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spaMM (version 2.6.1)

Mixed-Effect Models, Particularly Spatial Models

Description

Inference based on 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

2.6.1

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

January 14th, 2019

Functions in spaMM (2.6.1)

Loaloa

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

Confidence intervals for fixed-effect parameters
fixedLRT

Likelihood ratio test of fixed effects.
HLCor

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

Fit mixed models with given correlation matrix
arabidopsis

Arabidopsis genetic and climatic data
autoregressive

Fitting autoregressive models
fixed

Fixing some parameters
extractors

Functions to extract various components of a fit
fitme

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

Matern correlation function and Matern formula term.
CauchyCorr

Cauchy correlation function and Cauchy formula term
AIC

Extractors for informations criteria such as AIC
spaMM_glm.fit

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

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

Matern Correlation Structure as a corSpatial object
adjlg

Simulated data set for testing sparse-precision code
corrHLfit

Fits a mixed model, typically a spatial GLMM.
PLS-internals

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

Computation of “square root” of symmetric positive definite matrix
freight

Freight dataset
how

Extract information about how an object was obtained
get_matrix

Extract matrices from a fit
LRT

Likelihood ratio test of fixed effects.
multinomial

Analyzing multinomial data
covStruct

Specifying correlation structures
designL.from.Corr

Computation of “square root” of correlation matrix
scotlip

Lip cancer in Scotland 1975 - 1980
COMPoisson

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

Using a corrMatrix argument
negbin

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

spaMM options settings
corr_family

corr_family objects
get_ranPars

Operations on lists of parameters
pedigree

Fit mixed-effects models incorporating pedigrees
good-practice

Clear and trustworthy formulas
rankinfo

Checking the rank of the fixed-effects design matrix
seaMask

Masks of seas or lands
is_separated

Checking for (quasi-)separation in binomial-response model.
salamander

Salamander mating data
inverse.Gamma

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

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

Simulate realizations of a fitted model.
spaMM

Inference in mixed models, in particular spatial GLMMs
predict

Prediction from a model fit.
summary.HLfit

Summary and print methods for fit and test results.
make_scaled_dist

Scaled distances between unique locations
separation

Checking separation in binomial-response models
seeds

Seed germination data
sym_eigen

Singular Value Decomposition of a Symmetric Matrix
spaMM.filled.contour

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

Fitting random effects in the residual dispersion model
spaMM-conventions

spaMM conventions and differences from related fitting procedures
spaMM-internal

Internal spaMM Functions
spaMM_boot

Parametric bootstrap
plot.HLfit

Model checking plots for mixed models
sparse_precision

Sparse_precision algorithm
stripHLfit

Reduce the size of fitted objects
spaMM.colors

A flashy color palette.
spaMM-S3

S3 methods of generics defined in other packages
update.HLfit

Updates a fit
wafers

Data from a resistivity experiment for semiconductor materials.
welding

Welding data set
vcov

Extract covariance or correlation matrices from a fitted model object
MSFDR

Multiple-Stage False Discovery Rate procedure
blackcap

Genetic polymorphism in relation to migration in the blackcap