spaMM

v. 
by Franois Rousset
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Type Package
Encoding UTF-8
Date 2016-07-21
LinkingTo Rcpp, RcppEigen
NeedsCompilation yes
License CeCILL-2
URL http://www.r-project.org, http://kimura.univ-montp2.fr/~rousset/spaMM.htm
Packaged 2016-07-21 21:15:56 UTC; rousset
Repository CRAN
Date/Publication 2016-07-22 01:18:38

Mixed Models, Particularly Spatial GLMMs

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.

Functions in spaMM

Name Description
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.
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