Skip to content

Hua-Zhou/MultiResponseVarianceComponentModels.jl

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

MultiResponseVarianceComponentModels

Latest Stable Code Style: Blue License CI Codecov Repo Size Aqua QA

MultiResponseVarianceComponentModels.jl is a Julia package that allows fitting and testing multivariate response variance components linear mixed models of form

Installation

julia> ]
pkg> add https://github.com/Hua-Zhou/MultiResponseVarianceComponentModels.jl.git

Documentation

Latest

Examples

using MultiResponseVarianceComponentModels, LinearAlgebra, Random

# simulation
begin
    Random.seed!(1234)
    n = 1_000  # number of observations
    d = 4      # number of responses
    p = 10     # number of covariates
    m = 3      # number of variance components
    X = rand(n, p)
    B = rand(p, d) # fixed effects
    V = [zeros(n, n) for _ in 1:m] # kernel matrices
    Σ = [zeros(d, d) for _ in 1:m] # variance components
    Ω = zeros(n * d, n * d) # overall nd-by-nd covariance matrix Ω
    for i in 1:m
        Vi = randn(n, n)
        mul!(V[i], transpose(Vi), Vi)
        Σi = randn(d, d)
        mul!(Σ[i], transpose(Σi), Σi)
        kron_axpy!(Σ[i], V[i], Ω) # Ω = Σ[1]⊗V[1] + ... + Σ[m]⊗V[m]
    end
    Ωchol = cholesky(Ω)
    Y = X * B + reshape(Ωchol.L * randn(n * d), n, d)
end

# maximum likelihood estimation
model = MRVCModel(Y, X, V)
fit!(model)

# residual maximum likelihood estimation
model = MRVCModel(Y, X, V; reml = true)
fit!(model)

References

  • H. Zhou, L. Hu, J. Zhou, and K. Lange: MM algorithms for variance components models (2019) (link)
  • M. Kim: Gene regulation in the human brain and the biological mechanisms underlying psychiatric disorders (2022) (link)

See also

  • J. Kim, J. Shen, A. Wang, D.V. Mehrotra, S. Ko, J.J. Zhou, and H. Zhou: VCSEL: Prioritizing SNP-set by penalized variance component selection (2021) (link)
  • L. Hu, W. Lu, J. Zhou, and H. Zhou: MM algorithms for variance component estimation and selection in logistic linear mixed models (2019) (link)
  • J.J. Zhou, T. Hu, D. Qiao, M.H. Cho, and H. Zhou: Boosting gene mapping power and efficiency with efficient exact variance component tests of single nucleotide polymorphism sets (2016) (link)

Contributors

About

Multivariate Response Variance Component Models

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Contributors 3

  •  
  •  
  •  

Languages