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enhancer: cool functions to enhance mixed models

Extension of the sommer, lme4breeding, evola, and ASRi packages to fit special structures. It is a dependency for all these packages.

Installation

You can install the development version of coolFuns from GitHub:

devtools::install_github('covaruber/coolFuns')

In addition, the package is also available on CRAN:

install.packages("coolFuns")

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Version

Install

install.packages('enhancer')

Version

1.1.0

License

GPL (>= 2)

Maintainer

Giovanny Covarrubias-Pazaran

Last Published

November 17th, 2025

Functions in enhancer (1.1.0)

DT_example

Broad sense heritability calculation.
DT_envs

Simulated phenotypic records for a set of 100 environments and 200 entries.
DT_gryphon

Gryphon data from the Journal of Animal Ecology
DT_halfdiallel

half diallel data for corn hybrids
DT_ige

Data to fit indirect genetic effects.
DT_legendre

Simulated data for random regression
DT_sleepstudy

Reaction times in a sleep deprivation study
DT_technow

Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
DT_mohring

Full diallel data for corn hybrids
DT_polyploid

Genotypic and Phenotypic data for a potato polyploid population
DT_h2

Broad sense heritability calculation.
add.diallel.vars

add.diallel.vars
bbasis

Function for creating B-spline basis functions (Eilers & Marx, 2010)
atcg1234BackTransform

Letter to number converter
I.matr

Identity relationship matrix
DT_rice

Rice lines dataset
DT_yatesoats

Yield of oats in a split-block experiment
atcg1234

Letter to number converter
bathy.colors

Generate a sequence of colors for plotting bathymetric data.
LD.decay

Calculation of linkage disequilibrium decay
adiag1

Binds arrays corner-to-corner
DT_wheat

wheat lines dataset
manhattan

Creating a manhattan plot
imputev

Imputing a numeric or character vector
leg

Legendre polynomial matrix
jet.colors

Generate a sequence of colors alog the jet colormap.
overlay

Overlay Matrix
neMarker

Effective population size based on marker matrix
build.HMM

Build a hybrid marker matrix using parental genotypes from inbred individuals
enhancer-package

Mixed Effect Model Enhancing Functions
logspace

Decreasing logarithmic trend
transp

Creating color with transparency
tps

Get Tensor Product Spline Mixed Model Incidence Matrices
map.plot

Creating a genetic map plot
rrm

reduced rank matrix
replaceValues

Replace the values of a vector
simage2

Shortcut to sparse matrix image
stan

Standardize a vector of values in range 0 to 1
simGECorMat

Create a GE correlation matrix for simulation purposes.
simage

Image of sparsity between two variables
wald.test

Wald Test for Model Coefficients
redmm

Reduced Model Matrix
propMissing

Proportion of missing data
DT_expdesigns

Data for different experimental designs
A.matr

Additive relationship matrix
DT_fulldiallel

Full diallel data for corn hybrids
DT_btdata

Blue Tit Data for a Quantitative Genetic Experiment
DT_big

Big GxE Quantitative Genetic Simulation
DT_cpdata

Genotypic and Phenotypic data for a CP population
DT_augment

DT_augment design example.
DT_cornhybrids

Corn crosses and markers