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spaMM (version 3.1.2)

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

1,720

Version

3.1.2

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

February 12th, 2020

Functions in spaMM (3.1.2)

spaMM_glm.fit

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

Multiple-Stage False Discovery Rate procedure
MaternCorr

Matern correlation function and Matern formula term.
multIMRF

Interpolated Markov Random Field models
adjlg

Simulated data set for testing sparse-precision code
HLfit

Fit mixed models with given correlation matrix
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
COMPoisson

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

ZAXlist class and (cross) products for ZAL matrix
CauchyCorr

Cauchy correlation function and Cauchy formula term
convergence

Assessing convergence for fitted models
extractors

Functions to extract various components of a fit
LRT

Likelihood ratio test of fixed effects.
PLS-internals

Internal functions for procedure using the ((I,0),(Z,X)) block-order
AIC

Extractors for information criteria such as AIC
HLCor

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

Genetic polymorphism in relation to migration in the blackcap
confint.HLfit

Confidence intervals for fixed-effect parameters
corMatern

Matern Correlation Structure as a corSpatial object
fitme

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

Prediction from models with nearly-singular covariance matrices
arabidopsis

Arabidopsis genetic and climatic data
fixedLRT

Likelihood ratio test of fixed effects.
good-practice

Clear and trustworthy formulas
how

Extract information about how an object was obtained
corrMatrix

Using a corrMatrix argument
corrHLfit

Fits a mixed model, typically a spatial GLMM.
get_matrix

Extract matrices from a fit
get_ranPars

Operations on lists of parameters
plot.HLfit

Model checking plots for mixed models
plot_effects

Partial-dependence effects and plots
make_scaled_dist

Scaled distances between unique locations
autoregressive

Fitting autoregressive models
covStruct

Specifying correlation structures
inverse.Gamma

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

Salamander mating data
predict

Prediction from a model fit.
rankinfo

Checking the rank of the fixed-effects design matrix
mapMM

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

corr_family objects
designL.from.Corr

Computation of “square root” of correlation matrix
fixed

Fixing some parameters
options

spaMM options settings
is_separated

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

Lip cancer in Scotland 1975 - 1980
negbin

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

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

Freight dataset
simulate.HLfit

Simulate realizations of a fitted model.
spaMM.filled.contour

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

Masks of seas or lands
multinomial

Analyzing multinomial data
seeds

Seed germination data
eval_replicate

Evaluating bootstrap replicates
update.HLfit

Updates a fit
spaMM

Inference in mixed models, in particular spatial GLMMs
spaMM-S3

S3 methods of generics defined in other packages
pedigree

Fit mixed-effects models incorporating pedigrees
get_cPredVar

Estimation of prediction variance with bootstrap correction
get_inits_from_fit

Initiate a fit from another fit
vcov

Extract covariance or correlation components from a fitted model object
summary.HLfit

Summary and print methods for fit and test results.
wafers

Data from a resistivity experiment for semiconductor materials.
sym_eigen

Singular Value Decomposition of a Symmetric Matrix
phiHGLM

Fitting random effects in the residual dispersion model
spaMM.colors

A flashy color palette.
welding

Welding data set
spaMM_boot

Parametric bootstrap
Poisson

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

Applying post-fit procedures on spaMM results
spaMM-conventions

spaMM conventions and differences from related fitting procedures
stripHLfit

Reduce the size of fitted objects
sparse_precision

Sparse_precision algorithm
spaMM-internal

Internal spaMM Functions