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spaMM (version 2.7.1)

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). Both classical geostatistical models, and Markov random field models on irregular grids, can be fitted. 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

1,913

Version

2.7.1

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

April 14th, 2019

Functions in spaMM (2.7.1)

MSFDR

Multiple-Stage False Discovery Rate procedure
spaMM_glm.fit

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

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

Matern Correlation Structure as a corSpatial object
get_ranPars

Operations on lists of parameters
corrHLfit

Fits a mixed model, typically a spatial GLMM.
mapMM

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

Fit mixed models with given correlation matrix
mat_sqrt

Computation of “square root” of symmetric positive definite matrix
good-practice

Clear and trustworthy formulas
plot_effects

Partial-dependence effects and plots
predict

Prediction from a model fit.
AIC

Extractors for informations criteria such as AIC
Poisson

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

Confidence intervals for fixed-effect parameters
arabidopsis

Arabidopsis genetic and climatic data
blackcap

Genetic polymorphism in relation to migration in the blackcap
rankinfo

Checking the rank of the fixed-effects design matrix
spaMM.filled.contour

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

Interpolated Markov Random Field models
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
spaMM-internal

Internal spaMM Functions
spaMM_boot

Parametric bootstrap
fixedLRT

Likelihood ratio test of fixed effects.
spaMM.colors

A flashy color palette.
PLS-internals

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

Fixing some parameters
ZAXlist

ZAXlist class and (cross) products for ZAL matrix
covStruct

Specifying correlation structures
designL.from.Corr

Computation of “square root” of correlation matrix
spaMM

Inference in mixed models, in particular spatial GLMMs
is_separated

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

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

Sparse_precision algorithm
adjlg

Simulated data set for testing sparse-precision code
make_scaled_dist

Scaled distances between unique locations
LRT

Likelihood ratio test of fixed effects.
autoregressive

Fitting autoregressive models
vcov

Extract covariance or correlation matrices from a fitted model object
wafers

Data from a resistivity experiment for semiconductor materials.
salamander

Salamander mating data
extractors

Functions to extract various components of a fit
fitme

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

Lip cancer in Scotland 1975 - 1980
multinomial

Analyzing multinomial data
negbin

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

Freight dataset
phiHGLM

Fitting random effects in the residual dispersion model
separation

Checking separation in binomial-response models
seaMask

Masks of seas or lands
plot.HLfit

Model checking plots for mixed models
get_matrix

Extract matrices from a fit
seeds

Seed germination data
spaMM-S3

S3 methods of generics defined in other packages
spaMM-conventions

spaMM conventions and differences from related fitting procedures
how

Extract information about how an object was obtained
welding

Welding data set
simulate.HLfit

Simulate realizations of a fitted model.
stripHLfit

Reduce the size of fitted objects
summary.HLfit

Summary and print methods for fit and test results.
sym_eigen

Singular Value Decomposition of a Symmetric Matrix
update.HLfit

Updates a fit
inverse.Gamma

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

spaMM options settings
pedigree

Fit mixed-effects models incorporating pedigrees
CauchyCorr

Cauchy correlation function and Cauchy formula term
MaternCorr

Matern correlation function and Matern formula term.
corrMatrix

Using a corrMatrix argument
corr_family

corr_family objects