A.mat                   Additive relationship matrix
APY                     Construct an APY Relationship Precision Matrix
D.mat                   Dominance relationship matrix
E.mat                   Epistatic relationship matrix
GWAS                    Genome wide association study analysis
H.mat                   Combined relationship matrix H
MNR                     Multivariate Newton-Raphson algorithm
anova.mmes              anova form a GLMM fitted with mmes
antem                   Antedependence covariance structure
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.mmes               coef form a GLMM fitted with mmes
corImputation           Imputing a matrix using correlations
corgm                   General positive-definite correlation structure
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'
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
fam                     Factor-analytic covariance structure
familym                 Different distribution families for the traits
                        of a multi-trait model
fitted.mmes             fitted form a LMM fitted with mmes
fixm                    fixed indication matrix
ism                     Identity covariance structure
loadings_mmes           Extract factor-analytic loadings from a fitted
                        mmes model
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                    *m*ixed *m*odel *e*quations for *r* records
mmes                    *m*ixed *m*odel *e*quations *s*olver
ownm                    User-defined covariance structure
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
predict.mmes            Predict form of a LMM fitted with mmes
r2                      Reliability
randef                  extracting random effects
residuals.mmes          Residuals form a GLMM fitted with mmes
rotate_back_mmes        Back-transform rotated mmes random effects
rrm                     Reduced-rank covariance structure
sar                     Simultaneous autoregressive spatial covariance
                        structure
scores_mmes             Predict factor-analytic scores from a fitted
                        mmes model
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
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
usm                     Unstructured positive-definite covariance
                        structure
usr                     Unstructured covariance structure for 'mmer'
                        and 'vsr'
vcc                     Equality and scaling constraints between
                        variance parameters
vpredict                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
