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spaMM (version 4.1.20)

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

1,720

Version

4.1.20

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

December 12th, 2022

Functions in spaMM (4.1.20)

COMPoisson

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

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

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

Extractors for information criteria such as AIC
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
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
MSFDR

Multiple-Stage False Discovery Rate procedure
algebra

Control of matrix-algebraic methods
pseudoR2

Pseudo R-squared
WinterWheat

Example of yield stability analysis
ZAXlist

S4 classes for structured matrices
MaternIMRFa

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

Tests of fixed effects (LRTs and ANOVA tables).
adjlg

Simulated data set for testing sparse-precision code
MaternCorr

Matern correlation function and Matern formula term.
PLS-internals

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

Fitting autoregressive models
corMatern

Matern Correlation Structure as a corSpatial object
convergence

Assessing convergence for fitted models
beta_resp

Beta-response family object
composite-ranef

Composite random effects
blackcap

Genetic polymorphism in relation to migration in the blackcap
as_LMLT

Conversion to input for procedures from lmerTest package
arabidopsis

Arabidopsis genetic and climatic data
control.HLfit

Control parameters of the HLfit fitting algorithm
confint.HLfit

Confidence intervals
corr_family

corr_family objects
corrMatrix

Using a corrMatrix argument
div_info

Information about numerical problems
corrFamily-design

Designing new corrFamily descriptors for parametric correlation families
covStruct

Specifying correlation structures
corrFamily-definition

corrFamily definition
corrHLfit

Fits a mixed model, typically a spatial GLMM.
corrFamily

Using corrFamily constructors and descriptors.
diallel

Random-effect structures for diallel experiments and other dyadic interactions
dofuture

Interface for parallel computations
dopar

Interface for parallel computations
extreme_eig

Utilities for regularization of a matrix
extractors

Functions to extract various components of a fit.
fixedLRT

Likelihood ratio test of fixed effects.
eval_replicate

Evaluating bootstrap replicates
fix_predVar

Prediction from models with nearly-singular covariance matrices
drop1.HLfit

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

Fixing some parameters
fitmv

Fitting multivariate responses
fitme

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

Freight dataset
how

Extract information about how an object was obtained
get_matrix

Extract matrices from a fit
get_cPredVar

Estimation of prediction variance with bootstrap correction
get_ranPars

Operations on lists of parameters
get_RLRsim_args

Extractors of arguments for functions from package RLRsim
good-practice

Clear and trustworthy formulas and prior weights
hatvalues.HLfit

Leverage extractor for HLfit objects
get_inits_from_fit

Initiate a fit from another fit
inits

Controlling optimization strategy through initial values
inverse.Gamma

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

Scaled distances between unique locations
mat_sqrt

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

Virtual factor for multivariate responses
llm.fit

Link-linear regression models (LLMs)
method

Fitting methods (objective functions maximized)
external-libraries

Installing external libraries
mapMM

Colorful plots of predictions in two-dimensional space.
is_separated

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

Analyzing multinomial data
pedigree

Fit mixed-effects models incorporating pedigrees
negbin

Family function for negative binomial “2” response (including truncated variant).
post-fit

Applying post-fit procedures on spaMM results
numInfo

Information matrix
phiHGLM

Fitting random effects in the residual dispersion model
options

spaMM options settings
negbin1

Alternative negative-binomial family
plot_effects

Partial-dependence effects and plots
plot.HLfit

Model checking plots for mixed models
Poisson

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

Lip cancer in Scotland 1975 - 1980
random-effects

Structure of random effects
register_cF

Declare corrFamily constructor for use in formula
predVar

Prediction and response variances
residuals.HLfit

Extract model residuals
predict

Prediction from a model fit
residVar

Residual variance extractor
salamander

Salamander mating data
seaMask

Masks of seas or lands
rankinfo

Checking the rank of the fixed-effects design matrix
spaMM-internal

Internal spaMM Functions
spaMM-conventions

spaMM conventions and differences from related fitting procedures
stripHLfit

Reduce the size of fitted objects
spaMM.colors

A flashy color palette.
spaMM.filled.contour

Level (Contour) Plots with better aspect ratio control (for geographical maps, at least)
spaMM-S3

S3 methods of generics defined in other packages
simulate.HLfit

Simulate realizations of a fitted model.
seeds

Seed germination data
spaMM

Inference in mixed models, in particular spatial GLMMs
vcov

Extract covariance or correlation components from a fitted model object
update.HLfit

Updates a fit
welding

Welding data set
wafers

Data from a resistivity experiment for semiconductor materials.
spaMM_boot

Parametric bootstrap
wrap_parallel

Selecting interfaces for parallelisation
verbose

Tracking progress of fits
summary.HLfit

Summary and print methods for fit and test results.