popImprovByMateSel: Run population improvement using mate selection

In wolfemd/alphaSimHlpR: Functions added to AlphaSimR to simplify simulating breeding schemes

Description

Function to improve a simulated breeding population by one cycle. Also specify selCritPop="genomicMateSelCrit" and use the following new bsp arguments to control the predictions and selection:

• modelType: modelTypes: "A", "AD", "DirDom"

• crossSelCrit: "MeanBV" (modelTypes: "A", "AD", "DirDom"); "MeanTGV" (only with modelType="DirDom"); "UCparent" (modelTypes: "A", "AD", "DirDom"); "UCvariety" (modelTypes: "AD", "DirDom")

• propSel: 0-1, prop. of predicted crosses to select, used ONLY to calc the standardized selection intensity (i) and subsequently the usefulness criteria (μ + i \times σ).

Usage

popImprovByMateSel(records, bsp, SP)

Arguments

records	The breeding program records object. See fillPipeline for details
bsp	A list of breeding scheme parameters
SP	The AlphaSimR SimParam object

Details

My changes:

• nTrainPopCycles: draw training pop clones only from this number of recent cycles.

• nYrsAsCandidates: candidates for selection only from this number of recent years

• maxTrainingPopSize: From the lines in the most recent cycles (indicated by nTrainPopCycles), subsample this number of lines for training data. This is in addition to the "check" (bsp$checks@id) and the lines indicates as selection 'candidates' according to the setting of 'nYrsAsCandidates'. All "historical" data will always be used, but the number of maximum training lines will be held constant. Replaces the stage-specific 'bsp$trainingPopCycles', which will be unused in this pipeline, but not deleted from the package.

This function uses phenotypic records coming out of the product pipeline to choose individuals as parents to initiate the next breeding cycle

Value

A records object with a new F1 Pop-class object of progeny coming out of a population improvement scheme

wolfemd/alphaSimHlpR documentation built on Sept. 19, 2021, 6:25 p.m.