# Mixed-Effect Models, with or without Spatial Random Effects

## Documentation for package ‘spaMM’ version 4.6.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P R S T U V W X Z misc

spaMM-package | Inference in mixed models, in particular spatial GLMMs

## -- A --

adjacency | Fitting autoregressive models
adjlg | Simulated data set for testing sparse-precision code
adjlgMat | Simulated data set for testing sparse-precision code
AIC | Extractors for information criteria such as AIC
AIC.HLfit | Extractors for information criteria such as AIC
algebra | Control of matrix-algebraic methods
aliases | Variable aliases for multivariate-response fits
anova | ANOVA tables, and likelihood ratio tests of fixed and random effects.
anova.HLfit | ANOVA tables, and likelihood ratio tests of fixed and random effects.
anova.LMLT | ANOVA tables, and likelihood ratio tests of fixed and random effects.
antisym | Random-effect structures for symmetric or antisymmetric dyadic interactions
AR1 | Fitting autoregressive models
arabidopsis | Arabidopsis genetic and climatic data
ARMA | Random effect with AR(p) (autoregressive of order p) or ARMA(p,q) structure.
ARp | Random effect with AR(p) (autoregressive of order p) or ARMA(p,q) structure.
as_LMLT | Conversion to input for procedures from lmerTest package
as_precision | Specifying correlation structures
autoregressive | Fitting autoregressive models

## -- B --

barstyle | spaMM options settings
Beta | Fit mixed models with given correlation matrix
Beta-distribution-random-effects | Fit mixed models with given correlation matrix
betabin | Beta-binomial family object
beta_resp | Beta-distribution family object
beta_table | Extract covariance or correlation components from a fitted model object
binomialize | Analyzing multinomial data
blackcap | Genetic polymorphism in relation to migration in the blackcap

## -- C --

CAR | Fitting autoregressive models
Cauchy | Cauchy correlation function and Cauchy formula term
CauchyCorr | Cauchy correlation function and Cauchy formula term
CauchyCorr.default | Cauchy correlation function and Cauchy formula term
CauchyCorr.dgCMatrix | Cauchy correlation function and Cauchy formula term
CauchyCorr.dsCMatrix | Cauchy correlation function and Cauchy formula term
class:Kronfacto | S4 classes for structured matrices
class:LMLTslots | Conversion to input for procedures from lmerTest package
class:missingOrNULL | S4 classes for structured matrices
class:ZAXlist | S4 classes for structured matrices
clinics | Toy dataset for binomial response
coef.corMatern | Matern Correlation Structure as a corSpatial object
coef.HLfit | Functions to extract various components of a fit.
coef<-.corMatern | Matern Correlation Structure as a corSpatial object
combinepar | Interface for parallel computations
COMPoisson | Conway-Maxwell-Poisson (COM-Poisson) GLM family
composite-ranef | Composite random effects
confint | Confidence intervals
confint.HLfit | Confidence intervals
control.HLfit | Control parameters of the HLfit fitting algorithm
convergence | Assessing convergence for fitted models
corFactor.corMatern | Matern Correlation Structure as a corSpatial object
corMatern | Matern Correlation Structure as a corSpatial object
corMatrix.corMatern | Matern Correlation Structure as a corSpatial object
Corr | Extract covariance or correlation components from a fitted model 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 a corrMatrix argument
corrPars | Fixing some parameters
corr_family | 'corr_family' objects
covStruct | Specifying correlation structures
crossprod-method | S4 classes for structured matrices
crossprod-methods | S4 classes for structured matrices

## -- D --

deviance | Functions to extract various components of a fit.
deviance.HLfit | Functions to extract various components of a fit.
dev_resids | Functions to extract various components of a fit.
df.residual | Functions to extract various components of a fit.
df.residual.HLfit | Functions to extract various components of a fit.
DHARMa | Applying post-fit procedures from other packages on spaMM results
diagnose_conv | Information about numerical problems
diallel | Random-effect structures for symmetric or antisymmetric dyadic interactions
dim.Kronfacto | S4 classes for structured matrices
div_info | Information about numerical problems
DoF | Degrees of freedom extractor
dofuture | Interface for parallel computations
dopar | Interface for parallel computations
drop1 | Drop all possible single fixed-effect terms from a model
drop1.HLfit | Drop all possible single fixed-effect terms from a model
drop1.LMLT | Drop all possible single fixed-effect terms from a model
dyad | Correlated random effects in dyadic interactions

## -- E --

Earth | Scaled distances between unique locations
EarthChord | Scaled distances between unique locations
emmeans | Applying post-fit procedures from other packages on spaMM results
etaFix | Fixing some parameters
eval_replicate | Evaluating bootstrap replicates
extractAIC | Extractors for information criteria such as AIC
extractAIC.HLfit | Extractors for information criteria such as AIC
extractors | Functions to extract various components of a fit.
extreme_eig | Utilities for regularization of a matrix

## -- F --

family | Functions to extract various components of a fit.
family.HLfit | Functions to extract various components of a fit.
filled.mapMM | Colorful plots of predictions in two-dimensional space.
fitme | Fitting function for fixed- and mixed-effect models with GLM response.
fitmv | Fitting multivariate responses
fitted | Functions to extract various components of a fit.
fitted.HLfit | Functions to extract various components of a fit.
fitted.HLfitlist | Analyzing multinomial data
fixed | Fixing some parameters
fixedLRT | Likelihood ratio test of fixed effects.
fixef | Functions to extract various components of a fit.
fixef.HLfit | Functions to extract various components of a fit.
fixef.HLfitlist | Functions to extract various components of a fit.
fix_predVar | Prediction from models with nearly-singular covariance matrices
formula | Functions to extract various components of a fit.
formula.HLfit | Functions to extract various components of a fit.
formula_env | Clear and trustworthy formulas and prior weights
freight | Freight dataset

## -- G --

Gamma | Distribution families for Gamma and inverse Gamma-distributed random effects
geometric | Conway-Maxwell-Poisson (COM-Poisson) GLM family
getCovariate.corMatern | Matern Correlation Structure as a corSpatial object
getDistMat | Functions to extract various components of a fit.
get_any_IC | Extractors for information criteria such as AIC
get_cPredVar | Estimation of prediction variance with bootstrap correction
get_fittedPars | Operations on lists of parameters
get_fixefVar | Prediction from a model fit
get_inits_from_fit | Initiate a fit from another fit
get_intervals | Prediction from a model fit
get_matrix | Extract matrices from a fit
get_predCov_var_fix | Prediction from a model fit
get_predVar | Prediction from a model fit
get_rankinfo | Checking the rank of the fixed-effects design matrix
get_ranPars | Operations on lists of parameters
get_residVar | Prediction from a model fit
get_respVar | Prediction from a model fit
get_RLRsim_args | Extractors of arguments for functions from package RLRsim
get_RLRTSim_args | Extractors of arguments for functions from package RLRsim
get_ZALMatrix | Extract matrices from a fit
glht | Applying post-fit procedures from other packages on spaMM results
gof | Goodness of fit test
good-practice | Clear and trustworthy formulas and prior weights
Gryphon | Gryphon data
Gryphon_A | Gryphon data
Gryphon_df | Gryphon data
Gryphon_pedigree | Gryphon data
GxE | Example of yield stability analysis

## -- H --

hatvalues | Leverage extractor for HLfit objects
hatvalues.HLfit | Leverage extractor for HLfit objects
HLCor | Fits a (spatially) correlated mixed model, for given correlation parameters
HLfit | Fit mixed models with given correlation matrix
how | Extract information about how an object was obtained
how.default | Extract information about how an object was obtained
how.HLfit | Extract information about how an object was obtained
how.HLfitlist | Extract information about how an object was obtained
hyper | Interpolated Markov Random Field models

## -- I --

IMRF | Interpolated Markov Random Field models
Initialize.corMatern | Matern Correlation Structure as a corSpatial object
inits | Controlling optimization strategy through initial values
inla.spde2.matern | Interpolated Markov Random Field models
inla.spde2.pcmatern | Interpolated Markov Random Field models
intervals | Prediction from a model fit
inverse.Gamma | Distribution families for Gamma and inverse Gamma-distributed random effects
is_separated | Checking for (quasi-)separation in binomial-response model.
is_separated.formula | Checking for (quasi-)separation in binomial-response model.

## -- K --

keepInREML | Fixing some parameters
Kronfacto | S4 classes for structured matrices
Kronfacto-class | S4 classes for structured matrices

## -- L --

landMask | Masks of seas or lands
Leuca | Leucadendron data
lev2bool | Conversion of factor to 0/1 variable
LevenbergM | spaMM options settings
LL-family | Link-linear regression models (LLMs)
llm.fit | Link-linear regression models (LLMs)
lmerTest | Applying post-fit procedures from other packages on spaMM results
LMLTslots | Conversion to input for procedures from lmerTest package
LMLTslots-class | Conversion to input for procedures from lmerTest package
Loaloa | Loa loa prevalence in North Cameroon, 1991-2001
logDet.corMatern | Matern Correlation Structure as a corSpatial object
logLik | Functions to extract various components of a fit.
logLik.HLfit | Functions to extract various components of a fit.
logLik.HLfitlist | Analyzing multinomial data
LR2R2 | Pseudo R-squared
LRT | ANOVA tables, and likelihood ratio tests of fixed and random effects.

## -- M --

make_scaled_dist | Scaled distances between unique locations
mapMM | Colorful plots of predictions in two-dimensional space.
map_ranef | Colorful plots of predictions in two-dimensional space.
Matern | Matern correlation function and Matern formula term.
MaternCorr | Matern correlation function and Matern formula term.
MaternCorr.default | Matern correlation function and Matern formula term.
MaternCorr.dgCMatrix | Matern correlation function and Matern formula term.
MaternCorr.dsCMatrix | Matern correlation function and Matern formula term.
MaternIMRFa | corrFamily constructor for Interpolated Markov Random Field (IMRF) covariance structure approximating a 2D Matern correlation model.
mat_sqrt | Computation of "square root" of symmetric positive definite matrix
method | Fitting methods (objective functions maximized)
missingOrNULL | S4 classes for structured matrices
missingOrNULL-class | S4 classes for structured matrices
mm | Correlated random effects in dyadic interactions
mmfn | Correlated random effects in dyadic interactions
model.frame.HLfit | Functions to extract various components of a fit.
model.matrix.HLfit | Functions to extract various components of a fit.
model.matrix.LMLTslots | Conversion to input for procedures from lmerTest package
MSFDR | Multiple-Stage False Discovery Rate procedure
multcomp | Applying post-fit procedures from other packages on spaMM results
multi | Analyzing multinomial data
multIMRF | Interpolated Markov Random Field models
multinomial | Analyzing multinomial data
mv | Virtual factor for multivariate responses

## -- N --

negbin | Family function for negative binomial "2" response (including truncated variant).
negbin1 | Alternative negative-binomial family
negbin2 | Family function for negative binomial "2" response (including truncated variant).
Nmatrix | Lip cancer in Scotland 1975 - 1980
nobs | Functions to extract various components of a fit.
nobs.HLfit | Functions to extract various components of a fit.
numInfo | Information matrix

## -- O --

obsInfo | Fitting methods (objective functions maximized)
oceanmask | Masks of seas or lands

## -- P --

PAIRfn | Correlated random effects in dyadic interactions
pdep_effects | Partial-dependence effects and plots
pedigree | Fit mixed-effects models incorporating pedigrees
phi-resid.model | Residual dispersion model for gaussian and Gamma response
plot | Model checking plots for mixed models
plot.HLfit | Model checking plots for mixed models
plot_effects | Partial-dependence effects and plots
pois4mlogit | Fit multinomial logit models.
Poisson | Family function for GLMs and mixed models with Poisson and zero-truncated Poisson response.
post-fit | Applying post-fit procedures from other packages on spaMM results
predict | Prediction from a model fit
predict.HLfit | Prediction from a model fit
predict.pois4mlogit | Fit multinomial logit models.
Predictor | Specifying correlation structures
predVar | Prediction and response variances
preprocess_fix_corr | Prediction from a model fit
print | Summary and print methods for fit and test results.
print.corr_family | 'corr_family' objects
print.fixedLRT | Summary and print methods for fit and test results.
print.HLfit | Summary and print methods for fit and test results.
print.HLfitlist | Summary and print methods for fit and test results.
print.ranef | Functions to extract various components of a fit.
print.singeigs | Information matrix
prior.weights | Fit mixed models with given correlation matrix
pseudoR2 | Pseudo R-squared

## -- R --

ranCoefs | Fixing some parameters
ranCoefs_for_diag | Example of yield stability analysis
random-effects | Structure of random effects
ranef | Functions to extract various components of a fit.
ranef.HLfit | Functions to extract various components of a fit.
ranFix | Fixing some parameters
ranGCA | Random-effect structures for symmetric or antisymmetric dyadic interactions
rankinfo | Checking the rank of the fixed-effects design matrix
ranPars | Fixing some parameters
recalc.corMatern | Matern Correlation Structure as a corSpatial object
refit | Updates a fit
register_cF | Declare corrFamily constructor for use in formula
regularize | Utilities for regularization of a matrix
REMLformula | Fit mixed models with given correlation matrix
remove_from_parlist | Operations on lists of parameters
reshape2long | Fit multinomial logit models.
resid.model | Structured dispersion models
residuals | Extract model residuals
residuals.HLfit | Extract model residuals
residVar | Residual variance extractor
respName | Updates a fit
response | Functions to extract various components of a fit.
rho.mapping | Scaled distances between unique locations
RLRsim | Applying post-fit procedures from other packages on spaMM results

## -- S --

salamander | Salamander mating data
SAR_WWt | 'corr_family' objects
scotlip | Lip cancer in Scotland 1975 - 1980
seaMask | Masks of seas or lands
seeds | Seed germination data
separation | Checking for (quasi-)separation in binomial-response model.
setNbThreads | Parallel computations in fits
simulate | Simulate realizations of a fitted model.
simulate.HLfit | Simulate realizations of a fitted model.
simulate.HLfitlist | Simulate realizations of a fitted model.
simulate4boot | Simulate realizations of a fitted model.
simulate_ranef | Simulate realizations of a fitted model.
small_spde | Interpolated Markov Random Field models
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.getOption | spaMM options settings
spaMM.options | spaMM options settings
spaMM2boot | Parametric bootstrap
spaMMplot2D | Colorful plots of predictions in two-dimensional space.
spaMM_boot | Parametric bootstrap
spaMM_glm | Fitting generalized linear models without initial-value or divergence headaches
spaMM_glm.fit | Fitting generalized linear models without initial-value or divergence headaches
sparse_precision | Control of matrix-algebraic methods
str.inla.spde2 | Interpolated Markov Random Field models
stripHLfit | Reduce the size of fitted objects
summary | Summary and print methods for fit and test results.
summary.fixedLRT | Summary and print methods for fit and test results.
summary.HLfit | Summary and print methods for fit and test results.
summary.HLfitlist | Summary and print methods for fit and test results.

## -- T --

t.ZAXlist | S4 classes for structured matrices
tcrossprod-method | S4 classes for structured matrices
tcrossprod-methods | S4 classes for structured matrices
terms | Functions to extract various components of a fit.
terms.HLfit | Functions to extract various components of a fit.
Tnegbin | Family function for negative binomial "2" response (including truncated variant).
Tpoisson | Family function for GLMs and mixed models with Poisson and zero-truncated Poisson response.

## -- U --

unregister_cF | Declare corrFamily constructor for use in formula
update.formula | Updates a fit
update.HLfit | Updates a fit
update_formulas | Updates a fit
update_resp | Updates a fit

## -- V --

VarCorr | Extract covariance or correlation components from a fitted model object
VarCorr.HLfit | Extract covariance or correlation components from a fitted model object
Variogram.corMatern | Matern Correlation Structure as a corSpatial object
vcov | Extract covariance or correlation components from a fitted model object
vcov.HLfit | Extract covariance or correlation components from a fitted model object
verbose | Tracking progress of fits

## -- W --

wafers | Data from a resistivity experiment for semiconductor materials.
weights | Functions to extract various components of a fit.
weights.HLfit | Functions to extract various components of a fit.
welding | Welding data set
WinterWheat | Example of yield stability analysis
worldcountries | Masks of seas or lands
wrap_parallel | Selecting interfaces for parallelisation

## -- X --

X.antisym | Fixed-effect terms for dyadic interactions
X.GCA | Fixed-effect terms for dyadic interactions
X2X | Fitting multivariate responses

## -- Z --

ZAXlist | S4 classes for structured matrices
ZAXlist-class | S4 classes for structured matrices

## -- misc --

%*%-method | S4 classes for structured matrices
%*%-methods | S4 classes for structured matrices
.eval_replicate2 | Evaluating bootstrap replicates
`DHARMa-on-HLfit` | Model checking plots for mixed models