Solving Mixed Model Equations in R
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Documentation for package ‘sommer’ version 4.4.1
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A B C D E F G H I J L M N O P R S T U V W
-- A --
| 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.mmes | anova form a GLMM fitted with mmes |
| AR1 | Autocorrelation matrix of order 1. |
| ARMA | Autocorrelation Moving average. |
| atcg1234 | Letter to number converter |
| atcg1234BackTransform | Letter to number converter |
| atm | atm covariance structure |
| A_example | Broad sense heritability calculation. |
| A_gryphon | Gryphon data from the Journal of Animal Ecology |
| A_ige | Data to fit indirect genetic effects. |
-- B --
| bathy.colors | Generate a sequence of colors for plotting bathymetric data. |
| bbasis | Function for creating B-spline basis functions (Eilers & Marx, 2010) |
| build.HMM | Build a hybrid marker matrix using parental genotypes from inbred individuals |
-- C --
| coef.mmes | coef form a GLMM fitted with mmes |
| corImputation | Imputing a matrix using correlations |
| covm | covariance between random effects |
| CS | Compound symmetry matrix |
| csm | customized covariance structure |
-- D --
| D.mat | Dominance relationship matrix |
| dfToMatrix | data frame to matrix |
| dsm | 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 --
| E.mat | Epistatic relationship matrix |
-- F --
| fitted.mmes | fitted form a LMM fitted with mmes |
| fixm | fixed indication matrix |
-- G --
| 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 |
| GWAS | Genome wide association study analysis |
-- H --
| H.mat | Combined relationship matrix H |
-- I --
| imputev | Imputing a numeric or character vector |
| ism | identity covariance structure |
-- J --
| jet.colors | Generate a sequence of colors alog the jet colormap. |
-- L --
| LD.decay | Calculation of linkage disequilibrium decay |
| leg | Legendre polynomial matrix |
| logspace | Decreasing logarithmic trend |
-- M --
| 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) |
| Mf_technow | Genotypic and Phenotypic data from single cross hybrids (Technow et al.,2014) |
| mmer | *m*ixed *m*odel *e*quations for *r* records |
| mmes | *m*ixed *m*odel *e*quations *s*olver |
| MP_cpdata | Genotypic and Phenotypic data for a CP population |
| MP_polyploid | Genotypic and Phenotypic data for a potato polyploid population |
-- N --
| neMarker | Effective population size based on marker matrix |
-- O --
| overlay | Overlay Matrix |
-- P --
| plot.mmes | plot form a LMM plot with mmes |
| pmonitor | plot the change of VC across iterations |
| predict.mmes | Predict form of a LMM fitted with mmes |
| print.mmer | summary form a GLMM fitted with mmer |
| print.mmes | summary form a GLMM fitted with mmes |
| print.summary.mmer | summary form a GLMM fitted with mmer |
| print.summary.mmes | summary form a GLMM fitted with mmes |
| print.wald.test | Wald Test for Model Coefficients |
| propMissing | Proportion of missing data |
| P_gryphon | Gryphon data from the Journal of Animal Ecology |
-- R --
| r2 | Reliability |
| randef | extracting random effects |
| redmm | Reduced Model Matrix |
| residuals.mmes | Residuals form a GLMM fitted with mmes |
| rrm | reduced rank covariance structure |
-- S --
| simGECorMat | Create a GE correlation matrix for simulation purposes. |
| sommer | *So*lving *M*ixed *M*odel *E*quations in *R* |
| spl2Dc | Two-dimensional penalised tensor-product of marginal B-Spline basis. |
| spl2Dmats | Get Tensor Product Spline Mixed Model Incidence Matrices |
| stackTrait | Stacking traits in a dataset |
| summary.mmer | summary form a GLMM fitted with mmer |
| summary.mmes | summary form a GLMM fitted with mmes |
-- T --
| tps | Get Tensor Product Spline Mixed Model Incidence Matrices |
| tpsmmbwrapper | Get Tensor Product Spline Mixed Model Incidence Matrices |
| transp | Creating color with transparency |
-- U --
| unsm | unstructured indication matrix |
| usm | unstructured covariance structure |
-- V --
| vpredict | vpredict form of a LMM fitted with mmes |
| vpredict.mmes | vpredict form of a LMM fitted with mmes |
| vs | variance structure specification |
| vsm | variance structure specification |
| vsr | variance structure specification |
-- W --
| wald.test | Wald Test for Model Coefficients |