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spaMM (version 3.11.3)

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

3.11.3

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

March 23rd, 2022

Functions in spaMM (3.11.3)

spaMM_glm.fit

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

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

Fit mixed models with given correlation matrix
COMPoisson

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

Cauchy correlation function and Cauchy formula term
Gryphon

Gryphon data
multIMRF

Interpolated Markov Random Field models
MSFDR

Multiple-Stage False Discovery Rate procedure
LRT

Likelihood ratio test of fixed effects.
arabidopsis

Arabidopsis genetic and climatic data
PLS-internals

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

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

Simulated data set for testing sparse-precision code
algebra

Control of matrix-algebraic methods
ZAXlist

S4 classes for structured matrices
WinterWheat

Example of yield stability analysis
corrFamily

Using corrFamily constructors and descriptors.
corrFamily-definition

corrFamily definition
corrFamily-design

Designing new corrFamily descriptors for parametric correlation families
corrHLfit

Fits a mixed model, typically a spatial GLMM.
blackcap

Genetic polymorphism in relation to migration in the blackcap
autoregressive

Fitting autoregressive models
corMatern

Matern Correlation Structure as a corSpatial object
convergence

Assessing convergence for fitted models
MaternCorr

Matern correlation function and Matern formula term.
composite-ranef

Composite random effects
extreme_eig

Utilities for regularization of a matrix
extractors

Functions to extract various components of a fit
confint.HLfit

Confidence intervals
div_info

Information about numerical problems
dofuture

Interface for parallel computations
fitme

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

Specifying correlation structures
corrMatrix

Using a corrMatrix argument
corr_family

corr_family objects
fix_predVar

Prediction from models with nearly-singular covariance matrices
fixedLRT

Likelihood ratio test of fixed effects.
get_inits_from_fit

Initiate a fit from another fit
get_matrix

Extract matrices from a fit
how

Extract information about how an object was obtained
hatvalues.HLfit

Leverage extractor for HLfit objects
fixed

Fixing some parameters
eval_replicate

Evaluating bootstrap replicates
dopar

Interface for parallel computations
get_cPredVar

Estimation of prediction variance with bootstrap correction
diallel

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

Extractors of arguments for functions from package RLRsim
freight

Freight dataset
good-practice

Clear and trustworthy formulas and prior weights
get_ranPars

Operations on lists of parameters
plot.HLfit

Model checking plots for mixed models
plot_effects

Partial-dependence effects and plots
multinomial

Analyzing multinomial data
register_cF

Declare corrFamily constructor for use in formula
mv

Virtual factor for multivariate responses
pedigree

Fit mixed-effects models incorporating pedigrees
fitmv

Fitting multivariate responses
residuals.HLfit

Extract model residuals
phiHGLM

Fitting random effects in the residual dispersion model
seeds

Seed germination data
simulate.HLfit

Simulate realizations of a fitted model.
is_separated

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

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

Controlling optimization strategy through initial values
post-fit

Applying post-fit procedures on spaMM results
Poisson

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

Colorful plots of predictions in two-dimensional space.
make_scaled_dist

Scaled distances between unique locations
spaMM

Inference in mixed models, in particular spatial GLMMs
mat_sqrt

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

Salamander mating data
spaMM-internal

Internal spaMM Functions
residVar

Residual variance extractor
external-libraries

Installing external libraries
stripHLfit

Reduce the size of fitted objects
spaMM.colors

A flashy color palette.
options

spaMM options settings
spaMM-S3

S3 methods of generics defined in other packages
negbin

Family function for GLMs and mixed models with negative binomial and zero-truncated negative binomial response.
spaMM-conventions

spaMM conventions and differences from related fitting procedures
predVar

Prediction and response variances
predict

Prediction from a model fit
update.HLfit

Updates a fit
summary.HLfit

Summary and print methods for fit and test results.
vcov

Extract covariance or correlation components from a fitted model object
wafers

Data from a resistivity experiment for semiconductor materials.
wrap_parallel

Selecting interfaces for parallelisation
welding

Welding data set
scotlip

Lip cancer in Scotland 1975 - 1980
seaMask

Masks of seas or lands
method

Fitting methods (objective functions maximized)
rankinfo

Checking the rank of the fixed-effects design matrix
spaMM.filled.contour

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

Structure of random effects
spaMM_boot

Parametric bootstrap