millironx
/
beefblup
mirror of https://github.com/MillironX/beefblup
1
0
Fork 0
Code Issues Packages Releases Activity
Scripts and spreadsheets for performing single-variate Best Linear Unbiased Predictor (BLUP) to find beef cattle breeding values #KeepEPDsReal
You cannot select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
136 Commits
3 Branches
4 Tags
440 KiB
Julia 100%
 
gh-pages
develop
master
v0.2.2
v0.2.1
v0.2
v0.1
Branches Tags
${ item.name }
Create tag ${ searchTerm }
Create branch ${ searchTerm }
from 'develop'
${ noResults }
Go to file
Thomas A. Christensen II 62f5c4ea65
Update report generation to match new fixed effect format 		3 years ago
.github Make Julia version correct in docs CI 3 years ago
.vscode Fix documentation syntax bugs 3 years ago
data Use Julia error/warn systems instead of printing to stdout 3 years ago
docs Fix documentation syntax bugs 3 years ago
src Update report generation to match new fixed effect format 3 years ago
test Revamp fixed-effect algorithm 3 years ago
.gitattributes Mark beefblup CLI as Julia file 3 years ago
.gitignore Create debug config 3 years ago
.travis.yml More Travis GUI updates 3 years ago
CODE_OF_CONDUCT.md Add code of conduct 4 years ago
LICENSE Merge branch 'pkg-template' into develop 3 years ago
Project.toml Merge branch 'pkg-template' into develop 3 years ago
README.md Update badges to work on 'develop' branch 3 years ago
beefblup Mark beefblup CLI as Julia file 3 years ago

README.md

[🐮]: beefblup

Stable Dev Build Status Coverage 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