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CurrentModule = BeefBLUP

beefblup Command Line Interface (CLI) documentation

A work in progress

Notice: This document is a draft for what the command-line interface for beefblup would look like as of version 1.0, if beefblup was even a command-line application to begin with (it's not). It is modeled (loosely) after the man page format. It is not intended to be taken seriously, but instead to serve as a useful thought experiment and brainstorming ground on the future of beefblup. Please use it if it clarifies things for you. If it doesn't, ignore it.

Input file

beefblup requires a very specific format of input file. The format may be in comma-separated values (CSV) or Excel 2007+ (XLSX) format. CSV files should not be quoted (and therefore cannot have commas within cell values). Other formats may be forthcoming.

A beefblup data file must have at least six columns appearing in this order:

ID
Sire ID
Dam ID
Birthdate
Fixed effect(s)
Response variable(s)

The first row always contains column names. The values of column names are unimportant for the first four columns, as they will always be treated the same regardless of the name. The generated report will use the column names of fixed effects and response variables as given.

Each fixed effect should have its own column, to as many as are needed. There is no limit to the number of fixed effects as defined by beefblup, however its dependencies might have some. The same rules apply to response variables.

Unknown values should be left blank (,,). Do not substitute null placeholders (e.g. NULL, NA, 0, nothing, undefined, etc.) for unknown values.

An example spreadsheet might have the following format

ID	Sire ID	Dam ID	Birthdate	Sex	Weaning Weight
1			1/1/1990	Male	354
2	1		1/1/1990	Female	251
3	1		1/1/1991	Male	327
4	1	2	1/1/1991	Female	328
5		2	1/1/1991	Male	301
6			1/1/1991	Female	270
7			1/1/1992	Male	330

Synopsis

beefblup [-G SNPs_file] [-M num_response_vars] [-o report_spreadsheet]
[--no-aod] [--no-year] [--no-season] [--no-autob] [--maternal] input_file
[report_file]

Command line basic syntax

The most basic input is to simply pass the input file name to the program.

beefblup filename.csv

In this case beefblup will insert fixed-effects for age-of-dam, year, and season, and will calculate the EBVs for the response variable in the final column. The report will then be saved as filename_report.txt.

Suppressing automatically-calculated fixed effects

If you don't wish to include one of the automatically calculated fixed-effects from your model, you can pass arguments to suppress them.

Suppress Age-of-dam

beefblup --no-aod filename.csv

Suppress year

beefblup --no-year filename.csv

Suppress season

beefblup --no-season filename.csv

Suppress all calculated fixed effects

beefblup --no-autob filename.csv

The argument --no-autob comes from the nomenclature of assigning fixed-effects to the matrix b in Henderson's mixed-model equations.

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