AIC                     Extractors for information criteria such as AIC
ARp                     Random effect with AR(p) (autoregressive of
                        order p) or ARMA(p,q) structure.
COMPoisson              Conway-Maxwell-Poisson (COM-Poisson) GLM family
CauchyCorr              Cauchy correlation function and Cauchy formula
                        term
DoF                     Degrees of freedom extractor
Gryphon                 Gryphon data
HLCor                   Fits a (spatially) correlated mixed model, for
                        given correlation parameters
HLfit                   Fit mixed models with given correlation matrix
LRT                     Likelihood ratio tests of fixed and random
                        effects.
Leuca                   Leucadendron data
Loaloa                  Loa loa prevalence in North Cameroon, 1991-2001
MSFDR                   Multiple-Stage False Discovery Rate procedure
MaternCorr              Matern correlation function and Matern formula
                        term.
MaternIMRFa             corrFamily constructor for Interpolated Markov
                        Random Field (IMRF) covariance structure
                        approximating a 2D Matern correlation model.
Poisson                 Family function for GLMs and mixed models with
                        Poisson and zero-truncated Poisson response.
WinterWheat             Example of yield stability analysis
X.GCA                   Fixed-effect terms for dyadic interactions
X2X                     Fitting fixed-effects coefficients shared
                        between submodels
ZAXlist                 S4 classes for structured matrices
adjlg                   Simulated data set for testing sparse-precision
                        code
algebra                 Control of matrix-algebraic methods
aliases                 Variable aliases for multivariate-response fits
anova                   ANOVA tables (and likelihood ratio tests).
arabidopsis             Arabidopsis genetic and climatic data
as_LMLT                 Conversion to input for procedures from
                        lmerTest package
autoregressive          Fitting autoregressive models
beta_resp               Beta-distribution family object
betabin                 Beta-binomial family object
blackcap                Genetic polymorphism in relation to migration
                        in the blackcap
clinics                 Toy dataset for binomial response
composite-ranef         Composite random effects
confint.HLfit           Confidence intervals
control.HLfit           Control parameters of the HLfit fitting
                        algorithm
convergence             Assessing convergence for fitted models
corMatern               Matern Correlation Structure as a corSpatial
                        object
corrFamily              Using corrFamily constructors and descriptors.
corrFamily-definition   corrFamily definition
corrFamily-design       Designing new corrFamily descriptors for
                        parametric correlation families
corrHLfit               Fits a mixed model, typically a spatial GLMM.
corrMatrix              Using the 'corrMatrix' and 'distmatrix'
                        arguments
corr_family             'corr_family' objects
covStruct               Specifying correlation structures
diallel                 Random-effect structures for symmetric or
                        antisymmetric dyadic interactions
div_info                Information about numerical problems
dofuture                Interface for parallel computations
dopar                   Interface for parallel computations
drop1.HLfit             Drop all possible single fixed-effect terms
                        from a model
dyad                    Correlated random effects in dyadic
                        interactions
eval_replicate          Evaluating bootstrap replicates
extractors              Functions to extract various components of a
                        fit.
extreme_eig             Utilities for regularization of a matrix
fitme                   Fitting function for fixed- and mixed-effect
                        models with GLM response.
fitmv                   Fitting multivariate responses
fix_predVar             Prediction from models with nearly-singular
                        covariance matrices
fixed                   Fixing some parameters
fixedLRT                Likelihood ratio test of fixed effects.
freight                 Freight dataset
get_RLRsim_args         Extractors of arguments for functions from
                        package RLRsim
get_cPredVar            Estimation of prediction variance with
                        bootstrap correction
get_inits_from_fit      Initiate a fit from another fit
get_matrix              Extract matrices from a fit
get_ranPars             Operations on lists of parameters
gof                     Goodness of fit test
good-practice           Clear and trustworthy formulas and prior
                        weights
hatvalues.HLfit         Leverage extractor for HLfit objects
how                     Extract information about how an object was
                        obtained
inits                   Controlling optimization strategy through
                        initial values
inverse.Gamma           Distribution families for Gamma and inverse
                        Gamma-distributed random effects
is_separated            Checking for (quasi-)separation in
                        binomial-response model.
lev2bool                Conversion of factor to 0/1 variable
llm.fit                 Link-linear regression models (LLMs)
make_scaled_dist        Scaled distances between unique locations
mapMM                   Colorful plots of predictions in
                        two-dimensional space.
mat_sqrt                Computation of "square root" of symmetric
                        positive definite matrix
method                  Fitting methods (objective functions maximized)
multIMRF                Interpolated Markov Random Field models
multinomial             Analyzing multinomial data
mv                      Virtual factor for multivariate responses
negbin                  Family function for negative binomial "2"
                        response (including truncated variant).
negbin1                 Alternative negative-binomial family
numInfo                 Information matrix
optimBounds             Optimization bounds
pedigree                Fit mixed-effects models incorporating
                        pedigrees
phi-resid.model         Residual dispersion model for gaussian and
                        Gamma response
plot.HLfit              Model checking plots for mixed models
plot_effects            Partial-dependence effects and plots
pois4mlogit             Fit multinomial logit models and
                        multivariate-response models including them.
post-fit                Applying post-fit procedures from other
                        packages on spaMM results
predVar                 Prediction and response variances
predict                 Prediction from a model fit
pseudoR2                Pseudo R-squared
random-effects          Structure of random effects
rankinfo                Checking the rank of the fixed-effects design
                        matrix
register_cF             Declare corrFamily constructor for use in
                        formula
resid.model             Structured dispersion models
residVar                Residual variance extractor
residuals.HLfit         Extract model residuals
salamander              Salamander mating data
scotlip                 Lip cancer in Scotland 1975 - 1980
seaMask                 Masks of seas or lands
seeds                   Seed germination data
setNbThreads            Parallel computations in fits
simulate.HLfit          Simulate realizations of a fitted model.
spaMM                   Inference in mixed models, in particular
                        spatial GLMMs
spaMM-conventions       spaMM conventions and differences from related
                        fitting procedures
spaMM.colors            A flashy color palette.
spaMM.filled.contour    Level (Contour) Plots with better aspect ratio
                        control (for geographical maps, at least)
spaMM.options           spaMM options settings
spaMM_boot              Parametric bootstrap
spaMM_glm.fit           Fitting generalized linear models without
                        initial-value or divergence headaches
stripHLfit              Reduce the size of fitted objects
summary.HLfit           Summary and print methods for fit and test
                        results.
transffit               Transformation of the data.
update.HLfit            Updates a fit
vcov                    Extract covariance or correlation components
                        from a fitted model object
verbose                 Tracking progress of fits
wafers                  Data from a resistivity experiment for
                        semiconductor materials.
welding                 Welding data set
wrap_parallel           Selecting interfaces for parallelisation
