spaMM v2.2.0


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Mixed-Effect Models, Particularly Spatial Models

Inference in mixed-effect models, including generalized linear mixed models with spatial correlations and models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Variation in residual variance is handled and can be modelled as a linear model. Various approximations of likelihood or restricted likelihood are implement, in particular h-likelihood and Laplace approximation.

Functions in spaMM

Name Description
LRT Likelihood ratio test of fixed effects.
arabidopsis Arabidopsis genetic and climatic data
HLCor Fits a (spatially) correlated mixed model, for given correlation parameters
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.
PLS-internals Internal, Experimental Functions for procedure using the ((I,0),(Z,X)) block-order
Predictor Interface for model formulas
COMPoisson Conway-Maxwell-Poisson (COM-Poisson) GLM family Fitting generalized linear models without initial-value or divergence headaches
corrHLfit Fits a mixed model, typically a spatial GLMM.
corrMatrix Using a corrMatrix argument
extractors Functions to extract various components of a fit
fitme Fitting function for fixed- and mixed-effect models with GLM response.
confint.HLfit Confidence intervals for fixed-effect parameters
corMatern Matern Correlation Structure as a corSpatial object
make_scaled_dist Scaled distances between unique locations
mapMM Colorful plots of predicted responses in two-dimensional space.
good-practice Clear and trustworthy formulas
inverse.Gamma Distribution families for Gamma and inverse Gamma-distributed random effects
seeds Seed germination data
scotlip Lip cancer in Scotland 1975 - 1980
seaMask Masks of seas or lands
spaMM-internal Internal spaMM Functions
adjacency Fitting autoregressive models
blackcap Genetic polymorphism in relation to migration in the blackcap
pedigree Fit mixed-effects models incorporating pedigrees
multinomial Analyzing multinomial data
negbin Family function for negative binomial GLMs and mixed models.
predict Prediction from a model fit.
salamander Salamander mating data
spaMM-conventions spaMM conventions and differences from related fitting procedures
spaMM-Rcpp-internal Internal spaMM Functions using Rcpp/RcppEigen
update.HLfit Updates an HLCor or HLfit fit
wafers Data from a resistivity experiment for semiconductor materials.
options spaMM options settings
separation Checking separation in binomial-response models
spaMM.filled.contour Level (Contour) Plots with better aspect ratio control (for geographical maps, at least)
spaMM.colors A flashy color palette.
spaMM Inference in mixed models, in particular spatial GLMMs
covStruct Specifying correlation structures
designL.from.Corr Computation of “square root” of correlation matrix
fixedLRT Likelihood ratio test of fixed effects.
freight Freight dataset
phiHGLM Fitting random effects in the residual dispersion model
plot.HLfit Model checking plots for mixed models
sparse_precision Sparse_precision algorithm
stripHLfit Reduce the size of fitted objects
welding Welding data set
simulate.HLfit Simulate realizations of a fitted model.
spaMM-S3 S3 methods of generics defined in other packages
summary.HLfit Summary and print methods for fit and test results.
sym_eigen Singular Value Decomposition of a Symmetric Matrix
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Last month downloads


Type Package
Encoding UTF-8
Date 2017-10-03
LinkingTo Rcpp, RcppEigen
NeedsCompilation yes
License CeCILL-2
RoxygenNote 5.0.1
Packaged 2017-10-03 11:59:23 UTC; Francois.rousset
Repository CRAN
Date/Publication 2017-10-03 20:00:13 UTC

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