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spaMM (version 2.4.35)

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). 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

1,720

Version

2.4.35

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

May 19th, 2018

Functions in spaMM (2.4.35)

confint.HLfit

Confidence intervals for fixed-effect parameters
inverse.Gamma

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

Freight dataset
pedigree

Fit mixed-effects models incorporating pedigrees
good-practice

Clear and trustworthy formulas
predict

Prediction from a model fit.
Poisson

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

Welding data set
get_ranPars

More functions to extract various components of a fit
options

spaMM options settings
extractors

Functions to extract various components of a fit
simulate.HLfit

Simulate realizations of a fitted model.
fixed

Fixing some parameters
spaMM

Inference in mixed models, in particular spatial GLMMs
fixedLRT

Likelihood ratio test of fixed effects.
wafers

Data from a resistivity experiment for semiconductor materials.
separation

Checking separation in binomial-response models
spaMM-internal

Internal spaMM Functions
seeds

Seed germination data
spaMM-S3

S3 methods of generics defined in other packages
phiHGLM

Fitting random effects in the residual dispersion model
make_scaled_dist

Scaled distances between unique locations
stripHLfit

Reduce the size of fitted objects
multinomial

Analyzing multinomial data
mapMM

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

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

Checking the rank of the fixed-effects design matrix
summary.HLfit

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

spaMM conventions and differences from related fitting procedures
negbin

Family function for GLMs and mixed models with negative binomial and zero-truncated negative binomial response.
salamander

Salamander mating data
spaMM.colors

A flashy color palette.
plot.HLfit

Model checking plots for mixed models
spaMM-Rcpp-internal

Internal spaMM Functions using Rcpp/RcppEigen
scotlip

Lip cancer in Scotland 1975 - 1980
sparse_precision

Sparse_precision algorithm
sym_eigen

Singular Value Decomposition of a Symmetric Matrix
update.HLfit

Updates an HLCor or HLfit fit
seaMask

Masks of seas or lands
spaMM.filled.contour

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

Parametric bootstrap
MaternCorr

Matern correlation function and Matern formula term.
PLS-internals

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

Cauchy correlation function and Cauchy formula term
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
Predictor

Interface for model formulas
adjlg

Simulated data set for testing sparse-precision code
spaMM_glm.fit

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

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

Fit mixed models with given correlation matrix
COMPoisson

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

Fitting autoregressive models
LRT

Likelihood ratio test of fixed effects.
corrHLfit

Fits a mixed model, typically a spatial GLMM.
arabidopsis

Arabidopsis genetic and climatic data
designL.from.Corr

Computation of “square root” of correlation matrix
covStruct

Specifying correlation structures
blackcap

Genetic polymorphism in relation to migration in the blackcap
corMatern

Matern Correlation Structure as a corSpatial object
corrMatrix

Using a corrMatrix argument