# Mixed-Effects Models Enhancing Functions

## Documentation for package ‘enhancer’ version 1.1.1

- DESCRIPTION file.

## Help Pages

A.matr | Additive relationship matrix
add.diallel.vars | add.diallel.vars
adiag1 | Binds arrays corner-to-corner
Ad_technow | Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
Af_technow | Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
atcg1234 | Letter to number converter
atcg1234BackTransform | Letter to number converter
A_example | Broad sense heritability calculation.
A_gryphon | Gryphon data from the Journal of Animal Ecology
A_ige | Data to fit indirect genetic effects.
A_wheat | wheat lines dataset
bathy.colors | Generate a sequence of colors for plotting bathymetric data.
bbasis | Function for creating B-spline basis functions (Eilers & Marx, 2010)
build.HMM | Build a hybrid marker matrix using parental genotypes from inbred individuals
DTi_cornhybrids | Corn crosses and markers
DT_augment | DT_augment design example.
DT_big | Big GxE Quantitative Genetic Simulation
DT_btdata | Blue Tit Data for a Quantitative Genetic Experiment
DT_cornhybrids | Corn crosses and markers
DT_cpdata | Genotypic and Phenotypic data for a CP population
DT_envs | Simulated phenotypic records for a set of 100 environments and 200 entries.
DT_example | Broad sense heritability calculation.
DT_expdesigns | Data for different experimental designs
DT_fulldiallel | Full diallel data for corn hybrids
DT_gryphon | Gryphon data from the Journal of Animal Ecology
DT_h2 | Broad sense heritability calculation.
DT_halfdiallel | half diallel data for corn hybrids
DT_ige | Data to fit indirect genetic effects.
DT_legendre | Simulated data for random regression
DT_mohring | Full diallel data for corn hybrids
DT_polyploid | Genotypic and Phenotypic data for a potato polyploid population
DT_rice | Rice lines dataset
DT_sleepstudy | Reaction times in a sleep deprivation study
DT_technow | Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
DT_wheat | wheat lines dataset
DT_yatesoats | Yield of oats in a split-block experiment
enhancer | Mixed Effect Model Enhancing Functions
GTn_rice | Rice lines dataset
GT_cornhybrids | Corn crosses and markers
GT_cpdata | Genotypic and Phenotypic data for a CP population
GT_polyploid | Genotypic and Phenotypic data for a potato polyploid population
GT_rice | Rice lines dataset
GT_wheat | wheat lines dataset
I.matr | Identity relationship matrix
imputev | Imputing a numeric or character vector
jet.colors | Generate a sequence of colors alog the jet colormap.
LD.decay | Calculation of linkage disequilibrium decay
leg | Legendre polynomial matrix
logspace | Decreasing logarithmic trend
M | Simulated phenotypic records for a set of 100 environments and 200 entries.
manhattan | Creating a manhattan plot
map.plot | Creating a genetic map plot
Md_technow | Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
Mf_technow | Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
MP_cpdata | Genotypic and Phenotypic data for a CP population
MP_polyploid | Genotypic and Phenotypic data for a potato polyploid population
M_big | Big GxE Quantitative Genetic Simulation
neMarker | Effective population size based on marker matrix
overlay | Overlay Matrix
print.wald.test | Wald Test for Model Coefficients
propMissing | Proportion of missing data
P_gryphon | Gryphon data from the Journal of Animal Ecology
redmm | Reduced Model Matrix
replaceValues | Replace the values of a vector
rrm | reduced rank matrix
simage | Image of sparsity between two variables
simage2 | Shortcut to sparse matrix image
simGECorMat | Create a GE correlation matrix for simulation purposes.
stan | Standardize a vector of values in range 0 to 1
tps | Get Tensor Product Spline Mixed Model Incidence Matrices
transp | Creating color with transparency
W | Simulated phenotypic records for a set of 100 environments and 200 entries.
wald.test | Wald Test for Model Coefficients