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spaMM (version 3.5.0)

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

1,720

Version

3.5.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

October 3rd, 2020

Functions in spaMM (3.5.0)

Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
MSFDR

Multiple-Stage False Discovery Rate procedure
HLfit

Fit mixed models with given correlation matrix
HLCor

Fits a (spatially) correlated mixed model, for given correlation parameters
spaMM_glm.fit

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

Cauchy correlation function and Cauchy formula term
MaternCorr

Matern correlation function and Matern formula term.
multIMRF

Interpolated Markov Random Field models
AIC

Extractors for information criteria such as AIC
blackcap

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

Confidence intervals
COMPoisson

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

Assessing convergence for fitted models
corMatern

Matern Correlation Structure as a corSpatial object
ZAXlist

ZAXlist class and (cross) products for ZAL matrix
LRT

Likelihood ratio test of fixed effects.
PLS-internals

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

Arabidopsis genetic and climatic data
div_info

Information about numerical problems
autoregressive

Fitting autoregressive models
corrMatrix

Using a corrMatrix argument
adjlg

Simulated data set for testing sparse-precision code
corrHLfit

Fits a mixed model, typically a spatial GLMM.
covStruct

Specifying correlation structures
corr_family

corr_family objects
fix_predVar

Prediction from models with nearly-singular covariance matrices
get_cPredVar

Estimation of prediction variance with bootstrap correction
fitme

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

Fixing some parameters
eval_replicate

Evaluating bootstrap replicates
fixedLRT

Likelihood ratio test of fixed effects.
good-practice

Clear and trustworthy formulas
hatvalues.HLfit

Leverage extractor for HLfit objects
get_inits_from_fit

Initiate a fit from another fit
dopar

Interface for parallel computations
get_matrix

Extract matrices from a fit
get_ranPars

Operations on lists of parameters
extractors

Functions to extract various components of a fit
is_separated

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

Extractors of arguments for functions from package RLRsim
freight

Freight dataset
make_scaled_dist

Scaled distances between unique locations
mat_sqrt

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

Fitting methods (objective functions maximized)
how

Extract information about how an object was obtained
mapMM

Colorful plots of predicted responses in two-dimensional space.
inverse.Gamma

Distribution families for Gamma and inverse Gamma-distributed random effects
external-libraries

Installing external libraries
options

spaMM options settings
pedigree

Fit mixed-effects models incorporating pedigrees
random-effects

Structure of random effects
multinomial

Analyzing multinomial data
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
seaMask

Masks of seas or lands
post-fit

Applying post-fit procedures on spaMM results
predict

Prediction from a model fit.
spaMM

Inference in mixed models, in particular spatial GLMMs
sparse_precision

Sparse_precision algorithm
spaMM.filled.contour

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

Salamander mating data
scotlip

Lip cancer in Scotland 1975 - 1980
vcov

Extract covariance or correlation components from a fitted model object
seeds

Seed germination data
phiHGLM

Fitting random effects in the residual dispersion model
simulate.HLfit

Simulate realizations of a fitted model.
wafers

Data from a resistivity experiment for semiconductor materials.
spaMM-S3

S3 methods of generics defined in other packages
update.HLfit

Updates a fit
summary.HLfit

Summary and print methods for fit and test results.
spaMM_boot

Parametric bootstrap
plot.HLfit

Model checking plots for mixed models
spaMM.colors

A flashy color palette.
stripHLfit

Reduce the size of fitted objects
Poisson

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

spaMM conventions and differences from related fitting procedures
plot_effects

Partial-dependence effects and plots
spaMM-internal

Internal spaMM Functions
welding

Welding data set