Mixed-Effects REML Incorporating Generalized Inverses.

gremlin

R package for mixed-effects model REML incorporating Generalized Inverses (so, with some mental gymnastics: GREMLIN).

See the latest developments:

• gremlin NEWS page

Overview of main branches:

• 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

To install gremlin:

• From R:
  • see the package page for the latest release of gremlin on CRAN where you can download the source.
  • install the latest release of the package directly in R:

install.packages("gremlin")

then select your favorite CRAN mirror

• From GitHub:
  • install the latest versions directly in R using the devtools package https://github.com/hadley/devtools:

library(devtools)

# Install `master` branch
install_github("matthewwolak/gremlin")

# Install `devel` branch
install_github("matthewwolak/gremlin", ref = "devel")

Examples

• Estimating autosomal additive and dominance genetic variances

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)