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spaMM (version 2.6.0)

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

2.6.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

January 10th, 2019

Functions in spaMM (2.6.0)

arabidopsis

Arabidopsis genetic and climatic data
autoregressive

Fitting autoregressive models
fixed

Fixing some parameters
sparse_precision

Sparse_precision algorithm
update.HLfit

Updates a fit
adjlg

Simulated data set for testing sparse-precision code
fixedLRT

Likelihood ratio test of fixed effects.
LRT

Likelihood ratio test of fixed effects.
stripHLfit

Reduce the size of fitted objects
HLfit

Fit mixed models with given correlation matrix
options

spaMM options settings
pedigree

Fit mixed-effects models incorporating pedigrees
corrMatrix

Using a corrMatrix argument
extractors

Functions to extract various components of a fit
Poisson

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

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

Genetic polymorphism in relation to migration in the blackcap
mapMM

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

Matern Correlation Structure as a corSpatial object
corr_family

corr_family objects
freight

Freight dataset
corrHLfit

Fits a mixed model, typically a spatial GLMM.
predict

Prediction from a model fit.
mat_sqrt

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

Extract covariance or correlation matrices from a fitted model object
get_matrix

Extract matrices from a fit
how

Extract information about how an object was obtained
confint.HLfit

Confidence intervals for fixed-effect parameters
covStruct

Specifying correlation structures
seeds

Seed germination data
get_ranPars

Operations on lists of parameters
designL.from.Corr

Computation of “square root” of correlation matrix
inverse.Gamma

Distribution families for Gamma and inverse Gamma-distributed random effects
spaMM.filled.contour

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

Inference in mixed models, in particular spatial GLMMs
phiHGLM

Fitting random effects in the residual dispersion model
spaMM-conventions

spaMM conventions and differences from related fitting procedures
separation

Checking separation in binomial-response models
multinomial

Analyzing multinomial data
plot.HLfit

Model checking plots for mixed models
spaMM-internal

Internal spaMM Functions
negbin

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

Checking the rank of the fixed-effects design matrix
salamander

Salamander mating data
spaMM_boot

Parametric bootstrap
spaMM.colors

A flashy color palette.
summary.HLfit

Summary and print methods for fit and test results.
good-practice

Clear and trustworthy formulas
sym_eigen

Singular Value Decomposition of a Symmetric Matrix
is_separated

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

Scaled distances between unique locations
spaMM-S3

S3 methods of generics defined in other packages
seaMask

Masks of seas or lands
scotlip

Lip cancer in Scotland 1975 - 1980
simulate.HLfit

Simulate realizations of a fitted model.
wafers

Data from a resistivity experiment for semiconductor materials.
welding

Welding data set
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
MaternCorr

Matern correlation function and Matern formula term.
MSFDR

Multiple-Stage False Discovery Rate procedure
CauchyCorr

Cauchy correlation function and Cauchy formula term
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
AIC

Extractors for informations criteria such as AIC
spaMM_glm.fit

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

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