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spaMM (version 1.8.0)

Mixed Models, Particularly Spatial GLMMs

Description

Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity 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

1.8.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

April 8th, 2016

Functions in spaMM (1.8.0)

MaternCorr

Matern correlation function.
make_scaled_dist

Scaled Euclidean distances between unique locations
HLfit

Fit mixed models with given correlation matrix
spaMM

Inference in mixed models, in particular spatial GLMMs
wafers

Data from a resistivity experiment for semiconductor materials.
Predictor

Interface for model formulas
spaMM-internal

Internal spaMM Functions
designL.from.Corr

Computation of square root of correlation matrix
fixedLRT

Likelihood ratio test of fixed effects.
raster

Raster plots of predicted responses
spaMM.filled.contour

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

Functions to extract various components of a fit
options

spaMM options settings
spaMM-internal-migraineLike

Internal spaMM Functions
corMatern

Matern Correlation Structure as a corSpatial object
salamander

Salamander mating data
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
summary.HLfit

Summary and print methods for fit and test results.
multinomial

Analyzing multinomial data
blackcap

Genetic polymorphism in relation to migration in the blackcap
arabidopsis

Arabidopsis genetic and climatic data
corrHLfit

Fits a mixed model, typically a spatial GLMM.
spaMM_glm.fit

Fitting generalized linear models without initial-value or divergence headaches
spaMM-Rcpp-internal

Internal spaMM Functions using Rcpp/RcppEigen
COMPoisson

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

Fitting autoregressive models
mapMM

Colorful plots of predicted responses in two-dimensional space.
confint.HLfit

Confidence intervals for fixed-effect parameters
LRT

Likelihood ratio test of fixed effects.
seaMask

Masks of seas or lands
spaMM.colors

A flashy color palette.
seeds

Seed germination data
freight

Freight dataset
simulate.HLfit

Simulate realizations of a fitted mixed model.
scotlip

Lip cancer in Scotland 1975 - 1980
predict

Prediction from a model fit.
update.HLfit

Updates an HLCor or HLfit fit
HLCor

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

Internal Functions for COM-Poisson family
welding

Welding data set
plot.HLfit

Model checking plots for mixed models