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spaMM (version 2.4.8)

Mixed-Effect Models, Particularly Spatial Models

Description

Inference in mixed-effect models, including generalized linear mixed models with spatial correlations and models with non-Gaussian random effects (e.g., Beta-Binomial). Variation in residual variance (heteroscedasticity) can itself be represented by a generalized linear mixed model. Various approximations of likelihood or restricted likelihood are implemented, in particular h-likelihood (Lee and Nelder 2001 ) and Laplace approximation.

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Version

Install

install.packages('spaMM')

Monthly Downloads

5,527

Version

2.4.8

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

April 14th, 2018

Functions in spaMM (2.4.8)

HLfit

Fit mixed models with given correlation matrix
fitme

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

Analyzing multinomial data
corMatern

Matern Correlation Structure as a corSpatial object
designL.from.Corr

Computation of “square root” of correlation matrix
good-practice

Clear and trustworthy formulas
inverse.Gamma

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

Masks of seas or lands
scotlip

Lip cancer in Scotland 1975 - 1980
fixedLRT

Likelihood ratio test of fixed effects.
extractors

Functions to extract various components of a fit
rankinfo

Checking the rank of the fixed-effects design matrix
salamander

Salamander mating data
spaMM-internal

Internal spaMM Functions
simulate.HLfit

Simulate realizations of a fitted model.
corrHLfit

Fits a mixed model, typically a spatial GLMM.
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.
phiHGLM

Fitting random effects in the residual dispersion model
covStruct

Specifying correlation structures
stripHLfit

Reduce the size of fitted objects
summary.HLfit

Summary and print methods for fit and test results.
fixed

Fixing some parameters
plot.HLfit

Model checking plots for mixed models
seeds

Seed germination data
spaMM

Inference in mixed models, in particular spatial GLMMs
freight

Freight dataset
options

spaMM options settings
pedigree

Fit mixed-effects models incorporating pedigrees
spaMM.colors

A flashy color palette.
spaMM.filled.contour

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

Scaled distances between unique locations
separation

Checking separation in binomial-response models
spaMM_boot

Parametric bootstrap
sparse_precision

Sparse_precision algorithm
welding

Welding data set
wafers

Data from a resistivity experiment for semiconductor materials.
Poisson

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

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

Prediction from a model fit.
spaMM-conventions

spaMM conventions and differences from related fitting procedures
spaMM-Rcpp-internal

Internal spaMM Functions using Rcpp/RcppEigen
update.HLfit

Updates an HLCor or HLfit fit
sym_eigen

Singular Value Decomposition of a Symmetric Matrix
CauchyCorr

Cauchy correlation function and Cauchy formula term
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
COMPoisson

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

Genetic polymorphism in relation to migration in the blackcap
confint.HLfit

Confidence intervals for fixed-effect parameters
spaMM_glm.fit

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

Fits a (spatially) correlated mixed model, for given correlation parameters
PLS-internals

Internal, Experimental Functions for procedure using the ((I,0),(Z,X)) block-order
arabidopsis

Arabidopsis genetic and climatic data
corrMatrix

Using a corrMatrix argument
MaternCorr

Matern correlation function and Matern formula term.
autoregressive

Fitting autoregressive models
Predictor

Interface for model formulas
LRT

Likelihood ratio test of fixed effects.