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spaMM (version 1.4.1)

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

1.4.1

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

November 8th, 2014

Functions in spaMM (1.4.1)

make.scaled.dist

Scaled Euclidian distances between unique locations
spaMM-Rcpp-internal

Internal spaMM Functions using Rcpp/RcppEigen
multinomial

Analyzing multinomial data
summary.HLfit

Summary and print methods for fit and test results.
welding

Welding data set
spaMM-internal-blockDiag

Internal spaMM Functions
simulate.HLfit

Simulate realizations of a fitted mixed model.
spaMM-internal

Internal spaMM Functions
plot.HLfit

Model checking plots for mixed models
designL.from.Corr

Computation of square root of correlation matrix
spaMM-internal-migraineLike

Internal spaMM Functions
predict

Prediction from a model fit.
seeds

Seed germination data
confint.HLfit

Confidence intervals for fixed-effect parameters.
corMatern

Matern Correlation Structure as a corSpatial object
fixedLRT

Likelihood ratio test of fixed effects.
blackcap

Genetic polymorphism in relation to migration in the blackcap
HLfit

Fit mixed models with given correlation matrix
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
HLCor

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

Masks of seas or lands
corrHLfit

Fits a mixed model, typically a spatial GLMM.
spaMM.filled.contour

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

Likelihood ratio test of fixed effects.
options

spaMM options settings
Matern.corr

Matern correlation function.
arabidopsis

Arabidopsis genetic and climatic data
scotlip

Lip cancer in Scotland 1975 - 1980
extractors

Functions to extract various components of a fit
update.HLfit

Updates an HLCor or HLfit fit
spaMM.colors

A flashy color palette.
mapMM

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

Data from a resistivity experiment for semiconductor materials.
spaMM

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

Interface for model formulas
salamander

Salamander mating data