Solving Mixed Model Equations in R

Documentation for package ‘sommer’ version 4.5.12

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A.mat	Additive relationship matrix
analyze_mme_crossovers	Analyze Crossover Frontiers from MME Benchmarks
anova.mmer	anova form a GLMM fitted with mmes
anova.mmes	anova form a GLMM fitted with mmes
antem	Antedependence covariance structure
APY	Construct an APY Relationship Precision Matrix
ar1m	First-order autoregressive covariance structure
ar2m	Second-order autoregressive covariance structure
ar3m	Third-order autoregressive covariance structure
atm	Selected-level diagonal covariance structure
atr	Selected-level diagonal covariance structure for 'mmer' and 'vsr'
binm	Binomial proportion response with its number of trials
car	Proper conditional autoregressive spatial covariance structure
coef.mmer	coef form a GLMM fitted with mmes
coef.mmes	coef form a GLMM fitted with mmes
corgm	General positive-definite correlation structure
corImputation	Imputing a matrix using correlations
covm	Covariance Between Two Random Effects
covmatrix_mmes	Covariance and correlation matrix of a fitted term with standard errors
covparams_mmes	Extract native-scale covariance parameters from an mmes fit
covparams_mmes_se	Native-scale covariance parameters and standard errors
csm	Compound-symmetry covariance structure
csr	User-specified covariance-component structure for 'mmer' and 'vsr'
D.mat	Dominance relationship matrix
dfToMatrix	data frame to matrix
dsm	Diagonal heterogeneous covariance structure
dsr	Diagonal covariance structure for 'mmer' and 'vsr'
dsumm	Direct sum of residual covariance structures across sections
E.mat	Epistatic relationship matrix
fam	Factor-analytic covariance structure
familym	Different distribution families for the traits of a multi-trait model
fitted.mmer	fitted form a LMM fitted with mmes
fitted.mmes	fitted form a LMM fitted with mmes
fixm	fixed indication matrix
generate_mme_workload	Generate Parameterized MME Workloads for Solver Evaluation
GWAS	Genome wide association study analysis
H.mat	Combined relationship matrix H
ism	Identity covariance structure
loadings_mmes	Extract factor-analytic loadings from a fitted mmes model
ma1m	Moving-average covariance structures of order one or two
ma2m	Moving-average covariance structures of order one or two
mam	Moving-average covariance structures of order one or two
maternm	Matern spatial covariance structure
meffects_mmes	Marker effects recovered from a fitted relationship-based term
metricm	Distance-based (metric) spatial correlation structures
mmer	mixed model equations for r records
mmes	mixed model equations solver
mmes_control	Modular Numerical Controls for Mixed Models
mme_workload_grid	Generate a Factorial Grid of MME Workloads
MNR	Multivariate Newton-Raphson algorithm
ownm	User-defined covariance structure
plot.mmer	plot form a LMM plot with mmes
plot.mmes	plot form a LMM plot with mmes
pmonitor	plot the change of VC across iterations
postPEV	Post-fit prediction error variances and inverse coefficient matrix
postVarU	Post-fit Sampling Covariance of BLUPs
predict.mmer	Predict form of a LMM fitted with mmes
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.sommer_mmes_control	Print Modular Numerical Controls
print.sommer_mme_benchmark	Print method for sommer_mme_benchmark
print.sommer_mme_crossover	Print method for sommer_mme_crossover
print.sommer_mme_profile	Print method for sommer_mme_profile
print.summary.mmer	summary form a GLMM fitted with mmer
print.summary.mmes	summary form a GLMM fitted with mmes
print.wald.mmes	Wald tests for fixed effects with optional small-sample denominator df
profile_mme_workload	Profile an MME Workload by Phase
r2	Reliability
randef	extracting random effects
residuals.mmer	Residuals form a GLMM fitted with mmes
residuals.mmes	Residuals form a GLMM fitted with mmes
rotate_back_mmes	Back-transform rotated mmes random effects
rrm	Reduced-rank covariance structure
run_mme_benchmark	Run Experimental MME Benchmark Suite
sar	Simultaneous autoregressive spatial covariance structure
scores_mmes	Predict factor-analytic scores from a fitted mmes model
sommer	Solving Mixed Model Equations in R
spl2Da	Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Db	Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Dc	Two-dimensional penalised tensor-product of marginal B-Spline basis.
spl2Dmats	Get Tensor Product Spline Mixed Model Incidence Matrices
stackTraits	Stack several trait columns into the long format used by multi-trait models
strm	Covariance structure spanning several random terms
summary.mmer	summary form a GLMM fitted with mmer
summary.mmes	summary form a GLMM fitted with mmes
toeplitzm	General positive-definite Toeplitz correlation structure
tpsmmbwrapper	Get Tensor Product Spline Mixed Model Incidence Matrices
unsm	unstructured indication matrix
unsm2	unstructured indication matrix
usm	Unstructured positive-definite covariance structure
usr	Unstructured covariance structure for 'mmer' and 'vsr'
vcc	Equality and scaling constraints between variance parameters
vcParams	Equality and scaling constraints between variance parameters
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 model with arbitrary Kronecker covariance factors
vsr	variance structure specification
wald_mmes	Wald tests for fixed effects with optional small-sample denominator df