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: R install.packages("gremlin") then select your favorite CRAN mirror
• From GitHub:
  • install the latest versions directly in R using the remotes package https://github.com/r-lib/remotes:

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

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

Examples

Estimating autosomal additive and dominance genetic variances

library(gremlin)
library(nadiv)  #<-- needed for creating inverse relatedness matrices

# Add unique term for including individual effects of additive and dominance
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)

Summarize model

# Summary
nrow(warcolak)
summary(grAD)

Calculating combinations of (co)variances and quantifying uncertainty

Delta method

# Calculate proportions of phenotypic variances (and Std. Error)
deltaSE(h2 ~ V1 / (V1 + V2 + V3), grAD)
deltaSE(d2 ~ V2 / (V1 + V2 + V3), grAD)

Likelihood Ratio Test

• Hypothesis test: domimance variance=0

## Do this 2 alternative ways - both use `update()`:

### Either fix dominance variance to *almost* zero
grA_Dfxd <- update(grAD, Gstart = list(0.1, 1e-8), Gcon = list("P", "F"))

### Or drop dominance variance from the model
grA <- update(grAD, random = ~ ID)

## Compare log-likelihoods
logLik(grA_Dfxd)
logLik(grA)

## Do the Hypothesis test:
anova(grA, grAD)