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spaMM (version 2.1.0)

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, or negative-binomial mixed models). Variation in residual variance is handled and can be modelled as a linear model. The algorithms are currently various Laplace approximations methods for likelihood or restricted likelihood, in particular h-likelihood and penalized-likelihood methods.

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Version

Install

install.packages('spaMM')

Monthly Downloads

1,751

Version

2.1.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

May 25th, 2017

Functions in spaMM (2.1.0)

COMPoisson

Conway-Maxwell-Poisson (COM-Poisson) GLM family
spaMM_glm.fit

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

Loa loa prevalence in North Cameroon, 1991-2001
MaternCorr

Matern correlation function and Matern formula term.
HLCor

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

Fit mixed models with given correlation matrix
LRT

Likelihood ratio test of fixed effects.
arabidopsis

Arabidopsis genetic and climatic data
PLS-internals

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

Interface for model formulas
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.
corrMatrix

Using a corrMatrix argument
phiHGLM

Fitting random effects in the residual dispersion model
plot.HLfit

Model checking plots for mixed models
confint.HLfit

Confidence intervals for fixed-effect parameters
corMatern

Matern Correlation Structure as a corSpatial object
inverse.Gamma

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

Scaled distances between unique locations
freight

Freight dataset
good-practice

Clear and trustworthy formulas
seeds

Seed germination data
adjacency

Fitting autoregressive models
blackcap

Genetic polymorphism in relation to migration in the blackcap
mapMM

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

Analyzing multinomial data
negbin

Family function for negative binomial GLMs and mixed models.
options

spaMM options settings
spaMM-internal

Internal spaMM Functions
spaMM

Inference in mixed models, in particular spatial GLMMs
spaMM.filled.contour

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

A flashy color palette.
predict

Prediction from a model fit.
salamander

Salamander mating data
fitme

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

Likelihood ratio test of fixed effects.
spaMM-conventions

spaMM conventions and differences from related fitting procedures
simulate.HLfit

Simulate realizations of a fitted model.
sym_eigen

Singular Value Decomposition of a Symmetric Matrix
update.HLfit

Updates an HLCor or HLfit fit
scotlip

Lip cancer in Scotland 1975 - 1980
seaMask

Masks of seas or lands
wafers

Data from a resistivity experiment for semiconductor materials.
welding

Welding data set
spaMM-Rcpp-internal

Internal spaMM Functions using Rcpp/RcppEigen
stripHLfit

Reduce the size of fitted objects
summary.HLfit

Summary and print methods for fit and test results.