Learn R Programming

⚠️There's a newer version (4.5.0) of this package.Take me there.

spaMM (version 3.2.0)

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

1,824

Version

3.2.0

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

April 20th, 2020

Functions in spaMM (3.2.0)

HLCor

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

Functions to extract various components of a fit
get_cPredVar

Estimation of prediction variance with bootstrap correction
covStruct

Specifying correlation structures
good-practice

Clear and trustworthy formulas
AIC

Extractors for information criteria such as AIC
fitme

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

Confidence intervals for fixed-effect parameters
how

Extract information about how an object was obtained
pedigree

Fit mixed-effects models incorporating pedigrees
blackcap

Genetic polymorphism in relation to migration in the blackcap
dopar

Interface for parallel computations
spaMM.filled.contour

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

corr_family objects
eval_replicate

Evaluating bootstrap replicates
options

spaMM options settings
get_inits_from_fit

Initiate a fit from another fit
PLS-internals

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

Using a corrMatrix argument
autoregressive

Fitting autoregressive models
multIMRF

Interpolated Markov Random Field models
negbin

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

ZAXlist class and (cross) products for ZAL matrix
COMPoisson

Conway-Maxwell-Poisson (COM-Poisson) GLM family
inverse.Gamma

Distribution families for Gamma and inverse Gamma-distributed random effects
plot.HLfit

Model checking plots for mixed models
is_separated

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

Extract matrices from a fit
seeds

Seed germination data
predict

Prediction from a model fit.
rankinfo

Checking the rank of the fixed-effects design matrix
phiHGLM

Fitting random effects in the residual dispersion model
stripHLfit

Reduce the size of fitted objects
spaMM

Inference in mixed models, in particular spatial GLMMs
sparse_precision

Sparse_precision algorithm
get_ranPars

Operations on lists of parameters
corrHLfit

Fits a mixed model, typically a spatial GLMM.
mat_sqrt

Computation of “square root” of symmetric positive definite matrix
spaMM.colors

A flashy color palette.
spaMM-S3

S3 methods of generics defined in other packages
plot_effects

Partial-dependence effects and plots
simulate.HLfit

Simulate realizations of a fitted model.
spaMM-conventions

spaMM conventions and differences from related fitting procedures
seaMask

Masks of seas or lands
multinomial

Analyzing multinomial data
spaMM_boot

Parametric bootstrap
salamander

Salamander mating data
spaMM-internal

Internal spaMM Functions
fix_predVar

Prediction from models with nearly-singular covariance matrices
scotlip

Lip cancer in Scotland 1975 - 1980
CauchyCorr

Cauchy correlation function and Cauchy formula term
mapMM

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

Fixing some parameters
fixedLRT

Likelihood ratio test of fixed effects.
welding

Welding data set
vcov

Extract covariance or correlation components from a fitted model object
spaMM_glm.fit

Fitting generalized linear models without initial-value or divergence headaches
post-fit

Applying post-fit procedures on spaMM results
adjlg

Simulated data set for testing sparse-precision code
update.HLfit

Updates a fit
make_scaled_dist

Scaled distances between unique locations
LRT

Likelihood ratio test of fixed effects.
summary.HLfit

Summary and print methods for fit and test results.
Poisson

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

Data from a resistivity experiment for semiconductor materials.
freight

Freight dataset
MSFDR

Multiple-Stage False Discovery Rate procedure
arabidopsis

Arabidopsis genetic and climatic data
HLfit

Fit mixed models with given correlation matrix
Loaloa

Loa loa prevalence in North Cameroon, 1991-2001
MaternCorr

Matern correlation function and Matern formula term.
convergence

Assessing convergence for fitted models
corMatern

Matern Correlation Structure as a corSpatial object