Mixed-Effects Models Enhancing Functions

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Documentation for package ‘enhancer’ version 1.1.0

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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