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
4,314
Version
3.8
License
GPL (>= 2)
Maintainer
Giovanny Covarrubias-Pazaran
Last Published
January 2nd, 2019
Functions in sommer (3.8)
DT_polyploid
Genotypic and Phenotypic data for a potato polyploid population
MEMMA
Multivariate Efficient Mixed Model Association Algorithm
cs
customized covariance structure
ds
diagonal covariance structure
DT_technow
Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
DT_wheat
wheat lines dataset
EM
Expectation Maximization Algorithm
DT_halfdiallel
half diallel data for corn hybrids
DT_legendre
Simulated data for random regression
jet.colors
Generate a sequence of colors alog the jet colormap.
leg
Legendre polynomial matrix
atcg1234
Letter to number converter
at
at covariance structure
AR1
Autocorrelation matrix of order 1.
DT_yatesoats
Yield of oats in a split-block experiment
DT_h2
Broad sense heritability calculation.
DT_gryphon
Gryphon data from the Journal of Animal Ecology
GWAS
Genome wide association study
GWAS2
Genome wide association study
E.mat
Epistatic relationship matrix
map.plot
Creating a genetic map plot
DT_expdesigns
Data for different experimental designs
DT_fulldiallel
Full diallel data for corn hybrids
adiag1
Binds arrays corner-to-corner
sommer-package
Solving Mixed Model Equations in R
spatPlots
Spatial plots
fitted.mmer
fitted form a GLMM fitted with mmer
fcm
fixed effect constraint indication matrix
DT_rice
Rice lines dataset
mmer
mixed model equations in R
fill.design
Filling the design of an experiment
bathy.colors
Generate a sequence of colors for plotting bathymetric data.
uncm
unconstrained indication matrix
unsm
unstructured indication matrix
h2.fun
Obtain heritabilities with three different methods
fixm
fixed indication matrix
anova.mmer
anova form a GLMM fitted with mmer
pedtoK
Pedigree to matrix
imputev
Imputing a numeric or character vector
pin
pin functionality
randef
extracting random effects
residuals.mmer
Residuals form a GLMM fitted with mmer
transformConstraints
transformConstraints
transp
Creating color with transparency
spl2D
Two-dimensional penalised tensor-product of marginal B-Spline basis.
us
unstructured covariance structure
summary.mmer
summary form a GLMM fitted with mmer
bivariateRun
bivariateRun functionality
vs
variance structure
list2usmat
list or vector to unstructured matrix
build.HMM
Build a hybrid marker matrix using parental genotypes
coef.mmer
coef form a GLMM fitted with mmer
manhattan
Creating a manhattan plot
overlay
Overlay Matrix
plot.mmer
plot form a LMM plot with mmer
mmer2
mixed model equations in R
predict.mmer
Predict form a LMM fitted with mmer
ARMA
Autocorrelation Moving average.
CS
Compound symmetry matrix
A.mat
Additive relationship matrix
DT_cpdata
Genotypic and Phenotypic data for a CP population
DT_example
Broad sense heritability calculation.
D.mat
Dominance relationship matrix
DT_augment
DT_augment design example.
DT_btdata
Blue Tit Data for a Quantitative Genetic Experiment
DT_cornhybrids
Corn crosses and markers