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spaMM (version 4.5.0)

Mixed-Effect Models, with or without Spatial Random Effects

Description

Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 ), and Markov random field models on irregular grids (as considered in the 'INLA' package, ), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 ) are also implemented.

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Version

Install

install.packages('spaMM')

Monthly Downloads

2,256

Version

4.5.0

License

CeCILL-2

Maintainer

Last Published

June 9th, 2024

Functions in spaMM (4.5.0)

COMPoisson

Conway-Maxwell-Poisson (COM-Poisson) GLM family
DoF

Degrees of freedom extractor
ARp

Random effect with AR(p) (autoregressive of order p) or ARMA(p,q) structure.
HLCor

Fits a (spatially) correlated mixed model, for given correlation parameters
Gryphon

Gryphon data
HLfit

Fit mixed models with given correlation matrix
CauchyCorr

Cauchy correlation function and Cauchy formula term
spaMM_glm.fit

Fitting generalized linear models without initial-value or divergence headaches
multIMRF

Interpolated Markov Random Field models
ZAXlist

S4 classes for structured matrices
AIC

Extractors for information criteria such as AIC
adjlg

Simulated data set for testing sparse-precision code
MSFDR

Multiple-Stage False Discovery Rate procedure
MaternCorr

Matern correlation function and Matern formula term.
pseudoR2

Pseudo R-squared
WinterWheat

Example of yield stability analysis
algebra

Control of matrix-algebraic methods
as_LMLT

Conversion to input for procedures from lmerTest package
Leuca

Leucadendron data
arabidopsis

Arabidopsis genetic and climatic data
MaternIMRFa

corrFamily constructor for Interpolated Markov Random Field (IMRF) covariance structure approximating a 2D Matern correlation model.
PLS-internals

Internal functions for procedure using the ((I,0),(Z,X)) block-order
convergence

Assessing convergence for fitted models
clinics

Toy dataset for binomial response
LRT

ANOVA tables, and likelihood ratio tests of fixed and random effects.
control.HLfit

Control parameters of the HLfit fitting algorithm
composite-ranef

Composite random effects
confint.HLfit

Confidence intervals
corMatern

Matern Correlation Structure as a corSpatial object
autoregressive

Fitting autoregressive models
corrMatrix

Using a corrMatrix argument
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
betabin

Beta-binomial family object
corrFamily-definition

corrFamily definition
corrFamily-design

Designing new corrFamily descriptors for parametric correlation families
beta_resp

Beta-response family object
drop1.HLfit

Drop all possible single fixed-effect terms from a model
blackcap

Genetic polymorphism in relation to migration in the blackcap
corr_family

corr_family objects
extractors

Functions to extract various components of a fit.
extreme_eig

Utilities for regularization of a matrix
eval_replicate

Evaluating bootstrap replicates
X.GCA

Fixed-effect terms for dyadic interactions
div_info

Information about numerical problems
fix_predVar

Prediction from models with nearly-singular covariance matrices
fixedLRT

Likelihood ratio test of fixed effects.
fitme

Fitting function for fixed- and mixed-effect models with GLM response.
fitmv

Fitting multivariate responses
corrFamily

Using corrFamily constructors and descriptors.
corrHLfit

Fits a mixed model, typically a spatial GLMM.
dopar

Interface for parallel computations
dofuture

Interface for parallel computations
get_matrix

Extract matrices from a fit
get_ranPars

Operations on lists of parameters
good-practice

Clear and trustworthy formulas and prior weights
get_inits_from_fit

Initiate a fit from another fit
get_cPredVar

Estimation of prediction variance with bootstrap correction
llm.fit

Link-linear regression models (LLMs)
external-libraries

Installing external libraries
get_RLRsim_args

Extractors of arguments for functions from package RLRsim
covStruct

Specifying correlation structures
numInfo

Information matrix
make_scaled_dist

Scaled distances between unique locations
inits

Controlling optimization strategy through initial values
mapMM

Colorful plots of predictions in two-dimensional space.
hatvalues.HLfit

Leverage extractor for HLfit objects
is_separated

Checking for (quasi-)separation in binomial-response model.
mat_sqrt

Computation of “square root” of symmetric positive definite matrix
how

Extract information about how an object was obtained
options

spaMM options settings
method

Fitting methods (objective functions maximized)
inverse.Gamma

Distribution families for Gamma and inverse Gamma-distributed random effects
predVar

Prediction and response variances
predict

Prediction from a model fit
lev2bool

Conversion of factor to 0/1 variable
multinomial

Analyzing multinomial data
mv

Virtual factor for multivariate responses
plot_effects

Partial-dependence effects and plots
diallel

Random-effect structures for diallel experiments and other dyadic interactions
plot.HLfit

Model checking plots for mixed models
seaMask

Masks of seas or lands
setNbThreads

Parallel computations in fits
fixed

Fixing some parameters
simulate.HLfit

Simulate realizations of a fitted model.
pedigree

Fit mixed-effects models incorporating pedigrees
negbin

Family function for negative binomial “2” response (including truncated variant).
freight

Freight dataset
negbin1

Alternative negative-binomial family
rankinfo

Checking the rank of the fixed-effects design matrix
random-effects

Structure of random effects
spaMM.filled.contour

Level (Contour) Plots with better aspect ratio control (for geographical maps, at least)
spaMM_boot

Parametric bootstrap
phi-resid.model

Residual dispersion model for gaussian and Gamma response
scotlip

Lip cancer in Scotland 1975 - 1980
seeds

Seed germination data
spaMM-internal

Internal spaMM Functions
salamander

Salamander mating data
wrap_parallel

Selecting interfaces for parallelisation
spaMM

Inference in mixed models, in particular spatial GLMMs
post-fit

Applying post-fit procedures on spaMM results
Poisson

Family function for GLMs and mixed models with Poisson and zero-truncated Poisson response.
residVar

Residual variance extractor
residuals.HLfit

Extract model residuals
update.HLfit

Updates a fit
wafers

Data from a resistivity experiment for semiconductor materials.
summary.HLfit

Summary and print methods for fit and test results.
register_cF

Declare corrFamily constructor for use in formula
resid.model

Structured dispersion models
spaMM-conventions

spaMM conventions and differences from related fitting procedures
spaMM-S3

S3 methods of generics defined in other packages
welding

Welding data set
spaMM.colors

A flashy color palette.
stripHLfit

Reduce the size of fitted objects
vcov

Extract covariance or correlation components from a fitted model object
verbose

Tracking progress of fits