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spaMM (version 3.9.0)

Mixed-Effect Models, with or without Spatial Random Effects

Description

Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models, and Markov random field models on irregular grids (as considered in the 'INLA' package, ), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 ) are also implemented.

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Version

Install

install.packages('spaMM')

Monthly Downloads

1,866

Version

3.9.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

September 13th, 2021

Functions in spaMM (3.9.0)

MSFDR

Multiple-Stage False Discovery Rate procedure
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
Gryphon

Gryphon data
CauchyCorr

Cauchy correlation function and Cauchy formula term
algebra

Control of matrix-algebraic methods
LRT

Likelihood ratio test of fixed effects.
HLfit

Fit mixed models with given correlation matrix
ZAXlist

ZAXlist class and (cross) products for ZAL matrix
multIMRF

Interpolated Markov Random Field models
corrMatrix

Using a corrMatrix argument
AIC

Extractors for information criteria such as AIC
COMPoisson

Conway-Maxwell-Poisson (COM-Poisson) GLM family
spaMM_glm.fit

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

Simulated data set for testing sparse-precision code
PLS-internals

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

Genetic polymorphism in relation to migration in the blackcap
HLCor

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

Matern Correlation Structure as a corSpatial object
MaternCorr

Matern correlation function and Matern formula term.
fitme

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

Arabidopsis genetic and climatic data
corrHLfit

Fits a mixed model, typically a spatial GLMM.
autoregressive

Fitting autoregressive models
external-libraries

Installing external libraries
fitmv

Fitting multivariate responses
fixed

Fixing some parameters
freight

Freight dataset
negbin

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

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

Composite random effects
get_matrix

Extract matrices from a fit
phiHGLM

Fitting random effects in the residual dispersion model
pedigree

Fit mixed-effects models incorporating pedigrees
get_inits_from_fit

Initiate a fit from another fit
residVar

Residual variance extractor
dofuture

Interface for parallel computations
covStruct

Specifying correlation structures
div_info

Information about numerical problems
residuals.HLfit

Extract model residuals
corr_family

corr_family objects
dopar

Interface for parallel computations
fix_predVar

Prediction from models with nearly-singular covariance matrices
get_RLRsim_args

Extractors of arguments for functions from package RLRsim
fixedLRT

Likelihood ratio test of fixed effects.
multinomial

Analyzing multinomial data
mv

Virtual factor for multivariate responses
get_cPredVar

Estimation of prediction variance with bootstrap correction
get_ranPars

Operations on lists of parameters
how

Extract information about how an object was obtained
mat_sqrt

Computation of “square root” of symmetric positive definite matrix
hatvalues.HLfit

Leverage extractor for HLfit objects
method

Fitting methods (objective functions maximized)
plot.HLfit

Model checking plots for mixed models
Poisson

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

spaMM options settings
post-fit

Applying post-fit procedures on spaMM results
plot_effects

Partial-dependence effects and plots
confint.HLfit

Confidence intervals
convergence

Assessing convergence for fitted models
good-practice

Clear and trustworthy formulas
eval_replicate

Evaluating bootstrap replicates
simulate.HLfit

Simulate realizations of a fitted model.
spaMM.colors

A flashy color palette.
spaMM-S3

S3 methods of generics defined in other packages
spaMM-conventions

spaMM conventions and differences from related fitting procedures
spaMM_boot

Parametric bootstrap
predict

Prediction from a model fit
predVar

Prediction and response variances
spaMM-internal

Internal spaMM Functions
extractors

Functions to extract various components of a fit
wrap_parallel

Selecting interfaces for parallelisation
spaMM

Inference in mixed models, in particular spatial GLMMs
inits

Controlling optimization strategy through initial values
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)
update.HLfit

Updates a fit
make_scaled_dist

Scaled distances between unique locations
rankinfo

Checking the rank of the fixed-effects design matrix
random-effects

Structure of random effects
vcov

Extract covariance or correlation components from a fitted model object
mapMM

Colorful plots of predictions in two-dimensional space.
seaMask

Masks of seas or lands
wafers

Data from a resistivity experiment for semiconductor materials.
seeds

Seed germination data
welding

Welding data set
scotlip

Lip cancer in Scotland 1975 - 1980
stripHLfit

Reduce the size of fitted objects
summary.HLfit

Summary and print methods for fit and test results.
salamander

Salamander mating data