From 5f3d54e86da1c0cbbc0f1d3d9d42e8b8a8c35860 Mon Sep 17 00:00:00 2001 From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com> Date: Sat, 28 Sep 2019 00:20:02 -0700 Subject: [PATCH] Update README.md --- README.md | 36 +++++++++++++++++++++++++++--------- 1 file changed, 27 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 2a754a3..97d6c74 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ # beefblup -#### \# KeepEPDsReal +:cow: :cow: :cow: + +#### \#KeepEPDsReal MATLAB and Python scripts and Excel spreadsheets that can be used in conjunction to find breeding values for beef cattle. @@ -8,7 +10,7 @@ MATLAB and Python scripts and Excel spreadsheets that can be used in conjunction 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, add them into or directly after the Purple section +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. Download the entire `MATLAB` folder, and set it as your current MATLAB directory 5. Run `beefblup.m` 6. Select the spreadsheet file you just placed your data into @@ -17,20 +19,36 @@ MATLAB and Python scripts and Excel spreadsheets that can be used in conjunction ## Contributing -I will gladly take input on the following: +I will gladly accept pull requests that acomplish any of the following: -* Converting MATLAB scripts to Python +* Convert MATLAB scripts to Python + * The product must be able to be run from the native (non-python) terminal using only the default [Anaconda Python packages](https://anaconda.com/distribution) * Optimizing code sections -* Adding spreadsheets for additional traits -* Bug reports, usability issues, etc. + * 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 + -If you are writing code, please keep the code clean by: -* Indenting using the native editor's formating -* Naming variables in full word English using all lowercase for MATLAB and camelCase for Python, unless the matrix name is generally agreed upon in academic papers (i.e. A is the additive relationship matrix) +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 +Bug reports and suggestions will be gladly taken on the [issues](https://github.com/MillironX/beefblup/issues) page. There is no set format for issues, yet, but please at the minimum attach a filled-out spreadsheet that demonstrates your bug or how your suggestion would be useful. + ## License Distributed under the 3-Clause BSD License