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spaMM (version 1.3.0)

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

4,103

Version

1.3.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

September 9th, 2014

Functions in spaMM (1.3.0)

spaMM-internal-migraineLike

Internal spaMM Functions
Predictor

Interface for model formulas
mapMM

Colorful plots of predicted responses in two-dimensional space.
arabidopsis

Arabidopsis genetic and climatic data
HLfit

Fit mixed models with given correlation matrix
summary.HLfit

Summary and print methods for fit and test results.
spaMM-internal

Internal spaMM Functions
make.scaled.dist

Scaled Euclidian distances between unique locations
simulate.HLfit

Simulate realizations of a fitted mixed model.
spaMM

Inference in spatial GLMMs (and other non-spatial mixed models)
spaMM-internal-blockDiag

Internal spaMM Functions
spaMM-Rcpp-internal

Internal spaMM Functions using Rcpp/RcppEigen
confint.HLfit

Confidence intervals for fixed-effect parameters.
seaMask

Masks of seas or lands
scotlip

Lip cancer in Scotland 1975 - 1980
fixedLRT

Likelihood ratio test of fixed effects.
HLCor

Fits a (spatially) correlated mixed model, for given correlation parameters
spaMM.filled.contour

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

Fits a mixed model, typically a spatial GLMM.
salamander

Salamander mating data
spaMM.colors

A flashy color palette.
corMatern

Matern Correlation Structure as a corSpatial object
plot.HLfit

Model checking plots for mixed models
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
blackcap

Genetic polymorphism in relation to migration in the blackcap
Matern.corr

Matern correlation function.
wafers

Data from a resistivity experiment for semiconductor materials.
multinomial

Analyzing multinomial data
update.HLfit

Updates an HLCor or HLfit fit
LRT

Likelihood ratio test of fixed effects.
designL.from.Corr

Computation of square root of correlation matrix
predict

Prediction from a model fit.
options

spaMM options settings
extractors

Functions to extract various components of a fit