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@ -1,9 +1,13 @@
# [:cow:]: beefblup
beefblup is an easy-to-use program for ranchers to calculate expected breeding
values (EBVs) for their own beef cattle. Why? It's part of my effort to
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**
[:arrow_down_small: Download beefblup](https://github.com/MillironX/beefblup/archive/master.zip)
> **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
@ -24,7 +28,8 @@ values (EBVs) for their own beef cattle. Why? It's part of my effort to
(Again)
5. Type `choco install Julia -y` into PowerShell and press **Enter**
6. Close PowerShell once Chocolatey has finished
7. Download and unzip beefblup to somewhere you will remember it
7. [Download beefblup](https://github.com/MillironX/beefblup/archive/master.zip)
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"
@ -37,9 +42,28 @@ worry about `cd` commands or editing your `%PATH%`. That's good, right?
#### Mac
I don't know. I can't afford one. If any of you super-privileged Apple snobs
out there run beefblup, please add proper instructions here and submit a pull
request.
1. [Download and install Julia](https://julialang.org/downloads/)
2. Open terminal.app, and run the following
```bash
curl https://github.com/MillironX/beefblup/archive/master.zip -o beefblup.zip
unzip beefblup.zip
rm beefblup.zip
```
3. Quit terminal.app
4. Open julia.app, and run the following
```julia
cd("~/beefblup/beefblup-master/Julia")
include("install.jl")
```
5. 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
@ -47,28 +71,76 @@ 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
#### Fedora Linux (The best platform)
TODO: Add instructions here. I have this info, but it's on the work computer.
From a new terminal, run
## How to Use
```bash
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
```
1. Choose a spreadsheet appropriate to the trait you want to analyze from the `Excel` folder, and save it to your hard drive
2. Place your data into the structure described by the spreadsheet
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. Open MATLAB
5. Enter the following lines in the command window:
#### Other Platforms
```
websave('beefblup.zip','https://github.com/MillironX/beefblup/archive/master.zip');
unzip('beefblup.zip');
cd beefblup-master/MATLAB
beefblup
```
Seriously? If you're enough of a geek to be using something else, you can figure
this out on your own.
6. Select the spreadsheet file you just placed your data into
7. Select a file that you would like to save your results to
8. Breeding values and contemporary group adjustments will be outputted to the file you selected
### How to Use
> **Note:** beefblup and [Juno](https://junolab.org)/[Julia Pro](https://juliacomputing.com/products/juliapro.html) 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](https://github.com/MillironX/beefblup/raw/master/Excel/Master%20BLUP%20Worksheet.xlsx)
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
5. Remember where you downloaded beefblup to when you installed it
6. Hold down the **Shift** key, and **right-click** in a blank space in the
"Julia" folder of beefblup
7. Click **Open PowerShell window here"
8. Type `julia beefblup.jl` into PowerShell and press **Enter**
9. Select the spreadsheet you created in Step 4
10. Follow the on-screen prompts
11. **\#KeepEPDsReal!**
#### Mac
5. Open julia.app, and run the following
```julia
cd("~/beefblup/beefblup-master/Julia")
include("beefblup.jl")
```
6. Select the spreadsheet you created in Step 4
7. Follow the on-screen prompts
8. **\#KeepEPDsReal!**
#### All Linux
5. Open a new terminal, and type
```bash
cd beefblup/beefblup-master/Julia
julia beefblup.jl
```
6. Select the spreadsheet you created in Step 4
7. Follow the on-screen prompts
8. **\#KeepEPDsReal!**
## For Programmers
@ -86,34 +158,24 @@ TODO: Add instructions here. I have this info, but it's on the work computer.
| v0.8 | Maternal effects BLUP |
| v0.9 | Genomic BLUP |
| v0.10 | beefblup binaries |
| v1.0 | [Finally, RELEASE!!!](https://youtu.be/Zd-up5EgoMw?t=5049) |
| v1.0 | [Finally, RELEASE!!!](https://youtu.be/1CBjxGdgC1w?t=282) |
I will gladly take input on the following:
### Bug Reports
* Converting MATLAB scripts to Python
* Optimizing code sections
* Use triagonal shortcuts to generate the additive relationship matrix
* Solve implicit forms of the mixed-model equation
* Perform cannonical transformations for missing values
* Other similar improvements that I might not be aware of
* Creation of scripts to handle additional forms of BLUP
* Mult-trait (MBLUP)
* Maternal-trait
* Genomic-enhanced (GBLUP) - this will require the creation of a standard SNP spreadsheet format
* Creation of spreadsheets for additional traits
* Creation of wiki pages to explain what each script does
* 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
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
Note that I intend to implement all of the items above eventually, but progress is slow since I'm learning as I go.
If you are writing code, please keep the code clean:
* Run "Smart Indent" in the MATLAB editor on the entire file before checking it in
* 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)
* For MATLAB, functions go in a separate file
* Comments go before a code block: no inline comments
Although I doubt there will be many contributors here,
## License