1. Choose a spreadsheet appropriate to the trait you want to analyze from the `Excel` folder, and save it to your hard drive
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2. Place your data into the structure described by the spreadsheet
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3. If you wish to add more contemporary group traits to your analysis, replace or add them to the right of the Purple section
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4. Open MATLAB
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@ -25,12 +70,27 @@ MATLAB and Python scripts and Excel spreadsheets that can be used in conjunction
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7. Select a file that you would like to save your results to
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8. Breeding values and contemporary group adjustments will be outputted to the file you selected
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## Contributing
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## For Programmers
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I will gladly accept pull requests that acomplish any of the following:
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### Development Roadmap
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* Convert MATLAB scripts to Python
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* The product must be able to be run from the native (non-python) terminal using only the default [Anaconda Python packages](https://anaconda.com/distribution)
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| Version | Feature |
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| ------- | ------------------------------------------------------------------- |
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| v0.1 | Julia port of original MATLAB script |
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| v0.2 | Spreadsheet format redesign |
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| v0.3 | API rewrite (change to function calls instead of script running) |
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| v0.4 | Add GUI for all options |
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| v0.5 | Automatically calculated Age-Of-Dam, Year, and Season fixed-effects |
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| v0.6 | Repeated measurement BLUP (aka dairyblup) |
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| v0.7 | Multiple trait BLUP |
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| v0.8 | Maternal effects BLUP |
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| v0.9 | Genomic BLUP |
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| v0.10 | beefblup binaries |
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| v1.0 | [Finally, RELEASE!!!](https://youtu.be/Zd-up5EgoMw?t=5049) |
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I will gladly take input on the following:
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* Converting MATLAB scripts to Python
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* Optimizing code sections
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* Use triagonal shortcuts to generate the additive relationship matrix
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* Solve implicit forms of the mixed-model equation
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@ -55,8 +115,6 @@ If you are writing code, please keep the code clean:
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* For MATLAB, functions go in a separate file
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* Comments go before a code block: no inline comments
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Bug reports and suggestions will be gladly taken on the [issues](https://github.com/MillironX/beefblup/issues) page. There is no set format for issues, yet, but please at the minimum attach a filled-out spreadsheet that demonstrates your bug or how your suggestion would be useful.
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## License
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Distributed under the 3-Clause BSD License
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