spaMM: 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.

AuthorFran├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 publication2016-09-05 04:17:26
MaintainerFran├žois Rousset <francois.rousset@umontpellier.fr>
LicenseCeCILL-2
Version1.10.0
http://www.r-project.org, http://kimura.univ-montp2.fr/~rousset/spaMM.htm

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

Functions

adjacency Man page
AIC Man page
AIC.HLfit Man page
alternating Man page
anova Man page
anova.HLfit Man page
arabidopsis Man page
asStandardFormula Man page
auglinmodfit Man page
Bartlett.robust Man page
bessel_lnKnu Man page
Beta Man page
binomialize Man page
blackcap Man page
bloc_lambda Man page
calc_asDmLR_invV_from_fitobject Man page
calc_beta_cov Man page
calc_beta_w_cov Man page
calc_CARdispGammaGLM Man page
calc_clik Man page
calcD2hDv2 Man page
calc_dispGammaGLM Man page
calc.dlW_deta Man page
calc.dvdloglamMat Man page
calc_dvdlogphiMat Man page
calc_etaGLMblob Man page
calc_hatval Man page
calc_info_crits Man page
calc_inits Man page
calc_inits_ARphi Man page
calc_inits_Auto_rho Man page
calc_inits_by_glm Man page
calc_inits_dispPars Man page
calc_inits_geostat_rho Man page
calc_inits_nu Man page
calc_invColdoldList Man page
calc_invL Man page
calc_invL_coeffs Man page
calc_invS.X Man page
calc_logdisp_cov Man page
calc_maxrange Man page
calcNewCorrs Man page
calc.Pdiag Man page
calcPHI Man page
calc.plot.dims Man page
calcPredVar Man page
calc.p_v Man page
calcRanefPars Man page
calcResidVar Man page
calc_Sig_from_fitobject Man page
calc_sscaled Man page
calc_TT Man page
calc_tXinvS Man page
calcUniqueGeo Man page
calc_wAugX Man page
calc.w.resid Man page
calc_ZALMatrix Man page
canonizeRanPars Man page
CAR Man page
checkDistMatrix Man page
checkRandLink Man page
checkRandLinkS Man page
checkRespFam Man page
Cholwrap Man page
choose_QRmethod Man page
clean_cs Man page
coef<-.corMatern Man page
coef.corMatern Man page
compare.model.structures Man page
COMP_dnu_objfn Man page
COMP_maxn Man page
COMPoisson Man page
computeZAXlist Man page
COMP_Z Man page
COMP_Z_lfacn Man page
COMP_Z_n Man page
COMP_Z_n2 Man page
COMP_Z_n3 Man page
COMP_Z_ratio Man page
CondNormfn Man page
confint Man page
confint.HLfit Man page
connectedSets Man page
corFactor.corMatern Man page
corMatern Man page
corMatrix.corMatern Man page
Corr Man page
corrHLfit Man page
corrHLfit_body Man page
corrMatrix Man page
corrMM.LRT Man page
corrMM.LRT Man page
corrMM.LRT Man page
corr.notEQL.lambda Man page
crack Man page
create_get_beta_cov Man page
create_get_beta_w_cov Man page
create_get_glm_phi Man page
create_get_info_crits Man page
create_get_init_lambda Man page
create_get_init_phi Man page
create_get_inits_by_glm Man page
create_get_invColdoldList Man page
create_get_logdispObject Man page
create_get_qr Man page
create_get_w_h_coeffs Man page
create_get_ZALMatrix Man page
crossprodCpp Man page
d2mudeta2fn Man page
dCOMP Man page
DEPARSE Man page
designL.from.Corr Man page
deviance Man page
deviance.HLfit Man page
dev_resids Man page
Dim.corMatern Man page
dispFn Man page
dispInv Man page
e_LevenbergMsolveCpp Man page
e_LevenbergMstep Man page
elim.redundant.V Man page
eval.corrEst.args Man page
eval_gain_LevM_GLM Man page
eval_gain_LevM_HGLM Man page
eval.update.call Man page
extract.check.coords Man page
extractors Man page
extrapolhull Man page
filled.mapMM Man page
findbarsMM Man page
findOffset Man page
findplus Man page
findSpatial Man page
fitme Man page
fitme_body Man page
fitted Man page
fitted.HLfit Man page
fitted.HLfitlist Man page
fixedLRT Man page
fixef Man page
fixef.HLfit Man page
freight Man page
freight Man page
fullrho Man page
Gamma Man page
generateFileName Man page
generateInitPhi Man page
generateName Man page
get_any_IC Man page
get_beta_cov_any_version Man page
getCall.HLfit Man page
getCovariate.corMatern Man page
get_DispCorrPars Man page
getDistMat Man page
get_fixefVar Man page
getgroups Man page
get_HLCorcall Man page
getHLfit Man page
get_intervals Man page
get_LSmatrix Man page
get_methods_ranefs Man page
getPar Man page
get_predVar Man page
getProcessed Man page
get_residVar Man page
get_respVar Man page
get_RLRTSim_args Man page
get_valid_beta_coefs Man page
getValidData Man page
get_ZAlist Man page
get_ZALMatrix Man page
glm.reformat Man page
HLCor Man page
HLCor_body Man page
HLCor.obj Man page
HLfit Man page
HLfit_body Man page
HLfit.obj Man page
HLframes Man page
HL_process.args Man page
HL_strictify Man page
\%id*id\% Man page
Initialize.corMatern Man page
initialize.v_h Man page
intervals Man page
intervalStep Man page
inverse.Gamma Man page
invscalefnfn Man page
is.identity Man page
iterateSEMSmooth Man page
labelfn Man page
landMask Man page
largeLambdaMessages Man page
legend_lambda Man page
LevenbergMsolveCpp Man page
LevenbergMstep Man page
LevenbergMstepCallingCpp Man page
leverages Man page
LevPerturbedQCpp Man page
lmwithQ Man page
Loaloa Man page
locatePointinvT Man page
locatePointinvT Man page
locoptim Man page
LogAbsDetCpp Man page
LogAbsDetWrap Man page
logDet.corMatern Man page
loglfn.ranU Man page
loglfn.ranU Man page
logL_from_SEMsample Man page
logLik Man page
logLik.HLfit Man page
logLik.HLfitlist Man page
LRT Man page
LRT.corrHL Man page
makeCheckGeoMatrices Man page
makeCovEst1 Man page
makeCovEst2 Man page
make_lambda_object Man page
makeLowerUpper Man page
makenewname Man page
make_scaled_dist Man page
makeTicks Man page
mapMM Man page
Matern Man page
Matern.corr Man page
MaternCorr Man page
MaternCorr.default Man page
MaternCorr.ff Man page
member_extractors Man page
MLmess Man page
muetafn Man page
multi Man page
multinomial Man page
NAcleaning Man page
negbin Man page
newetaFix Man page
nextPoints Man page
niceLabels Man page
Nmatrix Man page
nobarsMM Man page
nobarsMM_ Man page
nobarsNooffset Man page
noNonSpatialbarsMM Man page
noOffset Man page
noOffset_ Man page
noReForm Man page
nuFn Man page
nuInv Man page
oceanmask Man page
old.nextPoints Man page
optimthroughSmooth Man page
overcat Man page
parseBars Man page
pastefrom Man page
phiHGLM Man page
plot Man page
plot.HLfit Man page
plotScale Man page
pMVN Man page
post_process_ZAL Man page
post.process.ZALlist Man page
predict Man page
predict.HLfit Man page
Predictor Man page
preprocess Man page
print Man page
print.arglist Man page
print.fixedLRT Man page
print.HLfit Man page
print.HLfitlist Man page
print.predictions Man page
print.predictor Man page
print.ranef Man page
print.vcov.HLfit Man page
process_resglm_list Man page
provide_init_lambdas Man page
pseudoSolvediag Man page
QRwrap Man page
ranef Man page
ranef.HLfit Man page
raster Man page
RcppChol Man page
Rcpp_COMP_Z Man page
Rcpp_d2hdv2 Man page
Rcpp_gibbs Man page
Rcpp_gibbs_debug Man page
Rcpp_gibbs_iter Man page
Rcpp_pMVN Man page
Rcpp_QR Man page
Rcpp_qr_Q Man page
Rcpp_Sig Man page
recalc.corMatern Man page
reformat_verbose Man page
REMLmess Man page
resize_lambda Man page
rhoFn Man page
rhoInv Man page
rntneg Man page
rntpos Man page
rsimplex Man page
rtnorm.copy Man page
rvolTriangulation Man page
safesolve.qr.matrix Man page
safesolve.qr.vector Man page
salamander Man page
sampleGridFromLowUp Man page
sampleNearby Man page
sampleNextPars Man page
scalefnfn Man page
scotlip Man page
seaMask Man page
seeds Man page
selectLoglfn Man page
selfAdjointSolverCpp Man page
selfAdjointWrapper Man page
SEMbetalambda Man page
SEMdiagnosticPlot Man page
SEMdiagnosticPlot2D Man page
separator Man page
setControl Man page
setProcessed Man page
Sig_times_b Man page
Sigwrapper Man page
simple_WLS_with_Eigen Man page
simulate Man page
simulate.HLfit Man page
simulate.HLfitlist Man page
singularSigmaMessagesStop Man page
slashTerms Man page
solveWrap.matrix Man page
solveWrap.vector Man page
spaMM Man page
.SpaMM Man page
spaMM_bounds1D Man page
spaMM.colors Man page
spaMM-conventions Man page
spaMM.filled.contour Man page
spaMM_Gamma Man page
spaMM.getOption Man page
spaMM_glm Man page
spaMM_glm.fit Man page
spaMMLRT Man page
spaMM.options Man page
spaMM-package Man page
spaMMplot2D Man page
spaMM_rhullByEI Man page
spMMexpandSlash Man page
spMMFactorList Man page
subbarsMM Man page
subsimplices.volTriangulation Man page
summary Man page
summary.fixedLRT Man page
summary.HLfit Man page
summary.HLfitlist Man page
sweepZ1W Man page
sweepZ1Wwrapper Man page
tcrossprodCpp Man page
tcrossprodWrap Man page
theta.mu.canonical Man page
theta.mu.conjugate Man page
thetaMuDerivs Man page
tryCatch.W.E Man page
u_h_v_h_from_v_h Man page
ULI Man page
update Man page
update.HLCor Man page
update.HLfit Man page
updateWranef Man page
updateW_ranefS Man page
upperPoints Man page
validData Man page
validRangefn Man page
Variogram.corMatern Man page
vcov Man page
vcov.HLfit Man page
volTriangulation Man page
wafers Man page
welding Man page
worldcountries Man page
zrnorm Man page
ZtWZ Man page
ZtWZwrapper Man page
ZWZt Man page
ZWZtwrapper Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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