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.
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average-informationmixed-modelsrcpparmadilloopenblascppopenmp
12.84 score 59 stars 9 dependents 473 scripts 7.2k downloadslme4breeding - Breeding-Related 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'.
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7.07 score 14 stars 33 scripts 529 downloadsenhancer - Mixed-Effects Models Enhancing Functions
Special functions that enhance other mixed effect model packages by creating overlayed, reduced rank, and reduced model matrices together with multiple data sets to practice the use of these models. For more details see Covarrubias-Pazaran (2016) <doi:10.1371/journal.pone.0156744>.
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5.53 score 12 dependents 6.2k downloadsevola - Evolutionary Algorithm
Runs an evolutionary algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> .
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4.30 score 2 stars 7 scripts 277 downloads