gremlin

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

Cite as:

If your use of the gremlin package contributes to a publication, please cite the package as (and feel free to let me know!):

Wolak, M.E. 2018. gremlin: R package for mixed-effects model REML incorporating generalized Inverses. Version Insert version here. Zenodo http://doi.org/10.5281/zenodo.1476565.

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 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

gremlinR

• 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
tmpw <- warcolak[1:(72*10), ]  #<-- only use 10 units for poor young gremlin
tmpw$ID <- as.factor(as.character(tmpw$ID))
tmpw$IDD <- tmpw$ID

# Create generalized inverse matrices
Ainv <- makeAinv(tmpw[, 1:3])$Ainv
Dinv <- makeD(tmpw[, 1:3])$Dinv
  Dinv@Dimnames[[1]] <- as.character(tmpw$ID)

# Basic model structure is as follows:
## Fixed effects of sex
## ID  = autosomal additive genetic variance term
## IDD = autosomal dominance genetic variance term
system.time(grAD <- gremlinR(trait1 ~ sex-1,
	random = ~ ID + IDD,
	ginverse = list(ID = Ainv, IDD = Dinv),
	data = tmpw,
	maxit = 25, v = 2, vit = 1))

nrow(tmpw)
summary(grAD)