# Mixed-Effect Models, Particularly Spatial Models

## Documentation for package ‘spaMM’ version 2.2.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N O P R S U V W

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

## -- A --

adjacency | Fitting autoregressive models
AIC | Functions to extract various components of a fit
AIC.HLfit | Functions to extract various components of a fit
anova | Likelihood ratio test of fixed effects.
anova.HLfit | Likelihood ratio test of fixed effects.
arabidopsis | Arabidopsis genetic and climatic data

## -- B --

Beta-distribution-random-effects | Fit mixed models with given correlation matrix
binomialize | Analyzing multinomial data
blackcap | Genetic polymorphism in relation to migration in the blackcap

## -- C --

CAR | Fitting autoregressive models
coef.corMatern | Matern Correlation Structure as a corSpatial object
coef<-.corMatern | Matern Correlation Structure as a corSpatial object
COMPoisson | Conway-Maxwell-Poisson (COM-Poisson) GLM family
confint | Confidence intervals for fixed-effect parameters
confint.HLfit | Confidence intervals for fixed-effect parameters
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 | Functions to extract various components of a fit
corrHLfit | Fits a mixed model, typically a spatial GLMM.
corrMatrix | Using a corrMatrix argument
covStruct | Specifying correlation structures

## -- D --

designL.from.Corr | Computation of "square root" of correlation matrix
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

## -- E --

Earth | Scaled distances between unique locations
extractors | Functions to extract various components of a fit

## -- F --

filled.mapMM | Colorful plots of predicted responses in two-dimensional space.
fitme | Fitting function for fixed- and mixed-effect models with GLM response.
fitted | Functions to extract various components of a fit
fitted.HLfit | Functions to extract various components of a fit
fitted.HLfitlist | Analyzing multinomial data
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
freight | Freight dataset

## -- G --

Gamma | Distribution families for Gamma and inverse Gamma-distributed random effects
getCovariate.corMatern | Matern Correlation Structure as a corSpatial object
getDistMat | Functions to extract various components of a fit
get_any_IC | Functions to extract various components of a fit
get_boot_response | Functions to extract various components of a fit
get_fixefVar | Prediction from a model fit.
get_intervals | Prediction from a model fit.
get_predCov_var_fix | Prediction from a model fit.
get_predVar | Prediction from a model fit.
get_residVar | Prediction from a model fit.
get_respVar | Prediction from a model fit.
get_RLRTSim_args | Functions to extract various components of a fit
get_ZALMatrix | Functions to extract various components of a fit
good-practice | Clear and trustworthy formulas

## -- H --

HLCor | Fits a (spatially) correlated mixed model, for given correlation parameters
HLfit | Fit mixed models with given correlation matrix

## -- I --

Initialize.corMatern | Matern Correlation Structure as a corSpatial object
intervals | Prediction from a model fit.
inverse.Gamma | Distribution families for Gamma and inverse Gamma-distributed random effects

## -- L --

landMask | Masks of seas or lands
LevenbergM | spaMM options settings
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
LRT | Likelihood ratio test of fixed effects.

## -- M --

make_scaled_dist | Scaled distances between unique locations
mapMM | Colorful plots of predicted responses 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.ff | Matern correlation function and Matern formula term.
multi | Analyzing multinomial data
multinomial | Analyzing multinomial data

## -- N --

negbin | Family function for negative binomial GLMs and mixed models.
Nmatrix | Lip cancer in Scotland 1975 - 1980

## -- O --

oceanmask | Masks of seas or lands

## -- P --

pedigree | Fit mixed-effects models incorporating pedigrees
phiHGLM | Fitting random effects in the residual dispersion model
plot | Model checking plots for mixed models
plot.HLfit | Model checking plots for mixed models
predict | Prediction from a model fit.
predict.HLfit | Prediction from a model fit.
Predictor | Interface for model formulas
preprocess_fix_corr | Prediction from a model fit.
print | Summary and print methods for fit and test results.
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.

## -- R --

ranef | Functions to extract various components of a fit
ranef.HLfit | Functions to extract various components of a fit
recalc.corMatern | Matern Correlation Structure as a corSpatial object
residuals | Functions to extract various components of a fit
residuals.HLfit | Functions to extract various components of a fit
rho.mapping | Scaled distances between unique locations

## -- S --

salamander | Salamander mating data
scotlip | Lip cancer in Scotland 1975 - 1980
seaMask | Masks of seas or lands
seeds | Seed germination data
separation | Checking separation in binomial-response models
simulate | Simulate realizations of a fitted model.
simulate.HLfit | Simulate realizations of a fitted model.
simulate.HLfitlist | 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.getOption | spaMM options settings
spaMM.options | spaMM options settings
spaMMplot2D | Colorful plots of predicted responses in two-dimensional space.
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 | Sparse_precision algorithm
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.
sym_eigen | Singular Value Decomposition of a Symmetric Matrix

## -- U --

update | Updates an HLCor or HLfit fit
update.HLfit | Updates an HLCor or HLfit fit

## -- V --

Variogram.corMatern | Matern Correlation Structure as a corSpatial object
vcov | Functions to extract various components of a fit
vcov.HLfit | Functions to extract various components of a fit

## -- W --

wafers | Data from a resistivity experiment for semiconductor materials.
welding | Welding data set
worldcountries | Masks of seas or lands