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Merge tag 'v0.2' into develop

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Spreadsheet format redesign
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Thomas A. Christensen II 2021-06-18 13:27:52 -05:00
commit 80a21e42e0
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77
README.md
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@ -13,35 +13,34 @@ Why? It's part of my effort to
## Installation
1. [Download and install Julia](https://julialang.org/downloads/platform/)
2. Open a new Julia window and type the `]` key
3. Type `add XLSX Gtk` and press **Enter**
Alternatively, you can run the [install
script](https://github.com/MillironX/beefblup/raw/master/Julia/install.jl) from
Julia.
2. Download the [beefblup ZIP
file](https://github.com/MillironX/beefblup/archive/refs/tags/v0.2.zip) 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
> **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).
> 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.
1. Download the [beefblup ZIP
file](https://github.com/MillironX/beefblup/archive/v0.1.zip) and unzip it
someplace memorable
2. Make a copy of the "Master BLUP Worksheet" and replace the sample data 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 close
5. In your file explorer, copy the address of the "Julia" folder
6. Launch Julia
7. Type `cd("<the address copied in step 5")` and press **Enter** (For example,
`cd("C:\Users\MillironX\Documents\beefblup\Julia")`)
8. Type `include("beefblup.jl")` and press **Enter**
9. Select the spreadsheet you created in steps 1-4
10. Follow the on-screen prompts
11. **#KeepEPDsReal!**
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
@ -51,19 +50,19 @@ Julia.
### Development Roadmap
| Version | Feature |
| ------- | ------------------------------------------------------------------- |
| 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!!!](https://youtu.be/1CBjxGdgC1w?t=282) |
| Version | Feature | Status |
| ------- | ----------------------------------------------------------------------------------- | ------------------ |
| v0.1 | Julia port of original MATLAB script | :heavy_check_mark: |
| v0.2 | Spreadsheet format redesign | :heavy_check_mark: |
| 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!!!](https://youtu.be/1CBjxGdgC1w?t=282) | |
### Bug Reports

8
src/beefblup.jl
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@ -6,7 +6,7 @@ exec julia --project=$(realpath $(dirname $(dirname "${BASH_SOURCE[0]}"))) "${BA
# Main script for performing single-variate BLUP to find beef cattle
# breeding values
# Usage: julia beefblup.jl
# (C) 2020 Thomas A. Christensen II
# (C) 2021 Thomas A. Christensen II
# Licensed under BSD-3-Clause License
# cSpell:includeRegExp #.*
# cSpell:includeRegExp ("""|''')[^\1]*\1
@ -19,8 +19,8 @@ using Dates
using Gtk
# Display stuff
println("beefblup v 0.1")
println("(C) 2020 Thomas A. Christensen II")
println("beefblup v 0.2")
println("(C) 2021 Thomas A. Christensen II")
println("https://github.com/millironx/beefblup")
print("\n")
@ -218,7 +218,7 @@ traitname = names(data)[end]
# Start printing results to output
fileID = open(savepath, "w")
write(fileID, "beefblup Results Report\n")
write(fileID, "Produced using beefblup for Julia (")
write(fileID, "Produced using beefblup (")
write(fileID, "https://github.com/millironx/beefblup")
write(fileID, ")\n\n")
write(fileID, "Input:\t")