sommer
To install this source on your computer type in the R terminal
library(devtools)
install_github('covaruber/sommer')
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Version
Install
install.packages('sommer')Monthly Downloads
7,425
Version
4.1.1
License
GPL (>= 2)
Maintainer
Giovanny Covarrubias-Pazaran
Last Published
September 30th, 2020
Functions in sommer (4.1.1)
D.mat
Dominance relationship matrix
AR1
Autocorrelation matrix of order 1.
CS
Compound symmetry matrix
ARMA
Autocorrelation Moving average.
DT_cpdata
Genotypic and Phenotypic data for a CP population
A.mat
Additive relationship matrix
DT_btdata
Blue Tit Data for a Quantitative Genetic Experiment
DT_example
Broad sense heritability calculation.
DT_cornhybrids
Corn crosses and markers
DT_augment
DT_augment design example.
DT_halfdiallel
half diallel data for corn hybrids
DT_legendre
Simulated data for random regression
DT_rice
Rice lines dataset
DT_polyploid
Genotypic and Phenotypic data for a potato polyploid population
DT_expdesigns
Data for different experimental designs
DT_technow
Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
DT_wheat
wheat lines dataset
DT_h2
Broad sense heritability calculation.
DT_fulldiallel
Full diallel data for corn hybrids
DT_gryphon
Gryphon data from the Journal of Animal Ecology
at
at covariance structure
adiag1
Binds arrays corner-to-corner
DT_yatesoats
Yield of oats in a split-block experiment
E.mat
Epistatic relationship matrix
GWAS2
Genome wide association study
GWAS
Genome wide association study analysis
atcg1234
Letter to number converter
anova.mmer
anova form a GLMM fitted with mmer
fill.design
Filling the design of an experiment
fcm
fixed effect constraint indication matrix
cs
customized covariance structure
MEMMA
Multivariate Efficient Mixed Model Association Algorithm
EM
Expectation Maximization Algorithm
list2usmat
list or vector to unstructured matrix
leg
Legendre polynomial matrix
jet.colors
Generate a sequence of colors alog the jet colormap.
ds
diagonal covariance structure
manhattan
Creating a manhattan plot
pedtoK
Pedigree to matrix
randef
extracting random effects
bathy.colors
Generate a sequence of colors for plotting bathymetric data.
pin
pin functionality
fitted.mmer
fitted form a GLMM fitted with mmer
bivariateRun
bivariateRun functionality
unsm
unstructured indication matrix
fixm
fixed indication matrix
residuals.mmer
Residuals form a GLMM fitted with mmer
us
unstructured covariance structure
imputev
Imputing a numeric or character vector
h2.fun
Obtain heritabilities with three different methods
vs
variance structure specification
simGECorMat
Create a GE correlation matrix for simulation purposes.
wald.test
Wald Test for Model Coefficients
sommer-package
Solving Mixed Model Equations in R
spatPlots
Spatial plots
mmer2
mixed model equations in R
build.HMM
Build a hybrid marker matrix using parental genotypes
transp
Creating color with transparency
spl2D
Two-dimensional penalised tensor-product of marginal B-Spline basis.
coef.mmer
coef form a GLMM fitted with mmer
uncm
unconstrained indication matrix
overlay
Overlay Matrix
predict.mmer
Predict form a LMM fitted with mmer
map.plot
Creating a genetic map plot
mmer
mixed model equations in R
plot.mmer
plot form a LMM plot with mmer
transformConstraints
transformConstraints
summary.mmer
summary form a GLMM fitted with mmer