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spaMM (version 2.2.0)

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. Various approximations of likelihood or restricted likelihood are implement, in particular h-likelihood and Laplace approximation.

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Version

Install

install.packages('spaMM')

Monthly Downloads

1,712

Version

2.2.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

October 3rd, 2017

Functions in spaMM (2.2.0)

LRT

Likelihood ratio test of fixed effects.
arabidopsis

Arabidopsis genetic and climatic data
HLCor

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

Fit mixed models with given correlation matrix
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
MaternCorr

Matern correlation function and Matern formula term.
PLS-internals

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

Interface for model formulas
COMPoisson

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

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

Fits a mixed model, typically a spatial GLMM.
corrMatrix

Using a corrMatrix argument
extractors

Functions to extract various components of a fit
fitme

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

Confidence intervals for fixed-effect parameters
corMatern

Matern Correlation Structure as a corSpatial object
make_scaled_dist

Scaled distances between unique locations
mapMM

Colorful plots of predicted responses in two-dimensional space.
good-practice

Clear and trustworthy formulas
inverse.Gamma

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

Seed germination data
scotlip

Lip cancer in Scotland 1975 - 1980
seaMask

Masks of seas or lands
spaMM-internal

Internal spaMM Functions
adjacency

Fitting autoregressive models
blackcap

Genetic polymorphism in relation to migration in the blackcap
pedigree

Fit mixed-effects models incorporating pedigrees
multinomial

Analyzing multinomial data
negbin

Family function for negative binomial GLMs and mixed models.
predict

Prediction from a model fit.
salamander

Salamander mating data
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
wafers

Data from a resistivity experiment for semiconductor materials.
options

spaMM options settings
separation

Checking separation in binomial-response models
spaMM.filled.contour

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

A flashy color palette.
spaMM

Inference in mixed models, in particular spatial GLMMs
covStruct

Specifying correlation structures
designL.from.Corr

Computation of “square root” of correlation matrix
fixedLRT

Likelihood ratio test of fixed effects.
freight

Freight dataset
phiHGLM

Fitting random effects in the residual dispersion model
plot.HLfit

Model checking plots for mixed models
sparse_precision

Sparse_precision algorithm
stripHLfit

Reduce the size of fitted objects
welding

Welding data set
simulate.HLfit

Simulate realizations of a fitted model.
spaMM-S3

S3 methods of generics defined in other packages
summary.HLfit

Summary and print methods for fit and test results.
sym_eigen

Singular Value Decomposition of a Symmetric Matrix