Man pages for sommer
Solving Mixed Model Equations in R

add.diallel.vars	add.diallel.vars
adiag1	Binds arrays corner-to-corner
A.mat	Additive relationship matrix
anova_mmes	anova form a GLMM fitted with mmes
AR1mat	Autocorrelation matrix of order 1.
ARMAmat	Autocorrelation Moving average.
atcg1234	Letter to number converter
atcg1234BackTransform	Letter to number converter
atm	atm covariance structure
bathy.colors	Generate a sequence of colors for plotting bathymetric data.
bbasis	Function for creating B-spline basis functions (Eilers &...
build.HMM	Build a hybrid marker matrix using parental genotypes from...
coef_mmes	coef form a GLMM fitted with mmes
corImputation	Imputing a matrix using correlations
covm	covariance between random effects
csm	customized covariance structure
CSmat	Compound symmetry matrix
DEPRECATED_GWAS	Genome wide association study analysis
DEPRECATED_MMER	mixed model equations for r records
DEPRECATED_summary_mmer	summary form a GLMM fitted with mmer
DEPRECATED_VS	variance structure specification
DEPRECATED_VSR	variance structure specification
dfToMatrix	data frame to matrix
D.mat	Dominance relationship matrix
dsm	diagonal covariance structure
DT_augment	DT_augment design example.
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_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...
DT_rice	Rice lines dataset
DT_sleepstudy	Reaction times in a sleep deprivation study
DT_technow	Genotypic and Phenotypic data from single cross hybrids...
DT_wheat	wheat lines dataset
DT_yatesoats	Yield of oats in a split-block experiment
E.mat	Epistatic relationship matrix
fitted_mmes	fitted form a LMM fitted with mmes
fixm	fixed indication matrix
H.mat	Combined relationship matrix H
impute	Imputing a numeric or character vector
ism	identity covariance structure
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
manhattan	Creating a manhattan plot
map.plot	Creating a genetic map plot
mmes	mixed model equations solver
neMarker	Effective population size based on marker matrix
overlay	Overlay Matrix
plot_mmes	plot form a LMM plot with mmes
plot.monitor	plot the change of VC across iterations
predict_mmes	Predict form of a LMM fitted with mmes
propMissing	Proportion of missing data
r2	Reliability
randef	extracting random effects
redmm	Reduced Model Matrix
residuals_mmes	Residuals form a GLMM fitted with mmes
rrm	reduced rank covariance structure
simGECorMat	Create a GE correlation matrix for simulation purposes.
sommer-package	Solving Mixed Model Equations in R
spl2Dc	Two-dimensional penalised tensor-product of marginal B-Spline...
spl2Dmats	Get Tensor Product Spline Mixed Model Incidence Matrices
stackTrait	Stacking traits in a dataset
stan	Standardize a vector of values in range 0 to 1
summary_mmes	summary form a GLMM fitted with mmes
tps	Get Tensor Product Spline Mixed Model Incidence Matrices
tpsmmbwrapper	Get Tensor Product Spline Mixed Model Incidence Matrices
transp	Creating color with transparency
unsm	unstructured indication matrix
usm	unstructured covariance structure
vpredict	vpredict form of a LMM fitted with mmes
vsm	variance structure specification
wald	Wald Test for Model Coefficients