- MASS  
- pedigree  

Simple R-codes (2 scripts) for multi-trait simulations

-function : 'makebasepop'

-function : 'makeoff'

• User defined number of traits

• User defined number of generations (Numgen=)

• selection of parents based on (sd=)
  A) random - no selection (rnd)
  B) Phenotypic selection (Phen/h or Phen/l)
  C) TBV ('tbv/h' or 'tbv/l')
  D) selection index based on TBV ('index/h' or 'index/l')
  D) selection index based on phenotypes ('phenindex/h' or 'phenindex/l')

• index weight (selindex=c())
  The index weight sums to 1 and it should have the same length as the number of traits It should be the same order as the traits specified

• mating design for selected animals (md=)
  A) random mating with random union of gamete (rnd_ug) [leads to pseudo-overlapping generations: mostly used in cattle breeding]
  B) nested mating designs (nested), i.e. specific mating ratio (e.g. 1:2 ; 1:25) [purely non-overlapping generations: mostly used in fish breeding]
  C) factorial design (factorial[n]); please specify in the square braket the number of mating pairs

• litter size per dam (ls=)

• which of the traits you want to select when selection is not random (trsel=)

• Sex ratio is fixed at 50% male and 50% female
• G and R covariance structure are needed in matrix format (even for a single triat simulation)

- Generation
- Pedigree structure (ID, Sire, Dam)
- Sex
- Inbreeding (Fped)
- True breeding values (number of columns equals number of traits)
- Residuals (number of columns equals number of traits)
- Phenotypes ((number of columns equals number of traits))

- Panya Sae-Lim  (panya.sae-lim@nofima.no)
- Binyam Dagnachew  
- Kristine Hov Martinsen  (kristine.martinsen@nofima.no)
- Bjarne Gjerde  (bjarne.gjerde@Nofima.no)