extract_selections: Extract selections from current generation
In arfesta/SimBreeder: Forward population breeding simulator

Description Usage Arguments Examples

View source: R/extract_selections.R

This function extracts selections from the current generation

extract_selections(num.cores = NULL, map.info, cross.design, past.tgv,
  past.phenos, parent.info, progeny.info, progeny.TGV, progeny.phenos,
  selection.strategy, among.family.selection = NULL,
  within.family.selection = NULL, num.selections.within.family = 1,
  num.selections.among.family = NULL, relationship.matrix.type = "pedigree",
  prefix = NULL, rep.num = NULL, reduced = F, weighted = F)

`num.cores`	Number of cores used to create marker based relatedness matrix
`map.info`	Object returned from create_genetic_map()
`cross.design`	Object returned from create_cross_design()
`past.tgv`	Object returned from previous generation
`past.phenos`	Object returned from previous generation
`parent.info`	Object returned from previous generation;
`progeny.info`	Object returned from make_crosses()
`progeny.TGV`	Object returned from calc_progeny_TGV()
`progeny.phenos`	Object returned from sim_progeny_phenos()
`selection.strategy`	Type of selection strategy to use. Currently either: "among.family" or "within.family". Default: "within.familiy"
`among.family.selection`	Type of selection strategy to use for among family selection: "ABLUP", "GBLUP", "Phenotype"
`within.family.selection`	Type of selection strategy to use for within family selection: "ABLUP", "GBLUP", "Phenotype"
`num.selections.within.family`	The number of selections that should be made within each family
`num.selections.among.family`	The number of selections that should be made among all families
`relationship.matrix.type`	The type of relationship matrix to estimate for selections: "markers" or "pedigree"
`prefix`	A prefix to add to the file if writing the file out
`rep.num`	The rep number of the current generation
`reduced`	logical. Set to TRUE if selecting less individuals than are in the total population
`weighted`	logical. Should relationship matrix be weighted by A matrix prior to BLUP estimation.
`save`	logical. Saves the output of genetic map (Default: FALSE)

progeny1.extractions <- extract_selections(num.cores = 3,map.info = the.map,cross.design = cross.file,progeny.info = progeny1,
parent.info = op.families,progeny.TGV = progeny1.TGV,progeny.phenos = progeny1.PHENOS,num.selections.among.family = 64,reduced = T,
relationship.matrix.type = "markers",among.family.selection = "GBLUP",within.family.selection = "NO",selection.strategy = "within.family",
past.tgv = parent.TGV,past.phenos = parent.PHENOS)