spaMM: Mixed-Effect Models, Particularly Spatial Models
Version 2.0.0

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.

AuthorFrançois Rousset [aut, cre, cph], Jean-Baptiste Ferdy [aut, cph], Alexandre Courtiol [aut], GSL authors [ctb] (src/gsl_bessel.*)
Date of publication2017-04-06 22:05:00 UTC
MaintainerFrançois Rousset <francois.rousset@umontpellier.fr>
LicenseCeCILL-2
Version2.0.0
URL https://www.r-project.org http://kimura.univ-montp2.fr/~rousset/spaMM.htm
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("spaMM")

Popular man pages

COMPoisson: Conway-Maxwell-Poisson (COM-Poisson) GLM family
corMatern: Matern Correlation Structure as a corSpatial object
designL.from.Corr: Computation of "square root" of correlation matrix
fitme: Fitting function for fixed- and mixed-effect models with GLM...
fixed.LRT: Likelihood ratio test of fixed effects.
inverse.Gamma: Distribution families for Gamma and inverse Gamma-distributed...
spaMM-conventions: spaMM conventions and differences from related fitting...
See all...

All man pages Function index File listing

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...
good-practice: Clear and trustworthy formulas
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 distances between unique locations
mapMM: Colorful plots of predicted responses in two-dimensional...
Matern.corr: Matern correlation function and Matern formula term.
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
PLS-internals: Internal, Experimental Functions for procedure using the...
predict: Prediction from a model fit.
Predictor: Interface for model formulas
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: spaMM conventions and differences from related fitting...
spaMM.filled.contour: Level (Contour) Plots with better aspect ratio control (for...
spaMM-internal: Internal spaMM Functions
spaMM-internal-Rcpp: Internal spaMM Functions using Rcpp/RcppEigen
stripHLfit: Reduce the size of fitted objects
summary.HL: Summary and print methods for fit and test results.
sym_svd: Singular Value Decomposition of a Symmetric Matrix
update: Updates an HLCor or HLfit fit
wafers: Data from a resistivity experiment for semiconductor...
welding: Welding data set

Functions

.SpaMM Man page
.noRanef Man page
AIC Man page
AIC.HLfit Man page Source code
AUGI0_ZX_sparsePrecision Source code
Bartlett.robust Man page
Beta Man page Source code
CAR Man page
COMP_Z Man page Source code
COMP_Z_lfacn Man page Source code
COMP_Z_n Man page Source code
COMP_Z_n2 Man page Source code
COMP_Z_n3 Man page Source code
COMP_Z_ratio Man page Source code
COMP_dnu_objfn Man page Source code
COMP_maxn Man page Source code
COMPoisson Man page Source code
Cholwrap Man page Source code
Corr Man page Source code
DEPARSE Source code
Dim.corMatern Man page Source code
Dist.earth.mat Source code
Earth Man page
Gamma Man page
HLCor Man page Source code
HLCor.obj Man page
HLCor_body Man page Source code
HL_process.args Man page Source code
HL_strictify Man page Source code
HLfit Man page Source code
HLfit.obj Man page
HLfit_body Man page Source code
HLframes Man page Source code
Initialize.corMatern Man page Source code
LRT Man page Source code
LevMar_cpp Man page Source code
LevPerturbedQCpp Man page Source code
LevenbergMsolveCpp Man page Source code
LevenbergMsolve_Matrix Man page Source code
LevenbergMstepCallingCpp Man page Source code
Loaloa Man page
LogAbsDetCpp Man page Source code
LogAbsDetWrap Man page Source code
MLmess Source code
Matern Man page
Matern.corr Man page
MaternCorr Man page
MaternCorr.default Man page Source code
MaternCorr.ff Man page Source code
Matrix_times_Dvec Man page Source code
Nmatrix Man page
PLS-internals Man page
Predictor Man page Source code
QRsolveWrap Man page
QRwrap Man page Source code
REMLmess Source code
RcppChol Man page Source code
Rcpp_COMP_Z Man page Source code
Rcpp_Sig Man page Source code
Rcpp_chol_R Man page Source code
Rcpp_d2hdv2 Man page Source code
Rcpp_pMVN Man page
Sig_times_b Man page Source code
Sigwrapper Man page Source code
ULI Man page Source code
Variogram.corMatern Man page Source code
ZWZt Man page Source code
ZWZtwrapper Source code
ZtWZ Man page Source code
ZtWZwrapper Source code
\%id*id\% Man page
adjacency Man page
anova Man page
anova.HLfit Man page Source code
arabidopsis Man page
asStandardFormula Man page Source code
as_call_family Man page Source code
bessel_lnKnu Source code
binomialize Man page Source code
blackcap Man page
bloc_lambda Source code
calc.plot.dims Man page Source code
calc.w.resid Man page
calcD2hDv2 Man page Source code
calcNewCorrs Man page Source code
calcPHI Man page Source code
calcPredVar Man page Source code
calcRanefPars Man page Source code
calcResidVar Man page Source code
calcUniqueGeo Man page Source code
calc_APHLs_from_ZX Man page Source code
calc_CARdispGammaGLM Man page Source code
calc_Sig_from_fitobject Source code
calc_TT Source code
calc_asDmLR_invV_from_fitobject Source code
calc_beta_cov Source code
calc_clik Source code
calc_corr_from_dist Source code
calc_corr_list Source code
calc_dispGammaGLM Man page Source code
calc_dlW_deta Source code
calc_dvdloglamMat_new Source code
calc_dvdlogphiMat_new Source code
calc_etaGLMblob Man page Source code
calc_inits Source code
calc_inits_ARphi Source code
calc_inits_Auto_rho Source code
calc_inits_dispPars Source code
calc_inits_geostat_rho Source code
calc_inits_nu Source code
calc_invL Source code
calc_invL_coeffs Source code
calc_invV.dV_info Source code
calc_latentL Source code
calc_logdisp_cov Man page Source code
calc_logdisp_cov_new Source code
calc_logdisp_cov_old Source code
calc_loglamInfo Source code
calc_maxrange Man page Source code
calc_new_X_ZAC Source code
calc_old_corr Source code
calc_sXaug_Re Man page Source code
calc_sscaled_new Source code
calc_wAugX Man page Source code
calc_zAug_not_LMM Source code
canonizeRanPars Man page Source code
checkDistMatrix Man page Source code
checkRandLink Man page Source code
checkRandLinkS Man page Source code
checkRespFam Man page Source code
check_binomial_formula Source code
check_conv_glm_reinit Source code
check_nb_cores Source code
choose_QRmethod Source code
clean_cs Man page Source code
coef.corMatern Man page Source code
coef<-.corMatern Man page
compare.model.structures Man page
compare_model_structures Source code
compute_ZAXlist Source code
confint Man page
confint.HLfit Man page Source code
corFactor.corMatern Man page Source code
corMatern Man page Source code
corMatrix.corMatern Man page Source code
corr.notEQL.lambda Man page Source code
corrHLfit Man page Source code
corrHLfit_body Man page Source code
corrHLfit_future Source code
corrMM.LRT Man page Man page Man page
corrMatrix Man page
crack Man page
create_sXaug_EigenDense_QRP_scaled Man page Source code
create_sXaug_EigenDense_QR_scaled Man page
create_sXaug_EigenSparse_LDLP_scaled Man page Source code
create_sXaug_EigenSparse_LDL_scaled Man page Source code
create_sXaug_EigenSparse_LLP_scaled Man page Source code
create_sXaug_EigenSparse_QRP_scaled Man page Source code
create_sXaug_EigenSparse_QR_scaled Man page Source code
create_sXaug_Matrix_QRP_scaled Man page
create_sXaug_Matrix_cholP_scaled Man page Source code
create_sXaug_baseDense_QRP_scaled Man page Source code
crossprod Source code
crossprodCpp Man page Source code
d2mudeta2fn Man page Source code
dCOMP Man page Source code
def_AUGI0_ZX_sparsePrecision Man page Source code
def_call_corrHLfit_body Source code
def_call_fitme_body Source code
def_sXaug_EigenDense_QRP_scaled Man page Source code
def_sXaug_EigenDense_QR_scaled Man page Source code
def_sXaug_EigenSparse_LDLP_scaled Man page Source code
def_sXaug_EigenSparse_LDL_scaled Man page Source code
def_sXaug_EigenSparse_LLP_scaled Man page Source code
def_sXaug_EigenSparse_QRP_scaled Man page Source code
def_sXaug_EigenSparse_QR_scaled Man page Source code
def_sXaug_Matrix_QRP_scaled Man page Source code
def_sXaug_Matrix_cholP_scaled Man page Source code
def_sXaug_baseDense_QRP_scaled Man page Source code
designL.from.Corr Man page
dev_resids Man page Source code
deviance Man page
deviance.HLfit Man page Source code
dispFn Man page Source code
dispInv Man page Source code
dwdloglam_fn_obsolete Source code
e_LevenbergMsolveCpp Man page Source code
eval.corrEst.args Man page Source code
eval.update.call Man page Source code
eval_as_mat_arg Source code
eval_boot_replicates Source code
eval_gain_LevM_GLM Man page Source code
extract.check.coords Man page
extractors Man page
filled.mapMM Man page
findOffset Man page Source code
findSpatial Man page Source code
findbarsMM Man page Source code
findplus Man page Source code
fit_as_ZX Man page Source code
fit_as_sparsePrecision Man page Source code
fitme Man page Source code
fitme_body Man page Source code
fitme_future Source code
fitted Man page
fitted.HLfit Man page Source code
fitted.HLfitlist Man page Source code
fixedLRT Man page Source code
fixef Man page
fixef.HLfit Man page Source code
freight Man page Man page
fullrho Man page Source code
generateFileName Man page
generateInitPhi Man page Source code
generateName Man page Source code
getCall.HLfit Man page Source code
getCovariate.corMatern Man page Source code
getDistMat Man page Source code
getHLfit Man page Source code
getPar Man page Source code
getProcessed Man page Source code
getValidData Man page Source code
get_CorrEst_and_RanFix Source code
get_HLCorcall Man page Source code
get_LSmatrix Man page Source code
get_RLRTSim_args Man page Source code
get_ZALMatrix Man page Source code
get_ZAlist Man page Source code
get_any_IC Man page Source code
get_beta_cov Source code
get_beta_cov_any_version Man page Source code
get_beta_w_cov Source code
get_fixefVar Man page Source code
get_from_MME Man page
get_from_MME.AUGI0_ZX_sparsePrecision Man page Source code
get_from_MME.default Man page Source code
get_from_MME.sXaug_EigenDense_QRP_scaled Man page Source code
get_from_MME.sXaug_EigenDense_QR_scaled Man page Source code
get_from_MME.sXaug_EigenSparse_LDLP_scaled Man page Source code
get_from_MME.sXaug_EigenSparse_LDL_scaled Man page Source code
get_from_MME.sXaug_EigenSparse_LLP_scaled Man page Source code
get_from_MME.sXaug_EigenSparse_QRP_scaled Man page Source code
get_from_MME.sXaug_EigenSparse_QR_scaled Man page Source code
get_from_MME.sXaug_Matrix_QRP_scaled Man page Source code
get_from_MME.sXaug_Matrix_cholP_scaled Man page Source code
get_from_MME.sXaug_baseDense_QRP_scaled Man page Source code
get_from_MME.sparseMatrix Man page Source code
get_from_MME_default Man page
get_from_MME_default.Matrix Man page Source code
get_from_MME_default.matrix Man page Source code
get_glm_phi Source code
get_hatvalues Source code
get_info_crits Source code
get_init_lambda Source code
get_init_phi Source code
get_inits_by_glm Source code
get_intervals Man page Source code
get_invColdoldList Source code
get_logdispObject Source code
get_methods_ranefs Man page Source code
get_predCov_var_fix Man page Source code
get_predVar Man page Source code
get_residVar Man page Source code
get_respVar Man page Source code
get_valid_beta_coefs Man page Source code
getgroups Man page Source code
glm.reformat Man page Source code
good-practice Man page
initialize_v_h Man page Source code
internal_LRT Man page Source code
intervals Man page
inverse.Gamma Man page
is.identity Man page Source code
landMask Man page
largeLambdaMessages Man page Source code
legend_lambda Man page Source code
leverages Man page Source code
lmwithQR Man page Source code
lmwithQRP Man page Source code
lmwith_sparse_LDLp Man page Source code
lmwith_sparse_LLp Man page Source code
lmwith_sparse_QRp Man page Source code
locoptim Man page Source code
logDet.corMatern Man page Source code
logLik Man page
logLik.HLfit Man page Source code
logLik.HLfitlist Man page Source code
loglamInfo_fn_obsolete Source code
loglfn_ranU Source code
makeCheckGeoMatrices Man page Source code
makeCovEst1 Man page Source code
makeCovEst2 Man page Source code
makeLowerUpper Man page Source code
makeTicks Man page Source code
make_Xscal Man page Source code
make_corr_list Source code
make_lambda_object Source code
make_scaled_dist Man page
makelong Source code
makenewname Man page Source code Source code
mapMM Man page Source code
merge_parlist Man page Source code
minimalErrorHandler Source code
modify_list Man page Source code
muetafn Man page Source code
multi Man page Source code
multinomial Man page
negbin Man page Source code
newetaFix Source code
nextPoints Man page
niceLabels Man page Source code
nit_resp_z_corrections_new Source code
noNonSpatialbarsMM Man page Source code
noOffset Man page Source code
noOffset_ Man page Source code
noRanef Source code
nobarsMM Man page Source code
nobarsMM_ Man page Source code
nobarsNooffset Man page Source code
ntervalStep_I0ZX Source code
ntervalStep_ZX Source code
nuFn Man page Source code
nuInv Man page Source code
oceanmask Man page
onLoad Source code
overcat Man page Source code
pMVN Man page
parseBars Man page Source code
pastefrom Man page Source code
phiHGLM Man page
plot Man page
plot.HLfit Man page
plotScale Man page Source code
post_process_ZALlist Source code
post_process_family Man page Source code
predict Man page
predict.HLfit Man page Source code
preprocess Man page Source code
preprocess_fix_corr Man page Source code
print Man page
print.HLfit Man page Source code
print.HLfitlist Man page Source code
print.arglist Man page Source code
print.fixedLRT Man page Source code
print.predictions Man page Source code
print.predictor Man page Source code
print.vcov.HLfit Man page Source code
process_resglm_list Man page Source code
process_variances Source code
provide_init_lambdas Man page
pseudoSolvediag Man page Source code
ranef Man page
ranef.HLfit Man page Source code
recalc.corMatern Man page Source code
reformat_verbose Man page Source code
residuals Man page
residuals.HLfit Man page Source code
resize_lambda Man page Source code
rhoFn Man page Source code
rhoInv Man page Source code
sXaug_EigenDense_QR_scaled Source code
sXaug_Matrix_QRP_scaled Source code
s_separated Source code
safesolve.qr.matrix Man page
safesolve.qr.vector Man page
salamander Man page
scotlip Man page
seaMask Man page
seeds Man page
selectLoglfn Man page
selfAdjointSolverCpp Source code
separator Man page
setControl Man page Source code
setProcessed Man page Source code
simulate Man page
simulate.HLfit Man page Source code
simulate.HLfitlist Man page Source code
singularSigmaMessagesStop Man page Source code
slashTerms Man page Source code
solveWrap.matrix Man page Source code
solveWrap.vector Man page Source code
spMMFactorList Source code
spMMexpandSlash Source code
spaMM Man page
spaMM-conventions Man page
spaMM-package Man page
spaMM.colors Man page
spaMM.filled.contour Man page
spaMM.getOption Man page Source code
spaMM.options Man page Source code
spaMM_Gamma Man page Source code
spaMM_glm Man page Source code
spaMM_glm.fit Man page Source code
spaMMplot2D Man page Source code
sparse_LDLp_from_XtX Man page Source code
sparse_LLp_from_XtX Man page Source code
stripFormula Source code
stripHLfit Man page Source code
subbarsMM Man page Source code
summary Man page
summary.HLfit Man page
summary.HLfitlist Man page Source code
summary.fixedLRT Man page Source code
sweepZ1W Man page Source code
sweepZ1Wwrapper Source code
sym_eigen Man page Source code
tcrossprod Source code
tcrossprodCpp Man page Source code
theta.mu.canonical Man page
theta.mu.conjugate Man page
thetaMuDerivs Source code
timerraw Source code
traceAB Source code
traceDB Source code
tryCatch.W.E Man page Source code
u_h_v_h_from_v_h Source code
update Man page
update.HLCor Man page
update.HLfit Man page Source code
updateW_ranefS Source code
updateWranef Source code
validData Man page
vcov Man page
vcov.HLfit Man page Source code
wafers Man page
warn_intervalStep Source code
welding Man page
worldcountries Man page
zrnorm Man page

Files

inst
inst/CITATION
inst/NEWS.Rd
tests
tests/testthat
tests/testthat/test-predVar.R
tests/testthat/test-spaMM.filled.contour.R
tests/testthat/test-HLfit.R
tests/testthat/test-corrHLfit.txt
tests/testthat/test-fixedLRT.R
tests/testthat/test-HLCor.R
tests/testthat/test-random-slope.R
tests/testthat/test-salamander.R
tests/testthat/test-spaMM.R
tests/testthat/test-sparsePrecision.R
tests/testthat/test-inverse.Gamma.R
tests/testthat/test-Nugget.R
tests/testthat/test-confint.R
tests/testthat/test-COMPoisson.R
tests/testthat/test-multinomial.R
tests/testthat/test-spaMM_glm.R
tests/testthat/test-LRT-boot.R
tests/testthat/test-dhglm.R
tests/testthat/test-CAR.R
tests/testthat/test-filled.mapMM.R
tests/testthat/test-blackbox.R
tests/testthat/test-corMatern.R
tests/testthat/test-sp-nsp.R
tests/test-all.R
src
src/gsl_bessel.cpp
src/COMPoisson.cpp
src/PLS.h
src/gsl_bessel.h
src/PLS.cpp
src/Makevars.win
src/init.c
src/RcppExports.cpp
src/spaMM_linear.cpp
src/corMatern.cpp
src/spaMM_linear.h
NAMESPACE
data
data/blackcap.RData
data/seeds.RData
data/welding.RData
data/wafers.RData
data/freight.RData
data/Loaloa.RData
data/oceanmask.RData
data/seaMask.RData
data/salamander.RData
data/arabidopsis.RData
data/crack.RData
data/worldcountries.RData
data/landMask.RData
data/scotlip.RData
R
R/update.HL.R
R/generateName.R
R/utils.R
R/sXaug_base_QRP.R
R/subbarsMM.R
R/calc_LRT.R
R/is.diagonal.R
R/HLfit_body.R
R/fitme.R
R/cov_new_fix.R
R/corrMM.LRT.R
R/COMPoisson.R
R/spaMM.data.R
R/preprocess_internals.R
R/dispGammaGLM.R
R/corrHLfit_body.R
R/HLCor.R
R/preprocess.R
R/findplus.R
R/sXaug_Matrix_QRP.R
R/predict.R
R/MakeCovEst.R
R/predictor.R
R/profile.R
R/sXaug_EigenDense_QR.R
R/calc_logdisp_cov.R
R/inverse.Gamma.R
R/sXaug_Matrix_cholP.R
R/extractors.R
R/Beta.R
R/pastefrom.R
R/calc_logdisp_cov_old.R
R/multinomial.R
R/plot.HLfit.R
R/corMatern.R
R/sXaug_Eigen_LDL.R
R/LR.R
R/corrHLfit.R
R/expandSlash.R
R/mapMM.R
R/HLfit_b_internals.R
R/merge_parlist.R
R/CanonizeRanPars.R
R/fit_as_ZX.R
R/RcppExports.R
R/corrHLfit-internals.R
R/LevenbergMstep.R
R/confint.R
R/negbin.R
R/fit_as_sparsePrecision.R
R/save.R
R/simulate.HL.R
R/HLframes.R
R/sXaug_EigenSparse_LLP.R
R/HLfit.R
R/fitme_body.R
R/bloc_lambda.R
R/sXaug_Eigen_LDLP.R
R/slashTerms.R
R/newPLS.R
R/locoptim.R
R/HLfit_Internals.R
R/HLCor_body.R
R/GLM.fit.R
R/summary.HL.R
R/separator.R
R/HLFactorList.R
R/correlationFns.R
R/sXaug_sparsePrecision.R
R/glm.reformat.R
R/sXaug_sparse_QRP.R
R/sXaug_sparse_QR.R
R/structures.R
R/sXaug_EigenDense_QRP_scaled.R
MD5
DESCRIPTION
man
man/sym_svd.Rd
man/spaMM.Rd
man/fixed.LRT.Rd
man/spaMM-conventions.Rd
man/scotlip.Rd
man/Loaloa.Rd
man/plot.HL.Rd
man/stripHLfit.Rd
man/summary.HL.Rd
man/arabidopsis.Rd
man/welding.Rd
man/spaMM.filled.contour.Rd
man/good-practice.Rd
man/inverse.Gamma.Rd
man/update.Rd
man/spaMM-internal.Rd
man/Predictor.Rd
man/blackcap.Rd
man/predict.Rd
man/mapMM.Rd
man/options.Rd
man/designL.from.Corr.Rd
man/confint.Rd
man/Matern.corr.Rd
man/seeds.Rd
man/corrMatrix.Rd
man/wafers.Rd
man/fitme.Rd
man/freight.Rd
man/corrHLfit.Rd
man/simulate.HLCor.Rd
man/spaMM-internal-Rcpp.Rd
man/COMPoisson.Rd
man/PLS-internals.Rd
man/seaMask.Rd
man/phiHGLM.Rd
man/autoregressive.Rd
man/corMatern.Rd
man/HLCor.Rd
man/HLfit.Rd
man/make.scaled.dist.Rd
man/spaMMcolors.Rd
man/COMPoisson-internal.Rd
man/multinomial.Rd
man/negbin.Rd
man/anova.HLfit.Rd
man/salamander.Rd
man/extractors.Rd
man/GLM.fit.Rd
spaMM documentation built on May 20, 2017, 2:34 a.m.

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

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.