Vignettes:

Traits
  Background from existing vignette
    altAddTraitAD (its own section?)
  
  Practical examples
    How to get effects
    Manual adjustments 
    importation
      Mixture distributions
    rescaleTrait


SimpleGeneticSimulations
  In this vignette I will show how genetic simulations work using a simple examples. 
  I will start by showing how to simulate phenotypes from genotypes. I will then 
  show how to simulate new genotypes from existing genotypes.
  
  ## Simulating phenotypes from genotypes
  
  Simulating phenotypes from genotypes is a straightforward process that can be 
  done fairly easily using just base R functionality. 


QuantGen
  Introduction
    Point to vignette on traits as first step
    History
      Fisher (response to selection, variance components)
      Bulmer (genic variance)
    
  Decomposition of genetic values
    Reference population (HWE vs non-HWE)
    Breeding value
    Dominance deviations
    Epistatic deviations
    Variance, genic variance, LD covariance

Misc
  Introduction
  
  Explain individual level slot
    set/get
  
  Explain population slot
  
  Finalize pop?


GenomicSelection
  Introduction
    Point to genome (QTL/SNP) and trait
  
  How to build a training population
    Mention fixed effect
  
  How to fit a model
  
  How to get GEBVs
    Accuracy of selection (vs BV or GV, train vs pred)
  
  How to do selections
  
  Explain models
    Use Guilherme's paper
    Explain 1 vs 2
    
  How to use external software


DataImport
  Pull from example script
