[{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"CurrentModule = BeefBLUP","category":"page"},{"location":"beefblup-cli/#beefblup-Command-Line-Interface-(CLI)-documentation","page":"CLI Reference (WIP)","title":"beefblup Command Line Interface (CLI) documentation","text":"","category":"section"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"A work in progress","category":"page"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"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.","category":"page"},{"location":"beefblup-cli/#Input-file","page":"CLI Reference (WIP)","title":"Input file","text":"","category":"section"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"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.","category":"page"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"A beefblup data file must have at least six columns appearing in this order:","category":"page"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"ID\nSire ID\nDam ID\nBirthdate\nFixed effect(s)\nResponse variable(s)","category":"page"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"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.","category":"page"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"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.","category":"page"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"Unknown values should be left blank (,,). Do not substitute null placeholders (e.g. NULL, NA, 0, nothing, undefined, etc.) for unknown values.","category":"page"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"An example spreadsheet might have the following format","category":"page"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"ID Sire ID Dam ID Birthdate Sex Weaning Weight\n1 1/1/1990 Male 354\n2 1 1/1/1990 Female 251\n3 1 1/1/1991 Male 327\n4 1 2 1/1/1991 Female 328\n5 2 1/1/1991 Male 301\n6 1/1/1991 Female 270\n7 1/1/1992 Male 330","category":"page"},{"location":"beefblup-cli/#Synopsis","page":"CLI Reference (WIP)","title":"Synopsis","text":"","category":"section"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"beefblup [-G SNPs_file] [-M num_response_vars] [-o report_spreadsheet]\n[--no-aod] [--no-year] [--no-season] [--no-autob] [--maternal] input_file\n[report_file]","category":"page"},{"location":"beefblup-cli/#Command-line-basic-syntax","page":"CLI Reference (WIP)","title":"Command line basic syntax","text":"","category":"section"},{"location":"beefblup-cli/","page":"CLI Reference (WIP)","title":"CLI Reference (WIP)","text":"Themostbasicinputistosimplyp
