Learn R Programming

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

spaMM (version 3.3.0)

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). 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.

Copy Link

Version

Install

install.packages('spaMM')

Monthly Downloads

2,454

Version

3.3.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

May 30th, 2020

Functions in spaMM (3.3.0)

MSFDR

Multiple-Stage False Discovery Rate procedure
COMPoisson

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

Interpolated Markov Random Field models
CauchyCorr

Cauchy correlation function and Cauchy formula term
HLfit

Fit mixed models with given correlation matrix
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
confint.HLfit

Confidence intervals
MaternCorr

Matern correlation function and Matern formula term.
HLCor

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

ZAXlist class and (cross) products for ZAL matrix
fix_predVar

Prediction from models with nearly-singular covariance matrices
adjlg

Simulated data set for testing sparse-precision code
AIC

Extractors for information criteria such as AIC
autoregressive

Fitting autoregressive models
extractors

Functions to extract various components of a fit
fixedLRT

Likelihood ratio test of fixed effects.
PLS-internals

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

Genetic polymorphism in relation to migration in the blackcap
arabidopsis

Arabidopsis genetic and climatic data
get_inits_from_fit

Initiate a fit from another fit
get_cPredVar

Estimation of prediction variance with bootstrap correction
convergence

Assessing convergence for fitted models
corMatern

Matern Correlation Structure as a corSpatial object
LRT

Likelihood ratio test of fixed effects.
dopar

Interface for parallel computations
eval_replicate

Evaluating bootstrap replicates
fitme

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

Specifying correlation structures
spaMM_glm.fit

Fitting generalized linear models without initial-value or divergence headaches
good-practice

Clear and trustworthy formulas
options

spaMM options settings
pedigree

Fit mixed-effects models incorporating pedigrees
get_matrix

Extract matrices from a fit
get_ranPars

Operations on lists of parameters. A distinct documentation exists for get_inits_from_fit which is most useful to extract parameters from a fit in a form suitable to initialize another fit. VarCorr is yet another extractor for dispersion parameters.
mat_sqrt

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

Leverage extractor for HLfit objects
corrHLfit

Fits a mixed model, typically a spatial GLMM.
method

Fitting methods (objective functions maximized)
corr_family

corr_family objects
fixed

Fixing some parameters
corrMatrix

Using a corrMatrix argument
plot_effects

Partial-dependence effects and plots
how

Extract information about how an object was obtained
freight

Freight dataset
post-fit

Applying post-fit procedures on spaMM results
multinomial

Analyzing multinomial data
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.
predict

Prediction from a model fit.
salamander

Salamander mating data
external-libraries

Installing external libraries
inverse.Gamma

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

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

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

Lip cancer in Scotland 1975 - 1980
phiHGLM

Fitting random effects in the residual dispersion model
spaMM

Inference in mixed models, in particular spatial GLMMs
mapMM

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

Parametric bootstrap
random-effects

Structure of random effects
update.HLfit

Updates a fit
spaMM.colors

A flashy color palette.
plot.HLfit

Model checking plots for mixed models
summary.HLfit

Summary and print methods for fit and test results.
seeds

Seed germination data
spaMM-S3

S3 methods of generics defined in other packages
make_scaled_dist

Scaled distances between unique locations
simulate.HLfit

Simulate realizations of a fitted model.
rankinfo

Checking the rank of the fixed-effects design matrix
vcov

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

spaMM conventions and differences from related fitting procedures
spaMM-internal

Internal spaMM Functions
wafers

Data from a resistivity experiment for semiconductor materials.
welding

Welding data set
sparse_precision

Sparse_precision algorithm
stripHLfit

Reduce the size of fitted objects
seaMask

Masks of seas or lands