A.mat |
Additive relationship matrix |
add.diallel.vars |
add.diallel.vars |
adiag1 |
Binds arrays corner-to-corner |
Ad_technow |
Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014) |
Af_technow |
Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014) |
anova.mmer |
anova form a GLMM fitted with mmer |
AR1 |
Autocorrelation matrix of order 1. |
ARMA |
Autocorrelation Moving average. |
at |
at covariance structure |
atcg1234 |
Letter to number converter |
A_example |
Broad sense heritability calculation. |
A_gryphon |
Gryphon data from the Journal of Animal Ecology |
A_ige |
Data to fit indirect genetic effects. |
bathy.colors |
Generate a sequence of colors for plotting bathymetric data. |
bbasis |
Function for creating B-spline basis functions (Eilers & Marx, 2010) |
bivariateRun |
bivariateRun functionality |
build.HMM |
Build a hybrid marker matrix using parental genotypes from inbred individuals |
coef.mmer |
coef form a GLMM fitted with mmer |
CS |
Compound symmetry matrix |
cs |
customized covariance structure |
D.mat |
Dominance relationship matrix |
dfToMatrix |
data frame to matrix |
ds |
diagonal covariance structure |
DTi_cornhybrids |
Corn crosses and markers |
DT_augment |
DT_augment design example. |
DT_btdata |
Blue Tit Data for a Quantitative Genetic Experiment |
DT_cornhybrids |
Corn crosses and markers |
DT_cpdata |
Genotypic and Phenotypic data for a CP population |
DT_example |
Broad sense heritability calculation. |
DT_expdesigns |
Data for different experimental designs |
DT_fulldiallel |
Full diallel data for corn hybrids |
DT_gryphon |
Gryphon data from the Journal of Animal Ecology |
DT_h2 |
Broad sense heritability calculation. |
DT_halfdiallel |
half diallel data for corn hybrids |
DT_ige |
Data to fit indirect genetic effects. |
DT_legendre |
Simulated data for random regression |
DT_mohring |
Full diallel data for corn hybrids |
DT_polyploid |
Genotypic and Phenotypic data for a potato polyploid population |
DT_rice |
Rice lines dataset |
DT_sleepstudy |
Reaction times in a sleep deprivation study |
DT_technow |
Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014) |
DT_wheat |
wheat lines dataset |
DT_yatesoats |
Yield of oats in a split-block experiment |
E.mat |
Epistatic relationship matrix |
EM |
Expectation Maximization Algorithm |
fcm |
fixed effect constraint indication matrix |
fitted.mmer |
fitted form a LMM fitted with mmer |
fixm |
fixed indication matrix |
GTn_rice |
Rice lines dataset |
GT_cornhybrids |
Corn crosses and markers |
GT_cpdata |
Genotypic and Phenotypic data for a CP population |
GT_polyploid |
Genotypic and Phenotypic data for a potato polyploid population |
GT_rice |
Rice lines dataset |
GT_wheat |
wheat lines dataset |
gvs |
general variance structure specification |
GWAS |
Genome wide association study analysis |
GWAS2 |
Genome wide association study |
H.mat |
Combined relationship matrix H |
h2.fun |
Obtain heritabilities with three different methods |
imputev |
Imputing a numeric or character vector |
jet.colors |
Generate a sequence of colors alog the jet colormap. |
LD.decay |
Calculation of linkage disequilibrium decay |
leg |
Legendre polynomial matrix |
list2usmat |
list or vector to unstructured matrix |
manhattan |
Creating a manhattan plot |
map.plot |
Creating a genetic map plot |
Md_technow |
Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014) |
MEMMA |
Multivariate Efficient Mixed Model Association Algorithm |
Mf_technow |
Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014) |
mmer |
*m*ixed *m*odel *e*quations in *R* |
mmer2 |
*m*ixed *m*odel *e*quations in *R* |
MP_cpdata |
Genotypic and Phenotypic data for a CP population |
MP_polyploid |
Genotypic and Phenotypic data for a potato polyploid population |
overlay |
Overlay Matrix |
plot.mmer |
plot form a LMM plot with mmer |
predict.mmer |
Predict form of a LMM fitted with mmer |
print.mmer |
summary form a GLMM fitted with mmer |
print.summary.mmer |
summary form a GLMM fitted with mmer |
print.wald.test |
Wald Test for Model Coefficients |
P_gryphon |
Gryphon data from the Journal of Animal Ecology |
randef |
extracting random effects |
residuals.mmer |
Residuals form a GLMM fitted with mmer |
simGECorMat |
Create a GE correlation matrix for simulation purposes. |
sommer |
*So*lving *M*ixed *M*odel *E*quations in *R* |
spl2Da |
Two-dimensional penalised tensor-product of marginal B-Spline basis. |
spl2Db |
Two-dimensional penalised tensor-product of marginal B-Spline basis. |
spl2Dmats |
Get Tensor Product Spline Mixed Model Incidence Matrices |
summary.mmer |
summary form a GLMM fitted with mmer |
tpsmmbwrapper |
Get Tensor Product Spline Mixed Model Incidence Matrices |
transformConstraints |
transformConstraints |
transp |
Creating color with transparency |
uncm |
unconstrained indication matrix |
unsm |
unstructured indication matrix |
us |
unstructured covariance structure |
vpredict |
vpredict form of a LMM fitted with mmer |
vpredict.mmer |
vpredict form of a LMM fitted with mmer |
vs |
variance structure specification |
wald.test |
Wald Test for Model Coefficients |