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spaMM (version 1.9.16)

Mixed Models, Particularly Spatial GLMMs

Description

Inference in mixed models, including GLMMs with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroscedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.

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Version

Install

install.packages('spaMM')

Monthly Downloads

1,720

Version

1.9.16

License

CeCILL-2

Maintainer

Franois Rousset

Last Published

July 21st, 2016

Functions in spaMM (1.9.16)

arabidopsis

Arabidopsis genetic and climatic data
corrMatrix

Using a corrMatrix argument
designL.from.Corr

Computation of “square root” of correlation matrix
corMatern

Matern Correlation Structure as a corSpatial object
blackcap

Genetic polymorphism in relation to migration in the blackcap
corrHLfit

Fits a mixed model, typically a spatial GLMM.
confint.HLfit

Confidence intervals for fixed-effect parameters
COMPoisson

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

Fitting autoregressive models
COMPoisson-internal

Internal Functions for COM-Poisson family
fitme

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

Freight dataset
make_scaled_dist

Scaled Euclidean distances between unique locations
spaMM_glm.fit

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

Fit mixed models with given correlation matrix
HLCor

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

Loa loa prevalence in North Cameroon, 1991-2001
extractors

Functions to extract various components of a fit
fixedLRT

Likelihood ratio test of fixed effects.
mapMM

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

Raster plots of predicted responses
MaternCorr

Matern correlation function.
scotlip

Lip cancer in Scotland 1975 - 1980
multinomial

Analyzing multinomial data
negbin

Family function for negative binomial GLMs and mixed models.
salamander

Salamander mating data
seaMask

Masks of seas or lands
plot.HLfit

Model checking plots for mixed models
Predictor

Interface for model formulas
predict

Prediction from a model fit.
spaMM

Inference in mixed models, in particular spatial GLMMs
seeds

Seed germination data
spaMM-Rcpp-internal

Internal spaMM Functions using Rcpp/RcppEigen
spaMM-internal-migraineLike

Internal spaMM Functions
update.HLfit

Updates an HLCor or HLfit fit
simulate.HLfit

Simulate realizations of a fitted mixed model.
summary.HLfit

Summary and print methods for fit and test results.
spaMM.filled.contour

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

A flashy color palette.
spaMM-internal

Internal spaMM Functions
welding

Welding data set
wafers

Data from a resistivity experiment for semiconductor materials.