Karl Broman (following the code in Nick Furlotte's pylmm)
In order to better understand pylmm, for linear mixed models for genome-wide association studies (GWAS), I wrote an R version of the algorithm.
Results compared to pylmm (and also the R package regress). [source]
Performance compared to pylmm. [source]
Install circplot from R-universe:
install.packages("lmmlite", repos=c("https://kbroman.r-universe.dev",
"https://cloud.r-project.org"))
Or install it from github using the remotes package:
install.packages("remotes")
library(remotes)
install_github("kbroman/lmmlite")
The Rcpp and RcppEigen packages will also be installed.
R/lmmlite is released under the GNU Affero GPL.
The code was developed following study of Nick Furlotte's pylmm code.