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README.md
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README.md
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# [:cow:]: beefblup
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[](https://github.com/MillironX/beefblup/blob/master/LICENSE.md)
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[](https://gitter.im/beefblup/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
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[](https://GitHub.com/MillironX/beefblup/releases)
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beefblup is a program for ranchers to calculate expected breeding
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values (EBVs) for their own beef cattle. It is intended to be usable by anyone
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without requiring any prior knowledge of computer programming or linear algebra.
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Why? It's part of my effort to
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**\#KeepEPDsReal**
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[:arrow_down_small: Download beefblup](https://github.com/MillironX/beefblup/archive/master.zip)
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## Installation
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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 off the ground, and beefblup for Julia has superceded it.
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1. [Download and install Julia](https://julialang.org/downloads/platform/)
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2. Open a new Julia window and type the `]` key
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3. Type `add XLSX Gtk` and press **Enter**
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## For Users
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Alternatively, you can run the [install
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script](https://github.com/MillironX/beefblup/raw/master/Julia/install.jl) from
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Julia.
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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 beefblup](https://github.com/MillironX/beefblup/archive/master.zip)
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and unzip it 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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1. [Download and install Julia](https://julialang.org/downloads/)
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2. Open terminal.app, and run the following
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```bash
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curl https://github.com/MillironX/beefblup/archive/master.zip -o beefblup.zip
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unzip beefblup.zip
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rm beefblup.zip
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```
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3. Quit terminal.app
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4. Open julia.app, and run the following
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```julia
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cd("~/beefblup/beefblup-master/Julia")
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include("install.jl")
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```
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5. Quit julia.app
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I don't know if these are right, since I can't afford a Mac. If any of you
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super-privileged Apple snobs out there use beefblup, please add proper
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instructions here and submit a pull 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 (The best platform)
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From a new terminal, run
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```bash
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sudo dnf install julia -y
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wget https://github.com/MillironX/beefblup/archive/master.zip -O beefblup.zip
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unzip beefblup.zip
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rm beefblup.zip
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cd beefblup/beefblup-master/Julia
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julia install.jl
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exit
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```
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#### Other Platforms
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Seriously? If you're enough of a geek to be using something else, you can figure
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this out on your own.
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### How to Use
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## How to Use
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> **Note:** beefblup and [Juno](https://junolab.org)/[Julia Pro](https://juliacomputing.com/products/juliapro.html) currently [don't get along](https://github.com/JunoLab/Juno.jl/issues/118).
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> Although it's tempting to just open up beefblup in Juno and press the big play
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> button, it won't work. Follow these instructions until it's fixed. If you
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> don't know what Juno is: ignore this message.
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#### All platforms
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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. Replace the sample data in the spreadsheet with your own
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1. Download the [beefblup ZIP
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file](https://github.com/MillironX/beefblup/archive/0.1.zip) and unzip it
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someplace memorable
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2. Make a copy of the "Master BLUP Worksheet" and replace the sample data with your own
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3. If you wish to add more contemporary group traits to your analysis, replace
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or add them to the right of the Purple section
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4. Save, and continue with your platform-specific instructions below
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#### Windows
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5. Remember where you downloaded beefblup to when you installed it
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6. 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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7. Click **Open PowerShell window here"
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8. Type `julia beefblup.jl` into PowerShell and press **Enter**
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9. Select the spreadsheet you created in Step 4
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4. Save and close
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5. In your file explorer, copy the address of the "Julia" folder
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6. Launch Julia
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7. Type `cd("<the address copied in step 5")` and press **Enter** (For example,
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`cd("C:\Users\MillironX\Documents\beefblup\Julia")`)
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8. Type `include("beefblup.jl")` and press **Enter**
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9. Select the spreadsheet you created in steps 1-4
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10. Follow the on-screen prompts
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11. **\#KeepEPDsReal!**
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#### Mac
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5. Open julia.app, and run the following
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```julia
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cd("~/beefblup/beefblup-master/Julia")
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include("beefblup.jl")
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```
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6. Select the spreadsheet you created in Step 4
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7. Follow the on-screen prompts
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8. **\#KeepEPDsReal!**
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#### All Linux
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5. Open a new terminal, and type
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```bash
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cd beefblup/beefblup-master/Julia
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julia beefblup.jl
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```
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6. Select the spreadsheet you created in Step 4
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7. Follow the on-screen prompts
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8. **\#KeepEPDsReal!**
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11. **#KeepEPDsReal!**
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## For Programmers
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@ -154,7 +55,7 @@ julia beefblup.jl
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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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| v0.3 | API rewrite (change to function calls and package format 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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@ -177,10 +78,6 @@ For every bug report, please include at least the following:
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- Expected behavior
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- A screenshot and/or REPL printout
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### Feature and Pull Requests
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Although I doubt there will be many contributors here,
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## License
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Distributed under the 3-Clause BSD License
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