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Scripts and spreadsheets for performing single-variate Best Linear Unbiased Predictor (BLUP) to find beef cattle breeding values #KeepEPDsReal
85 commits 3 branches 4 tags 440 KiB
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Thomas A. Christensen II 5048d3a1b8
Split into input and worker functions
2021-06-18 14:13:28 -05:00
.github/ISSUE_TEMPLATE Update issue templates 2020-03-05 20:56:44 -08:00
data Reformat spreadsheet 2021-01-04 02:24:39 -07:00
src Split into input and worker functions 2021-06-18 14:13:28 -05:00
.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
beefblup Create bash wrapper for function call 2021-06-18 13:51:37 -05:00
CODE_OF_CONDUCT.md Add code of conduct 2020-10-11 20:51:43 -06:00
LICENSE Create Github-template LICENSE file 2020-10-11 21:24:56 -06:00
Project.toml Add package info back into project manifest 2021-06-18 13:43:36 -05:00
README.md Change copyright/release numbers 2021-06-18 13:26:35 -05:00

README.md

[🐮]: beefblup

GitHub license Join the chat at https://gitter.im/beefblup/community Github all releases

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

Installation

  1. Download and install Julia
  2. Download the beefblup ZIP file and unzip it someplace memorable
  3. In your file explorer, copy the address of the "beefblup" folder
  4. Launch Julia
  5. Type cd("<the address copied in step 5") and press Enter (For example, cd("C:\Users\MillironX\Documents\beefblup"))
  6. Type the ] key
  7. Type activate . and press Enter
  8. Type instantiate and press Enter
  9. Installation is done: you can close the Julia window

How to Use

  1. Make a copy of the "sample.csv" spreadsheet and replace the data with your own
    1. The trait you wish to calculate EBVs for always goes in the rightmost column
    2. If you wish to add more contemporary group traits to your analysis, include them before the rightmost column
  2. Save and close
  3. In your file explorer, copy the address of the "beefblup" folder
  4. Launch Julia
  5. Type cd("<the address copied in step 5") and press Enter (For example, cd("C:\Users\MillironX\Documents\beefblup"))
  6. Type the ] key
  7. Type activate . and press Enter
  8. Press Backspace
  9. Type include("src/beefblup.jl") and press Enter
  10. Select the spreadsheet you created in steps 1-4
  11. Follow the on-screen prompts
  12. #KeepEPDsReal!

For Programmers

Also Note: beefblup was written on, and has only been tested with Julia v1.2.0 and higher. While this shouldn't affect most everyday users, it might affect you if you are stuck on the current LTS version of Julia (v1.0.5).

Development Roadmap

Version Feature Status
v0.1 Julia port of original MATLAB script ✔️
v0.2 Spreadsheet format redesign ✔️
v0.3 API rewrite (change to function calls and package format 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

License

Distributed under the 3-Clause BSD License