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
4,080
Version
4.0.9
License
GPL (>= 2)
Maintainer
Giovanny Covarrubias-Pazaran
Last Published
February 7th, 2020
Functions in sommer (4.0.9)
CS
Compound symmetry matrix
DT_augment
DT_augment design example.
D.mat
Dominance relationship matrix
AR1
Autocorrelation matrix of order 1.
A.mat
Additive relationship matrix
ARMA
Autocorrelation Moving average.
DT_cornhybrids
Corn crosses and markers
DT_example
Broad sense heritability calculation.
DT_cpdata
Genotypic and Phenotypic data for a CP population
DT_btdata
Blue Tit Data for a Quantitative Genetic Experiment
DT_wheat
wheat lines dataset
DT_technow
Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
DT_legendre
Simulated data for random regression
DT_polyploid
Genotypic and Phenotypic data for a potato polyploid population
DT_h2
Broad sense heritability calculation.
fitted.mmer
fitted form a GLMM fitted with mmer
DT_rice
Rice lines dataset
DT_gryphon
Gryphon data from the Journal of Animal Ecology
anova.mmer
anova form a GLMM fitted with mmer
adiag1
Binds arrays corner-to-corner
DT_halfdiallel
half diallel data for corn hybrids
fixm
fixed indication matrix
DT_expdesigns
Data for different experimental designs
DT_fulldiallel
Full diallel data for corn hybrids
EM
Expectation Maximization Algorithm
MEMMA
Multivariate Efficient Mixed Model Association Algorithm
build.HMM
Build a hybrid marker matrix using parental genotypes
jet.colors
Generate a sequence of colors alog the jet colormap.
leg
Legendre polynomial matrix
list2usmat
list or vector to unstructured matrix
coef.mmer
coef form a GLMM fitted with mmer
GWAS
Genome wide association study analysis
cs
customized covariance structure
ds
diagonal covariance structure
GWAS2
Genome wide association study
manhattan
Creating a manhattan plot
mmer
mixed model equations in R
map.plot
Creating a genetic map plot
simGECorMat
Create a GE correlation matrix for simulation purposes.
sommer-package
Solving Mixed Model Equations in R
at
at covariance structure
DT_yatesoats
Yield of oats in a split-block experiment
spatPlots
Spatial plots
fcm
fixed effect constraint indication matrix
atcg1234
Letter to number converter
spl2D
Two-dimensional penalised tensor-product of marginal B-Spline basis.
fill.design
Filling the design of an experiment
residuals.mmer
Residuals form a GLMM fitted with mmer
randef
extracting random effects
vs
variance structure specification
transp
Creating color with transparency
uncm
unconstrained indication matrix
E.mat
Epistatic relationship matrix
bivariateRun
bivariateRun functionality
bathy.colors
Generate a sequence of colors for plotting bathymetric data.
h2.fun
Obtain heritabilities with three different methods
imputev
Imputing a numeric or character vector
mmer2
mixed model equations in R
us
unstructured covariance structure
overlay
Overlay Matrix
plot.mmer
plot form a LMM plot with mmer
unsm
unstructured indication matrix
predict.mmer
Predict form a LMM fitted with mmer
pedtoK
Pedigree to matrix
transformConstraints
transformConstraints
pin
pin functionality
summary.mmer
summary form a GLMM fitted with mmer