spaMM v2.1.6

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by Franois Rousset

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. The algorithms are currently various Laplace approximations methods for likelihood or restricted likelihood, in particular h-likelihood and penalized-likelihood methods.

Functions in spaMM

Name Description
Loaloa Loa loa prevalence in North Cameroon, 1991-2001
MaternCorr Matern correlation function and Matern formula term.
LRT Likelihood ratio test of fixed effects.
arabidopsis Arabidopsis genetic and climatic data
PLS-internals Internal, Experimental Functions for procedure using the ((I,0),(Z,X)) block-order
Predictor Interface for model formulas
HLCor Fits a (spatially) correlated mixed model, for given correlation parameters
HLfit Fit mixed models with given correlation matrix
COMPoisson Conway-Maxwell-Poisson (COM-Poisson) GLM family
spaMM_glm.fit Fitting generalized linear models without initial-value or divergence headaches
adjacency Fitting autoregressive models
blackcap Genetic polymorphism in relation to migration in the blackcap
designL.from.Corr Computation of “square root” of correlation matrix
extractors Functions to extract various components of a fit
confint.HLfit Confidence intervals for fixed-effect parameters
corMatern Matern Correlation Structure as a corSpatial object
phiHGLM Fitting random effects in the residual dispersion model
inverse.Gamma Distribution families for Gamma and inverse Gamma-distributed random effects
make_scaled_dist Scaled distances between unique locations
predict Prediction from a model fit.
salamander Salamander mating data
plot.HLfit Model checking plots for mixed models
scotlip Lip cancer in Scotland 1975 - 1980
seaMask Masks of seas or lands
corrHLfit Fits a mixed model, typically a spatial GLMM.
corrMatrix Using a corrMatrix argument
negbin Family function for negative binomial GLMs and mixed models.
options spaMM options settings
spaMM-conventions spaMM conventions and differences from related fitting procedures
fitme Fitting function for fixed- and mixed-effect models with GLM response.
fixedLRT Likelihood ratio test of fixed effects.
freight Freight dataset
good-practice Clear and trustworthy formulas
spaMM-internal Internal spaMM Functions
spaMM Inference in mixed models, in particular spatial GLMMs
spaMM.filled.contour Level (Contour) Plots with better aspect ratio control (for geographical maps, at least)
spaMM.colors A flashy color palette.
mapMM Colorful plots of predicted responses in two-dimensional space.
multinomial Analyzing multinomial data
seeds Seed germination data
simulate.HLfit Simulate realizations of a fitted model.
wafers Data from a resistivity experiment for semiconductor materials.
welding Welding data set
spaMM-Rcpp-internal Internal spaMM Functions using Rcpp/RcppEigen
sym_eigen Singular Value Decomposition of a Symmetric Matrix
update.HLfit Updates an HLCor or HLfit fit
stripHLfit Reduce the size of fitted objects
summary.HLfit Summary and print methods for fit and test results.
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Details

Type Package
Encoding UTF-8
Date 2017-07-07
LinkingTo Rcpp, RcppEigen
NeedsCompilation yes
License CeCILL-2
URL https://www.r-project.org, http://kimura.univ-montp2.fr/~rousset/spaMM.htm
RoxygenNote 5.0.1
Packaged 2017-07-06 22:31:04 UTC; Francois.rousset
Repository CRAN
Date/Publication 2017-07-07 05:44:19 UTC

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