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spaMM (version 3.6.0)

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). Various approximations of likelihood or restricted likelihood are implemented, in particular Laplace approximation and h-likelihood (Lee and Nelder 2001 ). Both classical geostatistical models, and Markov random field models on irregular grids (as considered in the 'INLA' package, ), can be fitted. Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model.

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Version

Install

install.packages('spaMM')

Monthly Downloads

4,070

Version

3.6.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

January 15th, 2021

Functions in spaMM (3.6.0)

MaternCorr

Matern correlation function and Matern formula term.
HLCor

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

Extractors for information criteria such as AIC
COMPoisson

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

Multiple-Stage False Discovery Rate procedure
CauchyCorr

Cauchy correlation function and Cauchy formula term
multIMRF

Interpolated Markov Random Field models
ZAXlist

ZAXlist class and (cross) products for ZAL matrix
HLfit

Fit mixed models with given correlation matrix
PLS-internals

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

Confidence intervals
blackcap

Genetic polymorphism in relation to migration in the blackcap
arabidopsis

Arabidopsis genetic and climatic data
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
corMatern

Matern Correlation Structure as a corSpatial object
convergence

Assessing convergence for fitted models
autoregressive

Fitting autoregressive models
fitme

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

Fitting multivariate responses
corrMatrix

Using a corrMatrix argument
corrHLfit

Fits a mixed model, typically a spatial GLMM.
dopar

Interface for parallel computations
div_info

Information about numerical problems
adjlg

Simulated data set for testing sparse-precision code
covStruct

Specifying correlation structures
get_ranPars

Operations on lists of parameters
LRT

Likelihood ratio test of fixed effects.
good-practice

Clear and trustworthy formulas
fix_predVar

Prediction from models with nearly-singular covariance matrices
eval_replicate

Evaluating bootstrap replicates
corr_family

corr_family objects
spaMM_glm.fit

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

Functions to extract various components of a fit
get_RLRsim_args

Extractors of arguments for functions from package RLRsim
fixedLRT

Likelihood ratio test of fixed effects.
fixed

Fixing some parameters
method

Fitting methods (objective functions maximized)
external-libraries

Installing external libraries
get_cPredVar

Estimation of prediction variance with bootstrap correction
freight

Freight dataset
make_scaled_dist

Scaled distances between unique locations
get_inits_from_fit

Initiate a fit from another fit
hatvalues.HLfit

Leverage extractor for HLfit objects
mat_sqrt

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

Colorful plots of predictions in two-dimensional space.
plot.HLfit

Model checking plots for mixed models
phiHGLM

Fitting random effects in the residual dispersion model
plot_effects

Partial-dependence effects and plots
multinomial

Analyzing multinomial data
random-effects

Structure of random effects
pedigree

Fit mixed-effects models incorporating pedigrees
options

spaMM options settings
spaMM-conventions

spaMM conventions and differences from related fitting procedures
Poisson

Family function for GLMs and mixed models with Poisson and zero-truncated Poisson response.
spaMM-S3

S3 methods of generics defined in other packages
scotlip

Lip cancer in Scotland 1975 - 1980
get_matrix

Extract matrices from a fit
spaMM-internal

Internal spaMM Functions
rankinfo

Checking the rank of the fixed-effects design matrix
spaMM

Inference in mixed models, in particular spatial GLMMs
salamander

Salamander mating data
predict

Prediction from a model fit.
inverse.Gamma

Distribution families for Gamma and inverse Gamma-distributed random effects
post-fit

Applying post-fit procedures on spaMM results
residVar

Residual variance extractor
spaMM.filled.contour

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

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

Updates a fit
vcov

Extract covariance or correlation components from a fitted model object
spaMM_boot

Parametric bootstrap
seaMask

Masks of seas or lands
spaMM.colors

A flashy color palette.
mv

Virtual factor for multivariate responses
how

Extract information about how an object was obtained
negbin

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

Data from a resistivity experiment for semiconductor materials.
sparse_precision

Sparse_precision algorithm
welding

Welding data set
summary.HLfit

Summary and print methods for fit and test results.
stripHLfit

Reduce the size of fitted objects
simulate.HLfit

Simulate realizations of a fitted model.
seeds

Seed germination data