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
4,273
Version
4.1.2
License
GPL (>= 2)
Maintainer
Giovanny Covarrubias-Pazaran
Last Published
January 6th, 2021
Functions in sommer (4.1.2)
DT_cornhybrids
Corn crosses and markers
A.mat
Additive relationship matrix
D.mat
Dominance relationship matrix
AR1
Autocorrelation matrix of order 1.
DT_btdata
Blue Tit Data for a Quantitative Genetic Experiment
DT_augment
DT_augment design example.
DT_cpdata
Genotypic and Phenotypic data for a CP population
ARMA
Autocorrelation Moving average.
CS
Compound symmetry matrix
DT_example
Broad sense heritability calculation.
DT_rice
Rice lines dataset
DT_fulldiallel
Full diallel data for corn hybrids
DT_expdesigns
Data for different experimental designs
DT_gryphon
Gryphon data from the Journal of Animal Ecology
DT_h2
Broad sense heritability calculation.
DT_mohring
Full diallel data for corn hybrids
DT_polyploid
Genotypic and Phenotypic data for a potato polyploid population
DT_sleepstudy
Reaction times in a sleep deprivation study
DT_legendre
Simulated data for random regression
DT_halfdiallel
half diallel data for corn hybrids
DT_yatesoats
Yield of oats in a split-block experiment
DT_wheat
wheat lines dataset
MEMMA
Multivariate Efficient Mixed Model Association Algorithm
GWAS
Genome wide association study analysis
EM
Expectation Maximization Algorithm
E.mat
Epistatic relationship matrix
H.mat
Combined relationship matrix H
DT_technow
Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014)
LD.decay
Calculation of linkage disequilibrium decay
GWAS2
Genome wide association study
at
at covariance structure
bivariateRun
bivariateRun functionality
bathy.colors
Generate a sequence of colors for plotting bathymetric data.
atcg1234
Letter to number converter
fixm
fixed indication matrix
dfToMatrix
data frame to matrix
fitted.mmer
fitted form a LMM fitted with mmer
cs
customized covariance structure
ds
diagonal covariance structure
fcm
fixed effect constraint indication matrix
imputev
Imputing a numeric or character vector
h2.fun
Obtain heritabilities with three different methods
anova.mmer
anova form a GLMM fitted with mmer
list2usmat
list or vector to unstructured matrix
manhattan
Creating a manhattan plot
adiag1
Binds arrays corner-to-corner
build.HMM
Build a hybrid marker matrix using parental genotypes
jet.colors
Generate a sequence of colors alog the jet colormap.
coef.mmer
coef form a GLMM fitted with mmer
leg
Legendre polynomial matrix
plot.mmer
plot form a LMM plot with mmer
overlay
Overlay Matrix
mmer2
mixed model equations in R
residuals.mmer
Residuals form a GLMM fitted with mmer
randef
extracting random effects
map.plot
Creating a genetic map plot
mmer
mixed model equations in R
unsm
unstructured indication matrix
uncm
unconstrained indication matrix
predict.mmer
Predict form of a LMM fitted with mmer
spl2D
Two-dimensional penalised tensor-product of marginal B-Spline basis.
us
unstructured covariance structure
summary.mmer
summary form a GLMM fitted with mmer
simGECorMat
Create a GE correlation matrix for simulation purposes.
sommer-package
Solving Mixed Model Equations in R
transp
Creating color with transparency
transformConstraints
transformConstraints
vpredict
vpredict functionality
wald.test
Wald Test for Model Coefficients
vs
variance structure specification