preselselcand: Preselection of selection candidates

In AquaBPsim: Aquaculture Breeding Program Simulation

Preselection of selection candidates

Description

Function to preselect selection candidates based on their Index/EBV/phenotype. Fish are preselected from the fish that are available for selection (ped$selcand==1). Fish that are not preselected will be assigned a value of 2 for ped$selcand. These fish will not be used in the function select.

Usage

preselselcand(
  gen,
  batch = 0,
  select_on = "Index",
  trait,
  Ntraits = BPdata$Ntraits,
  Nm,
  Nf,
  N,
  within_FSfam = FALSE,
  max_FSfam = "all"
)

Arguments

gen	The generation of the selection candidates. A vector of generations can be provided.
batch	The batch of the selection candidates. Default is 0. It is possible to provide a vector with multiple batches.
select_on	Options: "Index", "EBV" or "Phenotype". For "EBV" and "Phenotype", also the trait need to be specified in 'trait'. Default is Index.
trait	Which trait or EBV the selection is based on when option "EBV" or "Phenotype" is choosen in 'select on'.
Ntraits	Number of simulated traits. Does not need to be specified if Ntraits is specified in a list called 'BPdata'.
Nm	Number of males to preselect (In total or per full sib family, depending on within_FSfam).
Nf	Number of females to preselect (In total or per full sib family, depending on within_FSfam).
N	Total number of pre-selected fish. Does not need to be specified if Nm and Nf are specified.
within_FSfam	If True, pre-selection takes place within a full sib family. Default is False. Only use within family selection in a family design. Each full sib family must have at least Nm male sibs and Nf female sibs (or N sibs).
max_FSfam	Maximum number of sibs that can be selected per full sib familie, in case selection does not take place within a full sib family. Default is 'all'.

Value

This function will change the data frame called 'ped'. Fish that are not preselected will be assigned a value of 2 for ped$selcand.

Examples

ped <- founderpopfam(Nm = 60,
                     Nf = 60,
                     Nm2 = 0,
                     Nf2 = 0,
                     Ntraits = 2,
                     TraitsIndex = 2,
                     Rgen = matrix(c(1.00   , 0.48,
                                    0.48   , 1.00),
                                 nrow = 2),
                     Rcom = matrix(c(1.00  , 0.5,
                                    0.5   , 1.00),
                                 nrow = 2),
                     Rres = matrix(c(1.00   , 0.32,
                                    0.32   , 1.00),
                                 nrow = 2),
                     mean = c(50,500),
                     a_var = c(200,8000),
                     c_var = c(150,1000),
                     e_var = c(250,12000))
                     
Mating <- randommating(gen = 0,
                       Nfam_FS = 120)

for(fam in 1: nrow(Mating)){
ped <- offspringFSfam(gen = 1,
                      No = 100,
                      probmale = 0.5,
                      sire = Mating$Sire[fam],
                      dam = Mating$Dam[fam],
                      Ntraits = 2,
                      TraitsIndex = 2,
                      Rgen = matrix(c(1.00   , 0.48,
                                    0.48   , 1.00),
                                 nrow = 2),
                      Rcom = matrix(c(1.00  , 0.5,
                                    0.5   , 1.00),
                                 nrow = 2),
                      Rres = matrix(c(1.00   , 0.32,
                                    0.32   , 1.00),
                                 nrow = 2),
                      a_var = c(200,8000),
                      c_var = c(150,1000),
                      e_var = c(250,12000))
}

ped <- preselphen(gen = 1,
                  Nenv = 2,
                  Npresel = c(25,15),
                  trait = 1,
                  Ntraits = 2)
                  
ped <- avail_selection(gen = 1,
                       presel = 1,
                       surv = 0.9)
                       
ped <- breeding_values(gen = 1,
                       TraitsIndex = 2,
                       EBV = "GEBV",
                       GenomLength = 11.3,
                       Ne = 100,
                       SizeTraining = nrow(ped[ped$preselected ==2,]),
                       Ntraits = 2,
                       a_var = c(200,8000),
                       h2 = c(0.33,0.38))
                       
ped <- preselselcand(gen = 1,
                 Nm = 300,
                 Nf = 300,
                 max_FSfam = 15,
                 Ntraits = 2)

AquaBPsim documentation built on March 18, 2022, 6:40 p.m.