Learn R Programming

⚠️There's a newer version (4.6.1) of this package.Take me there.

spaMM (version 3.13.0)

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 (Rousset and Ferdy 2014 ), 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.

Copy Link

Version

Install

install.packages('spaMM')

Monthly Downloads

1,866

Version

3.13.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

September 5th, 2022

Functions in spaMM (3.13.0)

Gryphon

Gryphon data
HLCor

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

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

Loa loa prevalence in North Cameroon, 1991-2001
CauchyCorr

Cauchy correlation function and Cauchy formula term
ARp

corrFamily constructors for random effect with AR(p) (autoregressive of order p) or ARMA(p,q) structure.
AIC

Extractors for information criteria such as AIC
multIMRF

Interpolated Markov Random Field models
spaMM_glm.fit

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

Fit mixed models with given correlation matrix
adjlg

Simulated data set for testing sparse-precision code
MaternIMRFa

corrFamily constructor for Interpolated Markov Random Field (IMRF) covariance structure approximating a 2D Matern correlation model.
WinterWheat

Example of yield stability analysis
algebra

Control of matrix-algebraic methods
ZAXlist

S4 classes for structured matrices
LRT

Likelihood ratio test of fixed effects.
MSFDR

Multiple-Stage False Discovery Rate procedure
arabidopsis

Arabidopsis genetic and climatic data
MaternCorr

Matern correlation function and Matern formula term.
PLS-internals

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

Fitting autoregressive models
confint.HLfit

Confidence intervals
blackcap

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

Control parameters of the HLfit fitting algorithm
composite-ranef

Composite random effects
corrFamily-design

Designing new corrFamily descriptors for parametric correlation families
corrFamily-definition

corrFamily definition
beta_resp

Beta-response family object
convergence

Assessing convergence for fitted models
corMatern

Matern Correlation Structure as a corSpatial object
corrHLfit

Fits a mixed model, typically a spatial GLMM.
covStruct

Specifying correlation structures
dopar

Interface for parallel computations
corrFamily

Using corrFamily constructors and descriptors.
div_info

Information about numerical problems
diallel

Random-effect structures for diallel experiments and other symmetric dyadic interactions
eval_replicate

Evaluating bootstrap replicates
corrMatrix

Using a corrMatrix argument
corr_family

corr_family objects
dofuture

Interface for parallel computations
fix_predVar

Prediction from models with nearly-singular covariance matrices
fixedLRT

Likelihood ratio test of fixed effects.
fixed

Fixing some parameters
extractors

Functions to extract various components of a fit
extreme_eig

Utilities for regularization of a matrix
freight

Freight dataset
fitme

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

Estimation of prediction variance with bootstrap correction
get_RLRsim_args

Extractors of arguments for functions from package RLRsim
fitmv

Fitting multivariate responses
get_matrix

Extract matrices from a fit
get_infomat

Information matrix of fitted model
is_separated

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

Leverage extractor for HLfit objects
how

Extract information about how an object was obtained
get_ranPars

Operations on lists of parameters
inverse.Gamma

Distribution families for Gamma and inverse Gamma-distributed random effects
good-practice

Clear and trustworthy formulas and prior weights
inits

Controlling optimization strategy through initial values
get_inits_from_fit

Initiate a fit from another fit
external-libraries

Installing external libraries
multinomial

Analyzing multinomial data
mat_sqrt

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

Virtual factor for multivariate responses
llm.fit

Link-linear regression models (LLMs)
method

Fitting methods (objective functions maximized)
make_scaled_dist

Scaled distances between unique locations
negbin1

Alternative negative-binomial family
negbin

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

Colorful plots of predictions in two-dimensional space.
predVar

Prediction and response variances
predict

Prediction from a model fit
phiHGLM

Fitting random effects in the residual dispersion model
post-fit

Applying post-fit procedures on spaMM results
plot_effects

Partial-dependence effects and plots
options

spaMM options settings
random-effects

Structure of random effects
Poisson

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

Model checking plots for mixed models
pedigree

Fit mixed-effects models incorporating pedigrees
spaMM-S3

S3 methods of generics defined in other packages
residVar

Residual variance extractor
residuals.HLfit

Extract model residuals
scotlip

Lip cancer in Scotland 1975 - 1980
simulate.HLfit

Simulate realizations of a fitted model.
salamander

Salamander mating data
seaMask

Masks of seas or lands
seeds

Seed germination data
register_cF

Declare corrFamily constructor for use in formula
rankinfo

Checking the rank of the fixed-effects design matrix
spaMM

Inference in mixed models, in particular spatial GLMMs
stripHLfit

Reduce the size of fitted objects
spaMM.colors

A flashy color palette.
spaMM-conventions

spaMM conventions and differences from related fitting procedures
update.HLfit

Updates a fit
spaMM.filled.contour

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

Extract covariance or correlation components from a fitted model object
spaMM-internal

Internal spaMM Functions
spaMM_boot

Parametric bootstrap
welding

Welding data set
wrap_parallel

Selecting interfaces for parallelisation
wafers

Data from a resistivity experiment for semiconductor materials.
summary.HLfit

Summary and print methods for fit and test results.