spaMM: Mixed Models, Particularly Spatial GLMMs

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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.

Author
Fran├žois Rousset [aut, cre, cph], Jean-Baptiste Ferdy [aut, cph], Alexandre Courtiol [ctb], Dirk Eddelbuettel [ctb] (ziggurat rnorm sources), GSL authors [ctb] (src/gsl_bessel.*)
Date of publication
2016-09-05 04:17:26
Maintainer
Fran├žois Rousset <francois.rousset@umontpellier.fr>
License
CeCILL-2
Version
1.10.0
URLs

View on CRAN

Man pages

anova.HLfit
Likelihood ratio test of fixed effects.
arabidopsis
Arabidopsis genetic and climatic data
autoregressive
Fitting autoregressive models
blackcap
Genetic polymorphism in relation to migration in the blackcap
COMPoisson
Conway-Maxwell-Poisson (COM-Poisson) GLM family
COMPoisson-internal
Internal Functions for COM-Poisson family
confint
Confidence intervals for fixed-effect parameters
corMatern
Matern Correlation Structure as a corSpatial object
corrHLfit
Fits a mixed model, typically a spatial GLMM.
corrMatrix
Using a corrMatrix argument
designL.from.Corr
Computation of "square root" of correlation matrix
extractors
Functions to extract various components of a fit
fitme
Fitting function for fixed- and mixed-effect models with GLM...
fixed.LRT
Likelihood ratio test of fixed effects.
freight
Freight dataset
GLM.fit
Fitting generalized linear models without initial-value or...
HLCor
Fits a (spatially) correlated mixed model, for given...
HLfit
Fit mixed models with given correlation matrix
inverse.Gamma
Distribution families for Gamma and inverse Gamma-distributed...
Loaloa
Loa loa prevalence in North Cameroon, 1991-2001
make.scaled.dist
Scaled Euclidean distances between unique locations
mapMM
Colorful plots of predicted responses in two-dimensional...
Matern.corr
Matern correlation function and Matern formula term.
member_extractors
Member functions to extract various components of a fit
multinomial
Analyzing multinomial data
negbin
Family function for negative binomial GLMs and mixed models.
options
spaMM options settings
phiHGLM
Fitting random effects in the residual dispersion model
plot.HL
Model checking plots for mixed models
predict
Prediction from a model fit.
Predictor
Interface for model formulas
raster
Raster plots of predicted responses
salamander
Salamander mating data
scotlip
Lip cancer in Scotland 1975 - 1980
seaMask
Masks of seas or lands
seeds
Seed germination data
simulate.HLCor
Simulate realizations of a fitted mixed model.
spaMM
Inference in mixed models, in particular spatial GLMMs
spaMMcolors
A flashy color palette.
spaMM-conventions
Difference between spaMM and common R practices
spaMM.filled.contour
Level (Contour) Plots with better aspect ratio control (for...
spaMM-internal
Internal spaMM Functions
spaMM-internal-migraine
Internal spaMM Functions
spaMM-internal-Rcpp
Internal spaMM Functions using Rcpp/RcppEigen
summary.HL
Summary and print methods for fit and test results.
update
Updates an HLCor or HLfit fit
wafers
Data from a resistivity experiment for semiconductor...
welding
Welding data set

Files in this package

spaMM
spaMM/inst
spaMM/inst/CITATION
spaMM/inst/NEWS.Rd
spaMM/tests
spaMM/tests/testthat
spaMM/tests/testthat/test-predVar.R
spaMM/tests/testthat/test-spaMM.filled.contour.R
spaMM/tests/testthat/test-HLfit.R
spaMM/tests/testthat/test-corrHLfit.txt
spaMM/tests/testthat/test-fixedLRT.R
spaMM/tests/testthat/test-HLCor.R
spaMM/tests/testthat/test-random-slope.R
spaMM/tests/testthat/test-salamander.R
spaMM/tests/testthat/test-spaMM.R
spaMM/tests/testthat/test-inverse.Gamma.R
spaMM/tests/testthat/test-Nugget.R
spaMM/tests/testthat/test-confint.R
spaMM/tests/testthat/test-COMPoisson.R
spaMM/tests/testthat/test-multinomial.R
spaMM/tests/testthat/test-dhglm.R
spaMM/tests/testthat/test-CAR.R
spaMM/tests/testthat/test-filled.mapMM.R
spaMM/tests/testthat/test-blackbox.R
spaMM/tests/testthat/test-corMatern.R
spaMM/tests/testthat/test-sp-nsp.R
spaMM/tests/test-all.R
spaMM/src
spaMM/src/Zigg.h
spaMM/src/gsl_bessel.cpp
spaMM/src/COMPoisson.cpp
spaMM/src/pMVN.cpp
spaMM/src/Rcpp_gibbs.cpp
spaMM/src/Ziggurat.h
spaMM/src/gsl_bessel.h
spaMM/src/zrnorm.cpp
spaMM/src/Makevars.win
spaMM/src/RcppExports.cpp
spaMM/src/spaMM_linear.cpp
spaMM/src/corMatern.cpp
spaMM/src/spaMM_linear.h
spaMM/NAMESPACE
spaMM/data
spaMM/data/blackcap.RData
spaMM/data/seeds.RData
spaMM/data/welding.RData
spaMM/data/wafers.RData
spaMM/data/freight.RData
spaMM/data/Loaloa.RData
spaMM/data/oceanmask.RData
spaMM/data/seaMask.RData
spaMM/data/salamander.RData
spaMM/data/arabidopsis.RData
spaMM/data/crack.RData
spaMM/data/worldcountries.RData
spaMM/data/landMask.RData
spaMM/data/scotlip.RData
spaMM/R
spaMM/R/update.HL.R
spaMM/R/generateName.R
spaMM/R/anyStruct.R
spaMM/R/utils.R
spaMM/R/iterateSmooth.R
spaMM/R/subbarsMM.R
spaMM/R/is.diagonal.R
spaMM/R/migraineLike.R
spaMM/R/HLfit_body.R
spaMM/R/fitme.R
spaMM/R/corrMM.LRT.R
spaMM/R/COMPoisson.R
spaMM/R/spaMM.data.R
spaMM/R/preprocess_internals.R
spaMM/R/locoptimthroughsmooth.R
spaMM/R/dispGammaGLM.R
spaMM/R/SEMbetalambda.R
spaMM/R/HLCor.R
spaMM/R/preprocess.R
spaMM/R/auglinmodfit.R
spaMM/R/findplus.R
spaMM/R/predict.R
spaMM/R/MakeCovEst.R
spaMM/R/predictor.R
spaMM/R/profile.R
spaMM/R/inverse.Gamma.R
spaMM/R/extractors.R
spaMM/R/Beta.R
spaMM/R/pastefrom.R
spaMM/R/multinomial.R
spaMM/R/calc.p_v.R
spaMM/R/plot.HLfit.R
spaMM/R/corMatern.R
spaMM/R/LR.R
spaMM/R/corrHLfit.R
spaMM/R/expandSlash.R
spaMM/R/mapMM.R
spaMM/R/HLfit_b_internals.R
spaMM/R/CanonizeRanPars.R
spaMM/R/RcppExports.R
spaMM/R/corrHLfit-internals.R
spaMM/R/LevenbergMstep.R
spaMM/R/confint.R
spaMM/R/negbin.R
spaMM/R/simulate.HL.R
spaMM/R/HLframes.R
spaMM/R/HLfit.R
spaMM/R/bloc_lambda.R
spaMM/R/slashTerms.R
spaMM/R/locoptim.R
spaMM/R/HLfit_Internals.R
spaMM/R/GLM.fit.R
spaMM/R/summary.HL.R
spaMM/R/separator.R
spaMM/R/HLFactorList.R
spaMM/R/correlationFns.R
spaMM/R/glm.reformat.R
spaMM/R/logL_from_SEMsample.R
spaMM/R/structures.R
spaMM/MD5
spaMM/DESCRIPTION
spaMM/man
spaMM/man/spaMM.Rd
spaMM/man/fixed.LRT.Rd
spaMM/man/spaMM-conventions.Rd
spaMM/man/scotlip.Rd
spaMM/man/Loaloa.Rd
spaMM/man/plot.HL.Rd
spaMM/man/summary.HL.Rd
spaMM/man/arabidopsis.Rd
spaMM/man/welding.Rd
spaMM/man/spaMM.filled.contour.Rd
spaMM/man/inverse.Gamma.Rd
spaMM/man/update.Rd
spaMM/man/spaMM-internal.Rd
spaMM/man/Predictor.Rd
spaMM/man/blackcap.Rd
spaMM/man/predict.Rd
spaMM/man/mapMM.Rd
spaMM/man/options.Rd
spaMM/man/designL.from.Corr.Rd
spaMM/man/confint.Rd
spaMM/man/spaMM-internal-migraine.Rd
spaMM/man/Matern.corr.Rd
spaMM/man/seeds.Rd
spaMM/man/corrMatrix.Rd
spaMM/man/wafers.Rd
spaMM/man/fitme.Rd
spaMM/man/freight.Rd
spaMM/man/corrHLfit.Rd
spaMM/man/member_extractors.Rd
spaMM/man/simulate.HLCor.Rd
spaMM/man/spaMM-internal-Rcpp.Rd
spaMM/man/COMPoisson.Rd
spaMM/man/seaMask.Rd
spaMM/man/phiHGLM.Rd
spaMM/man/autoregressive.Rd
spaMM/man/raster.Rd
spaMM/man/corMatern.Rd
spaMM/man/HLCor.Rd
spaMM/man/HLfit.Rd
spaMM/man/make.scaled.dist.Rd
spaMM/man/spaMMcolors.Rd
spaMM/man/COMPoisson-internal.Rd
spaMM/man/multinomial.Rd
spaMM/man/negbin.Rd
spaMM/man/anova.HLfit.Rd
spaMM/man/salamander.Rd
spaMM/man/extractors.Rd
spaMM/man/GLM.fit.Rd