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spaMM (version 3.8.23)

Mixed-Effect Models, Particularly Spatial Models

Description

Inference based on mixed-effect models, including generalized linear mixed models with spatial correlations, multivariate responses, and models with non-Gaussian random effects (e.g., Beta). Various approximations of likelihood or restricted likelihood are implemented, in particular Laplace approximation and h-likelihood (Lee and Nelder 2001 ). Both classical geostatistical models, and Markov random field models on irregular grids (as considered in the 'INLA' package, ), can be fitted. Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model.

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Version

Install

install.packages('spaMM')

Monthly Downloads

1,866

Version

3.8.23

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

August 5th, 2021

Functions in spaMM (3.8.23)

HLCor

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

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

Gryphon data
MSFDR

Multiple-Stage False Discovery Rate procedure
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
multIMRF

Interpolated Markov Random Field models
spaMM_glm.fit

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

Cauchy correlation function and Cauchy formula term
confint.HLfit

Confidence intervals
AIC

Extractors for information criteria such as AIC
HLfit

Fit mixed models with given correlation matrix
LRT

Likelihood ratio test of fixed effects.
ZAXlist

ZAXlist class and (cross) products for ZAL matrix
MaternCorr

Matern correlation function and Matern formula term.
covStruct

Specifying correlation structures
div_info

Information about numerical problems
blackcap

Genetic polymorphism in relation to migration in the blackcap
PLS-internals

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

Assessing convergence for fitted models
autoregressive

Fitting autoregressive models
extractors

Functions to extract various components of a fit
eval_replicate

Evaluating bootstrap replicates
adjlg

Simulated data set for testing sparse-precision code
dofuture

Interface for parallel computations
arabidopsis

Arabidopsis genetic and climatic data
corMatern

Matern Correlation Structure as a corSpatial object
corrHLfit

Fits a mixed model, typically a spatial GLMM.
get_inits_from_fit

Initiate a fit from another fit
dopar

Interface for parallel computations
get_ranPars

Operations on lists of parameters
fixedLRT

Likelihood ratio test of fixed effects.
fix_predVar

Prediction from models with nearly-singular covariance matrices
is_separated

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

Estimation of prediction variance with bootstrap correction
external-libraries

Installing external libraries
get_RLRsim_args

Extractors of arguments for functions from package RLRsim
hatvalues.HLfit

Leverage extractor for HLfit objects
get_matrix

Extract matrices from a fit
how

Extract information about how an object was obtained
corrMatrix

Using a corrMatrix argument
fitme

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

Clear and trustworthy formulas
plot.HLfit

Model checking plots for mixed models
corr_family

corr_family objects
multinomial

Analyzing multinomial data
plot_effects

Partial-dependence effects and plots
salamander

Salamander mating data
residVar

Residual variance extractor
predict

Prediction from a model fit
predVar

Prediction and response variances
method

Fitting methods (objective functions maximized)
scotlip

Lip cancer in Scotland 1975 - 1980
mat_sqrt

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

Controlling optimization strategy through initial values
fitmv

Fitting multivariate responses
inverse.Gamma

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

Fit mixed-effects models incorporating pedigrees
fixed

Fixing some parameters
simulate.HLfit

Simulate realizations of a fitted model.
seeds

Seed germination data
wrap_parallel

Selecting interfaces for parallelisation
mv

Virtual factor for multivariate responses
freight

Freight dataset
make_scaled_dist

Scaled distances between unique locations
random-effects

Structure of random effects
spaMM.filled.contour

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

Masks of seas or lands
stripHLfit

Reduce the size of fitted objects
spaMM_boot

Parametric bootstrap
update.HLfit

Updates a fit
rankinfo

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

A flashy color palette.
sparse_precision

Control of usage of sparse_precision methods
summary.HLfit

Summary and print methods for fit and test results.
phiHGLM

Fitting random effects in the residual dispersion model
spaMM

Inference in mixed models, in particular spatial GLMMs
spaMM-internal

Internal spaMM Functions
mapMM

Colorful plots of predictions in two-dimensional space.
wafers

Data from a resistivity experiment for semiconductor materials.
welding

Welding data set
vcov

Extract covariance or correlation components from a fitted model object
post-fit

Applying post-fit procedures on spaMM results
options

spaMM options settings
spaMM-conventions

spaMM conventions and differences from related fitting procedures
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.
Poisson

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