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spaMM (version 3.12.0)

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

3.12.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

June 19th, 2022

Functions in spaMM (3.12.0)

ARp

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

Interpolated Markov Random Field models
Gryphon

Gryphon data
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
spaMM_glm.fit

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

Likelihood ratio test of fixed effects.
MaternIMRFa

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

Cauchy correlation function and Cauchy formula term
PLS-internals

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

Arabidopsis genetic and climatic data
algebra

Control of matrix-algebraic methods
adjlg

Simulated data set for testing sparse-precision code
MSFDR

Multiple-Stage False Discovery Rate procedure
MaternCorr

Matern correlation function and Matern formula term.
ZAXlist

S4 classes for structured matrices
WinterWheat

Example of yield stability analysis
composite-ranef

Composite random effects
autoregressive

Fitting autoregressive models
corrFamily-definition

corrFamily definition
confint.HLfit

Confidence intervals
corMatern

Matern Correlation Structure as a corSpatial object
blackcap

Genetic polymorphism in relation to migration in the blackcap
corrFamily-design

Designing new corrFamily descriptors for parametric correlation families
convergence

Assessing convergence for fitted models
control.HLfit

Control parameters of the HLfit fitting algorithm
corrFamily

Using corrFamily constructors and descriptors.
corrHLfit

Fits a mixed model, typically a spatial GLMM.
div_info

Information about numerical problems
diallel

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

Evaluating bootstrap replicates
corr_family

corr_family objects
covStruct

Specifying correlation structures
dopar

Interface for parallel computations
dofuture

Interface for parallel computations
corrMatrix

Using a corrMatrix argument
extractors

Functions to extract various components of a fit
fixed

Fixing some parameters
get_inits_from_fit

Initiate a fit from another fit
fitmv

Fitting multivariate responses
extreme_eig

Utilities for regularization of a matrix
get_cPredVar

Estimation of prediction variance with bootstrap correction
fix_predVar

Prediction from models with nearly-singular covariance matrices
freight

Freight dataset
fixedLRT

Likelihood ratio test of fixed effects.
fitme

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

Extractors of arguments for functions from package RLRsim
external-libraries

Installing external libraries
inits

Controlling optimization strategy through initial values
how

Extract information about how an object was obtained
good-practice

Clear and trustworthy formulas and prior weights
hatvalues.HLfit

Leverage extractor for HLfit objects
make_scaled_dist

Scaled distances between unique locations
is_separated

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

Fitting random effects in the residual dispersion model
inverse.Gamma

Distribution families for Gamma and inverse Gamma-distributed random effects
plot.HLfit

Model checking plots for mixed models
mat_sqrt

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

Colorful plots of predictions in two-dimensional space.
get_ranPars

Operations on lists of parameters
get_matrix

Extract matrices from a fit
mv

Virtual factor for multivariate responses
negbin

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

Fitting methods (objective functions maximized)
pedigree

Fit mixed-effects models incorporating pedigrees
options

spaMM options settings
multinomial

Analyzing multinomial data
post-fit

Applying post-fit procedures on spaMM results
predict

Prediction from a model fit
residuals.HLfit

Extract model residuals
residVar

Residual variance extractor
predVar

Prediction and response variances
Poisson

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

Partial-dependence effects and plots
spaMM-conventions

spaMM conventions and differences from related fitting procedures
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)
seeds

Seed germination data
spaMM-internal

Internal spaMM Functions
seaMask

Masks of seas or lands
simulate.HLfit

Simulate realizations of a fitted model.
spaMM-S3

S3 methods of generics defined in other packages
vcov

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

Updates a fit
wafers

Data from a resistivity experiment for semiconductor materials.
welding

Welding data set
random-effects

Structure of random effects
wrap_parallel

Selecting interfaces for parallelisation
summary.HLfit

Summary and print methods for fit and test results.
register_cF

Declare corrFamily constructor for use in formula
rankinfo

Checking the rank of the fixed-effects design matrix
stripHLfit

Reduce the size of fitted objects
salamander

Salamander mating data
scotlip

Lip cancer in Scotland 1975 - 1980
spaMM.colors

A flashy color palette.
spaMM_boot

Parametric bootstrap