sommer - Solving Mixed Model Equations in R

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.

Last updated 19 days ago

average-informationmixed-modelsrcpparmadilloopenblascppopenmp

12.34 score 40 stars 9 dependents 280 scripts 3.8k downloads

lme4breeding - Relationship-Based Mixed-Effects Models

Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the 'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.

Last updated 4 days ago

5.16 score 6 stars 5 scripts 304 downloads

evola - Evolutionary Algorithm

Runs a genetic algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> and the coalescent simulator 'MaCS' <doi:10.1101/gr.083634.108>.

Last updated -1 hours ago

4.08 score 1 stars 3 scripts 212 downloads