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62 lines
2.8 KiB
Markdown
62 lines
2.8 KiB
Markdown
# beefblup
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:cow: :cow: :cow:
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#### \#KeepEPDsReal
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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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## 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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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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5. Enter the following lines in the command window:
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```
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websave('beefblup.zip','https://github.com/MillironX/beefblup/archive/master.zip');
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unzip('beefblup.zip');
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cd beefblup-master/MATLAB
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beefblup
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```
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6. Select the spreadsheet file you just placed your data into
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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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I will gladly accept pull requests that acomplish any of the following:
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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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* 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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* Perform cannonical transformations for missing values
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* Other similar improvements that I might not be aware of
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* Creation of scripts to handle additional forms of BLUP
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* Mult-trait (MBLUP)
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* Maternal-trait
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* Genomic-enhanced (GBLUP) - this will require the creation of a standard SNP spreadsheet format
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* Creation of spreadsheets for additional traits
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* Creation of wiki pages to explain what each script does
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* The general rule is that **every** wiki page should be understandable to anyone who's passed high school algebra, while still being correct and informative
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Note that I intend to implement all of the items above eventually, but progress is slow since I'm learning as I go.
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If you are writing code, please keep the code clean:
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* Run "Smart Indent" in the MATLAB editor on the entire file before checking it in
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* Name variables in full word English using all lowercase, unless the matrix name is generally agreed upon in academic papers (i.e. A is the additive relationship matrix)
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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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