sommer (version 3.2)
Solving Mixed Model Equations in R
Description
Structural multivariate-univariate linear mixed model solver for multiple random effects allowing the specification of variance-covariance structures for random effects and allowing the fit of heterogeneous variance models (Covarrubias-Pazaran, 2016Copy Link
Version
Install
install.packages('sommer')Monthly Downloads
7,425
Version
3.2
License
GPL-3
Maintainer
Giovanny Covarrubias-Pazaran
Last Published
January 9th, 2018
Functions in sommer (3.2)
F1geno
Genotypes from an F1(CP) cross to show phasing
FDdata
Full diallel data for corn hybrids
EM
Expectation Maximization Algorithm
ExpDesigns
Data for different experimental designs
D.mat
Dominance relationship matrix
E.mat
Epistatic relationship matrix
adiag1
Binds arrays corner-to-corner
and
and functionality
blockerT
Applying transversal postblocking in a field
brewer.pal
Generate a sequence of colors for groups.
anova.MMERM
anova form a GLMM fitted with mmer
at
at functionality
eig
eigen decomposition functionality
example
Broad sense heritability calculation.
BTdata
Blue Tit Data for a Quantitative Genetic Experiment
CPdata
Genotypic and Phenotypic data for a CP population
GWAS
Genome Wide Association Analysis
fill.design
Filling the design of an experiment
fitted.MMERM
fitted form a GLMM fitted with mmer
imputev
Imputing a numeric or character vector
is.diagonal.matrix
Test for diagonal square matrix
A.mat
Additive relationship matrix
AI
Average Information Algorithm
matrix.trace
The trace of a matrix
maxi.qtl
Peak search by first derivatives
randef
extracting random effects
gryphondata
Gryphon data from the Journal of Animal Ecology
h2.fun
Obtain heritabilities with three different methods
manhattan
Creating a manhattan plot
MNR
Multivariate Newton-Raphson Algorithm
PolyData
Genotypic and Phenotypic data for a potato polyploid population
bathy.colors
Generate a sequence of colors for plotting bathymetric data.
big.peaks.col
Peak search by first derivatives
h2example
Broad sense heritability calculation.
residuals.MMERM
Residuals form a GLMM fitted with mmer
map.plot
Creating a genetic map plot
overlay
Overlay Matrix
pedtoK
Pedigree to matrix
vctable
vctable functionality
RICE
Rice lines dataset
Technow_data
Genotypic and Phenotypic data from single cross hybrids (Technow et al. (2014))
blocker
Applying postblocking in a field
blockerL
Applying linear postblocking in a field
cornHybrid
Corn crosses and markers
design.score
design score for the model to be tested
vctable.help
vctable.help functionality
g
g functionality
grp
grouping functionality
plot.MMERM
plot form a LMM plot with mmer
plot.variogram.MMERM
Default variogram.MMERM plotting
wheatLines
wheat lines dataset
HDdata
half diallel data for corn hybrids
MEMMA
Multivariate Efficient Mixed Model Association Algorithm
fdr
False Discovery Rate calculation
hadamard.prod
Hadamard product of two matrices
my.colors
All typical colors in R easy to access.
nna
Nearest neighbour adjustment
phase.F1
Phasing F1 (CP) data in biparental populations
pin
pin functionality
us
us functionality
variogram
Sample variogram
yates.oats
Yield of oats in a split-block experiment
hdm
Half Diallel Matrix
hits
Creating a fixed effect matrix with significant GWAS markers
mmer
mixed model equations in R
mmer2
mixed model equations in R
summary.MMERM
summary form a GLMM fitted with mmer
transp
Creating color with transparency
fdr2
False Discovery Rate calculation
GWAS2
Genome Wide Association Analysis
atcg1234
Letter to number converter
augment
augment design example.
build.HMM
Build a hybrid marker matrix using parental genotypes
coef.MMERM
coef form a GLMM fitted with mmer
is.square.matrix
Test for square matrix
jet.colors
Generate a sequence of colors alog the jet colormap.
score.calcMV
Score calculation for markers
sommer-package
Solving Mixed Model Equations in R
