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spaMM (version 4.0.0)

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

1,866

Version

4.0.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

October 20th, 2022

Functions in spaMM (4.0.0)

multIMRF

Interpolated Markov Random Field models
HLCor

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

Loa loa prevalence in North Cameroon, 1991-2001
HLfit

Fit mixed models with given correlation matrix
AIC

Extractors for information criteria such as AIC
ARp

corrFamily constructors for random effect with AR(p) (autoregressive of order p) or ARMA(p,q) structure.
COMPoisson

Conway-Maxwell-Poisson (COM-Poisson) GLM family
spaMM_glm.fit

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

Control of matrix-algebraic methods
adjlg

Simulated data set for testing sparse-precision code
Gryphon

Gryphon data
MSFDR

Multiple-Stage False Discovery Rate procedure
MaternIMRFa

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

Matern correlation function and Matern formula term.
CauchyCorr

Cauchy correlation function and Cauchy formula term
PLS-internals

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

Example of yield stability analysis
LRT

Tests of fixed effects (LRTs and ANOVA tables).
control.HLfit

Control parameters of the HLfit fitting algorithm
arabidopsis

Arabidopsis genetic and climatic data
convergence

Assessing convergence for fitted models
composite-ranef

Composite random effects
beta_resp

Beta-response family object
corrFamily-definition

corrFamily definition
ZAXlist

S4 classes for structured matrices
corMatern

Matern Correlation Structure as a corSpatial object
confint.HLfit

Confidence intervals
as_LMLT

Conversion to input for procedures from lmerTest package
blackcap

Genetic polymorphism in relation to migration in the blackcap
autoregressive

Fitting autoregressive models
dofuture

Interface for parallel computations
corrFamily-design

Designing new corrFamily descriptors for parametric correlation families
corr_family

corr_family objects
diallel

Random-effect structures for diallel experiments and other symmetric dyadic interactions
corrHLfit

Fits a mixed model, typically a spatial GLMM.
div_info

Information about numerical problems
covStruct

Specifying correlation structures
corrFamily

Using corrFamily constructors and descriptors.
dopar

Interface for parallel computations
corrMatrix

Using a corrMatrix argument
extreme_eig

Utilities for regularization of a matrix
eval_replicate

Evaluating bootstrap replicates
fixedLRT

Likelihood ratio test of fixed effects.
fitme

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

Fixing some parameters
freight

Freight dataset
get_RLRsim_args

Extractors of arguments for functions from package RLRsim
fitmv

Fitting multivariate responses
fix_predVar

Prediction from models with nearly-singular covariance matrices
extractors

Functions to extract various components of a fit.
hatvalues.HLfit

Leverage extractor for HLfit objects
inits

Controlling optimization strategy through initial values
inverse.Gamma

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

Initiate a fit from another fit
get_ranPars

Operations on lists of parameters
get_matrix

Extract matrices from a fit
good-practice

Clear and trustworthy formulas and prior weights
how

Extract information about how an object was obtained
get_cPredVar

Estimation of prediction variance with bootstrap correction
get_infomat

Information matrix of fitted model
llm.fit

Link-linear regression models (LLMs)
method

Fitting methods (objective functions maximized)
external-libraries

Installing external libraries
is_separated

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

Colorful plots of predictions in two-dimensional space.
make_scaled_dist

Scaled distances between unique locations
mat_sqrt

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

Prediction and response variances
multinomial

Analyzing multinomial data
pedigree

Fit mixed-effects models incorporating pedigrees
phiHGLM

Fitting random effects in the residual dispersion model
plot.HLfit

Model checking plots for mixed models
plot_effects

Partial-dependence effects and plots
mv

Virtual factor for multivariate responses
predict

Prediction from a model fit
negbin1

Alternative negative-binomial family
options

spaMM options settings
scotlip

Lip cancer in Scotland 1975 - 1980
register_cF

Declare corrFamily constructor for use in formula
spaMM-S3

S3 methods of generics defined in other packages
seaMask

Masks of seas or lands
spaMM-conventions

spaMM conventions and differences from related fitting procedures
residVar

Residual variance extractor
negbin

Family function for negative binomial “2” response (including truncated variant).
spaMM.filled.contour

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

Seed germination data
simulate.HLfit

Simulate realizations of a fitted model.
spaMM_boot

Parametric bootstrap
random-effects

Structure of random effects
summary.HLfit

Summary and print methods for fit and test results.
update.HLfit

Updates a fit
Poisson

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

Extract model residuals
post-fit

Applying post-fit procedures on spaMM results
wrap_parallel

Selecting interfaces for parallelisation
salamander

Salamander mating data
rankinfo

Checking the rank of the fixed-effects design matrix
spaMM.colors

A flashy color palette.
stripHLfit

Reduce the size of fitted objects
spaMM-internal

Internal spaMM Functions
spaMM

Inference in mixed models, in particular spatial GLMMs
wafers

Data from a resistivity experiment for semiconductor materials.
vcov

Extract covariance or correlation components from a fitted model object
welding

Welding data set
verbose

Tracking progress of fits