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spaMM (version 1.4.0)

Mixed Models, Particularly Spatial GLMMs

Description

Implements a collection of functions for inference in mixed models. It was developed in particular for GLMMs with spatial correlations, but also fits models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroskedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.

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Version

Install

install.packages('spaMM')

Monthly Downloads

1,720

Version

1.4.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

November 8th, 2014

Functions in spaMM (1.4.0)

welding

Welding data set
HLfit

Fit mixed models with given correlation matrix
multinomial

Analyzing multinomial data
spaMM

Inference in spatial GLMMs (and other non-spatial mixed models)
LRT

Likelihood ratio test of fixed effects.
update.HLfit

Updates an HLCor or HLfit fit
spaMM-internal-blockDiag

Internal spaMM Functions
options

spaMM options settings
summary.HLfit

Summary and print methods for fit and test results.
HLCor

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

Colorful plots of predicted responses in two-dimensional space.
Matern.corr

Matern correlation function.
confint.HLfit

Confidence intervals for fixed-effect parameters.
wafers

Data from a resistivity experiment for semiconductor materials.
predict

Prediction from a model fit.
designL.from.Corr

Computation of square root of correlation matrix
extractors

Functions to extract various components of a fit
corrHLfit

Fits a mixed model, typically a spatial GLMM.
seaMask

Masks of seas or lands
make.scaled.dist

Scaled Euclidian distances between unique locations
plot.HLfit

Model checking plots for mixed models
arabidopsis

Arabidopsis genetic and climatic data
spaMM-internal-migraineLike

Internal spaMM Functions
scotlip

Lip cancer in Scotland 1975 - 1980
spaMM-Rcpp-internal

Internal spaMM Functions using Rcpp/RcppEigen
spaMM.filled.contour

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

Genetic polymorphism in relation to migration in the blackcap
spaMM.colors

A flashy color palette.
seeds

Seed germination data
spaMM-internal

Internal spaMM Functions
simulate.HLfit

Simulate realizations of a fitted mixed model.
Predictor

Interface for model formulas
fixedLRT

Likelihood ratio test of fixed effects.
salamander

Salamander mating data
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
corMatern

Matern Correlation Structure as a corSpatial object