R
package for
mixed-effects model REML incorporating
Generalized Inverses (so, with some
mental gymnastics: GREMLIN).
master
branch is the most recent production version
(often the same as what is available from the R CRAN mirrors)
devel
branch is a preview of the next release which
should be functional and error/bug free, but proceed with
caution
R install.packages("gremlin")
then select your favorite CRAN mirrordevtools
package https://github.com/hadley/devtools:
``` library(devtools)# Install master
branch
install_github(“matthewwolak/gremlin”)
# Install devel
branch
install_github(“matthewwolak/gremlin”, ref = “devel”) ```
library(gremlin)
library(nadiv) #<-- needed for creating inverse relatedness matrices
# Set up a subset of data for the example
warcolak$IDD <- warcolak$ID
# Create generalized inverse matrices
Ainv <- makeAinv(warcolak[, 1:3])$Ainv
Dinv <- makeD(warcolak[, 1:3])$Dinv
# Basic model structure is as follows:
## Fixed effects of sex
## ID = autosomal additive genetic variance term
## IDD = autosomal dominance genetic variance term
grAD <- gremlin(trait1 ~ sex-1,
random = ~ ID + IDD,
ginverse = list(ID = Ainv, IDD = Dinv),
data = warcolak)
# Summary
nrow(warcolak)
summary(grAD)