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spaMM (version 4.2.1)

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

4,070

Version

4.2.1

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

March 3rd, 2023

Functions in spaMM (4.2.1)

spaMM_glm.fit

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

Gryphon data
HLCor

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

Interpolated Markov Random Field models
HLfit

Fit mixed models with given correlation matrix
ARp

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

Extractors for information criteria such as AIC
Leuca

Leucadendron data
CauchyCorr

Cauchy correlation function and Cauchy formula term
COMPoisson

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

Example of yield stability analysis
algebra

Control of matrix-algebraic methods
adjlg

Simulated data set for testing sparse-precision code
MaternIMRFa

corrFamily constructor for Interpolated Markov Random Field (IMRF) covariance structure approximating a 2D Matern correlation model.
pseudoR2

Pseudo R-squared
ZAXlist

S4 classes for structured matrices
MSFDR

Multiple-Stage False Discovery Rate procedure
PLS-internals

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

Loa loa prevalence in North Cameroon, 1991-2001
MaternCorr

Matern correlation function and Matern formula term.
control.HLfit

Control parameters of the HLfit fitting algorithm
beta_resp

Beta-response family object
blackcap

Genetic polymorphism in relation to migration in the blackcap
convergence

Assessing convergence for fitted models
LRT

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

Confidence intervals
composite-ranef

Composite random effects
as_LMLT

Conversion to input for procedures from lmerTest package
autoregressive

Fitting autoregressive models
arabidopsis

Arabidopsis genetic and climatic data
corrFamily

Using corrFamily constructors and descriptors.
corrFamily-definition

corrFamily definition
covStruct

Specifying correlation structures
corrMatrix

Using a corrMatrix argument
corrHLfit

Fits a mixed model, typically a spatial GLMM.
corrFamily-design

Designing new corrFamily descriptors for parametric correlation families
diallel

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

Matern Correlation Structure as a corSpatial object
X.GCA

Fixed-effect terms for dyadic interactions
corr_family

corr_family objects
dopar

Interface for parallel computations
eval_replicate

Evaluating bootstrap replicates
extreme_eig

Utilities for regularization of a matrix
dofuture

Interface for parallel computations
fitme

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

Information about numerical problems
drop1.HLfit

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

Functions to extract various components of a fit.
fix_predVar

Prediction from models with nearly-singular covariance matrices
fitmv

Fitting multivariate responses
get_cPredVar

Estimation of prediction variance with bootstrap correction
fixedLRT

Likelihood ratio test of fixed effects.
good-practice

Clear and trustworthy formulas and prior weights
freight

Freight dataset
get_RLRsim_args

Extractors of arguments for functions from package RLRsim
hatvalues.HLfit

Leverage extractor for HLfit objects
fixed

Fixing some parameters
get_inits_from_fit

Initiate a fit from another fit
get_matrix

Extract matrices from a fit
get_ranPars

Operations on lists of parameters
how

Extract information about how an object was obtained
inits

Controlling optimization strategy through initial values
inverse.Gamma

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

Fitting methods (objective functions maximized)
mapMM

Colorful plots of predictions in two-dimensional space.
external-libraries

Installing external libraries
mat_sqrt

Computation of “square root” of symmetric positive definite matrix
llm.fit

Link-linear regression models (LLMs)
is_separated

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

Scaled distances between unique locations
plot.HLfit

Model checking plots for mixed models
negbin1

Alternative negative-binomial family
phi-resid.model

Residual dispersion model for gaussian and Gamma response
numInfo

Information matrix
mv

Virtual factor for multivariate responses
negbin

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

Partial-dependence effects and plots
pedigree

Fit mixed-effects models incorporating pedigrees
options

spaMM options settings
multinomial

Analyzing multinomial data
random-effects

Structure of random effects
register_cF

Declare corrFamily constructor for use in formula
predVar

Prediction and response variances
resid.model

Structured dispersion models
residVar

Residual variance extractor
predict

Prediction from a model fit
post-fit

Applying post-fit procedures on spaMM results
rankinfo

Checking the rank of the fixed-effects design matrix
Poisson

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

Extract model residuals
spaMM-conventions

spaMM conventions and differences from related fitting procedures
salamander

Salamander mating data
spaMM

Inference in mixed models, in particular spatial GLMMs
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
seaMask

Masks of seas or lands
seeds

Seed germination data
scotlip

Lip cancer in Scotland 1975 - 1980
spaMM-internal

Internal spaMM Functions
simulate.HLfit

Simulate realizations of a fitted model.
verbose

Tracking progress of fits
stripHLfit

Reduce the size of fitted objects
wrap_parallel

Selecting interfaces for parallelisation
vcov

Extract covariance or correlation components from a fitted model object
spaMM.colors

A flashy color palette.
spaMM_boot

Parametric bootstrap
update.HLfit

Updates a fit
summary.HLfit

Summary and print methods for fit and test results.
wafers

Data from a resistivity experiment for semiconductor materials.
welding

Welding data set