spaMM-package	spaMM
%*%,Kronfacto,numeric-method	ZAXlist
%*%,numeric,Kronfacto-method	ZAXlist
%*%,numeric,ZAXlist-method	ZAXlist
%*%,ZAXlist,Matrix-method	ZAXlist
%*%,ZAXlist,matrix-method	ZAXlist
%*%,ZAXlist,numeric-method	ZAXlist
%*%-methods	ZAXlist
.calc_CARdispGammaGLM	spaMM-internal
.calc_dispGammaGLM	spaMM-internal
.crossprod	spaMM-internal
.dispFn	spaMM-internal
.dispInv	spaMM-internal
.evalWrapper	spaMM-internal
.eval_replicate2	eval_replicate
.HLfit_body_augZXy	spaMM-internal
.is_spprec	spaMM-internal
.is_spprec_fit	spaMM-internal
.modify_list	spaMM-internal
.NB_shapeFn	spaMM-internal
.NB_shapeInv	spaMM-internal
.nuFn	spaMM-internal
.nuInv	spaMM-internal
.rhoFn	spaMM-internal
.rhoInv	spaMM-internal
.safe_opt	spaMM-internal
.setCluster	spaMM-internal
.solve_IRLS_as_spprec	spaMM-internal
.solve_IRLS_as_ZX	spaMM-internal
.stripOffset	spaMM-internal
.stripRanefs	spaMM-internal
.tcrossprod	spaMM-internal
.unloads4spaMM	spaMM-internal
.wrap_Ltri_t_chol	spaMM-internal
.ZWZt	spaMM-internal
adjacency	autoregressive
adjlg	adjlg
adjlgMat	adjlg
AIC	AIC
AIC.HLfit	AIC
algebra	algebra
aliases	aliases
anova	anova.HLfit
anova.HLfit	anova.HLfit
anova.LMLT	anova.HLfit
antisym	diallel
AR1	autoregressive
arabidopsis	arabidopsis
ARMA	ARp
ARp	ARp
as_LMLT	as_LMLT
as_precision	covStruct
autoregressive	autoregressive
barstyle	options
Beta	HLfit
Beta-distribution-random-effects	HLfit
betabin	betabin
beta_resp	beta_resp
beta_table	vcov
binomialize	multinomial
blackcap	blackcap
CAR	autoregressive
Cauchy	CauchyCorr
CauchyCorr	CauchyCorr
CauchyCorr.default	CauchyCorr
CauchyCorr.dgCMatrix	CauchyCorr
CauchyCorr.dsCMatrix	CauchyCorr
class:Kronfacto	ZAXlist
class:LMLTslots	as_LMLT
class:missingOrNULL	ZAXlist
class:ZAXlist	ZAXlist
clinics	clinics
coef	spaMM-internal
coef.corMatern	corMatern
coef.HLfit	extractors
coef<-	spaMM-internal
coef<-.corMatern	corMatern
combinepar	dopar
COMPoisson	COMPoisson
composite-ranef	composite_ranef
confint	confint
confint.HLfit	confint
control.HLfit	control.HLfit
convergence	convergence
corFactor	spaMM-internal
corFactor.corMatern	corMatern
corMatern	corMatern
corMatrix	spaMM-internal
corMatrix.corMatern	corMatern
Corr	vcov
corrFamily	corrFamily
corrFamily-definition	corrFamily-definition
corrFamily-design	corrFamily-design
corrHLfit	corrHLfit
corrHLfit_body	spaMM-internal
corrMatrix	corrMatrix
corrMM.LRT	spaMM-internal
corrPars	fixed
corr_family	corr_family
covStruct	covStruct
crack	spaMM-internal
crossprod,Kronfacto,Matrix-method	ZAXlist
crossprod,Kronfacto,matrix-method	ZAXlist
crossprod,Kronfacto,numeric-method	ZAXlist
crossprod,ZAXlist,Matrix-method	ZAXlist
crossprod,ZAXlist,matrix-method	ZAXlist
crossprod,ZAXlist,numeric-method	ZAXlist
crossprod-methods	ZAXlist
def_AUGI0_ZX_spprec	PLS-internals
def_sXaug_EigenDense_QRP_Chol_scaled	PLS-internals
def_sXaug_Matrix_CHM_H_scaled	PLS-internals
def_sXaug_Matrix_QRP_CHM_scaled	PLS-internals
deviance	extractors
deviance.HLfit	extractors
dev_resids	extractors
df.residual	extractors
df.residual.HLfit	extractors
DHARMa	post-fit
diagnose_conv	div_info
diallel	diallel
dim.Kronfacto	ZAXlist
dim.precision	spaMM-S3
dimnames.bigq	spaMM-internal
div_info	div_info
DoF	DoF
dofuture	dofuture
dopar	dopar
drop1	drop1.HLfit
drop1.HLfit	drop1.HLfit
drop1.LMLT	drop1.HLfit
dyad	PAIRfn
Earth	make.scaled.dist
EarthChord	make.scaled.dist
emmeans	post-fit
emm_basis.HLfit	spaMM-S3
etaFix	fixed
eval_replicate	eval_replicate
extractAIC	AIC
extractAIC.HLfit	AIC
extractors	extractors
extreme_eig	extreme_eig
family	extractors
family.HLfit	extractors
filled.mapMM	mapMM
fitme	fitme
fitme_body	spaMM-internal
fitmv	fitmv
fitmv_body	spaMM-internal
fitted	extractors
fitted.HLfit	extractors
fitted.HLfitlist	multinomial
fixed	fixed
fixedLRT	fixed.LRT
fixef	extractors
fixef.HLfit	extractors
fixef.HLfitlist	extractors
fix_predVar	fix_predVar
formula	extractors
formula.HLfit	extractors
formula_env	good-practice
freight	freight
Gamma	inverse.Gamma
geometric	COMPoisson
getCall.HLfit	spaMM-internal
getCovariate	spaMM-internal
getCovariate.corMatern	corMatern
getDistMat	extractors
getPar	spaMM-internal
get_any_IC	AIC
get_cPredVar	get_cPredVar
get_fittedPars	get_fittedPars
get_fixefVar	predict
get_from_MME	PLS-internals
get_from_MME.AUGI0_ZX_spprec	PLS-internals
get_from_MME.default	PLS-internals
get_from_MME.sparseMatrix	PLS-internals
get_from_MME.sXaug_EigenDense_QRP_Chol_scaled	PLS-internals
get_from_MME.sXaug_Matrix_CHM_H_scaled	PLS-internals
get_from_MME.sXaug_Matrix_QRP_CHM_scaled	PLS-internals
get_from_MME_default	PLS-internals
get_from_MME_default.Matrix	PLS-internals
get_from_MME_default.matrix	PLS-internals
get_HLCorcall	spaMM-internal
get_inits_from_fit	get_inits_from_fit
get_intervals	predict
get_matrix	get_matrix
get_predCov_var_fix	predict
get_predVar	predict
get_rankinfo	rankinfo
get_ranPars	get_fittedPars
get_residVar	predict
get_respVar	predict
get_RLRsim_args	get_RLRSim_args
get_RLRTSim_args	get_RLRSim_args
get_ZALMatrix	get_matrix
glht	post-fit
glm.nodev.fit	spaMM-internal
gof	gof
good-practice	good-practice
gridIMRF	spaMM-internal
Gryphon	Gryphon
Gryphon_A	Gryphon
Gryphon_df	Gryphon
Gryphon_pedigree	Gryphon
GxE	WinterWheat
hatvalues	hatvalues.HLfit
hatvalues.HLfit	hatvalues.HLfit
HLCor	HLCor
HLCor.obj	spaMM-internal
HLCor_body	spaMM-internal
HLfit	HLfit
HLfit.obj	spaMM-internal
HLfit_body	spaMM-internal
HLfit_body_old	spaMM-internal
how	how
how.default	how
how.HLfit	how
how.HLfitlist	how
hyper	IMRF
IMRF	IMRF
Initialize	spaMM-internal
Initialize.corMatern	corMatern
inits	inits
inla.spde2.matern	IMRF
inla.spde2.pcmatern	IMRF
intervals	predict
inverse.Gamma	inverse.Gamma
is_separated	is_separated
is_separated.formula	is_separated
keepInREML	fixed
Kronfacto	ZAXlist
Kronfacto-class	ZAXlist
landMask	seaMask
Leuca	Leuca
lev2bool	lev2bool
LevenbergM	options
LL-family	llm.fit
llm.fit	llm.fit
lmerTest	post-fit
LMLTslots	as_LMLT
LMLTslots-class	as_LMLT
Loaloa	Loaloa
logDet	spaMM-internal
logDet.corMatern	corMatern
logLik	extractors
logLik.HLfit	extractors
logLik.HLfitlist	multinomial
LR2R2	R2
LRT	anova.HLfit
makeTicks	spaMM-internal
make_scaled_dist	make.scaled.dist
mapMM	mapMM
map_ranef	mapMM
Matern	MaternCorr
Matern.corr	spaMM-internal
MaternCorr	MaternCorr
MaternCorr.default	MaternCorr
MaternCorr.dgCMatrix	MaternCorr
MaternCorr.dsCMatrix	MaternCorr
MaternIMRFa	MaternIMRF
mat_sqrt	mat_sqrt
method	method
missingOrNULL	ZAXlist
missingOrNULL-class	ZAXlist
mm	PAIRfn
mmfn	PAIRfn
model.frame.HLfit	extractors
model.matrix.HLfit	extractors
model.matrix.LMLTslots	as_LMLT
model.offset.HLfit	spaMM-internal
MSFDR	MSFDR
multcomp	post-fit
multi	multinomial
multIMRF	IMRF
multinomial	multinomial
mv	mv
negbin	negbin
negbin1	negbin1
negbin2	negbin
niceLabels	spaMM-internal
Nmatrix	scotlip
nobs	extractors
nobs.HLfit	extractors
numInfo	numInfo
obsInfo	method
oceanmask	seaMask
overcat	spaMM-internal
PAIRfn	PAIRfn
pdep_effects	plot_effect
pedigree	pedigree
phi-resid.model	phi-resid.model
plot	plot.HL
plot.HLfit	plot.HL
plot_effects	plot_effect
PLS-internals	PLS-internals
pois4mlogit	pois4mlogit
Poisson	poisson
post-fit	post-fit
predict	predict
predict.HLfit	predict
predict.pois4mlogit	pois4mlogit
Predictor	covStruct
predVar	predVar
preprocess_fix_corr	predict
print	summary.HL
print.arglist	spaMM-S3
print.bootci4print	spaMM-S3
print.corr_family	corr_family
print.fixedLRT	summary.HL
print.HLfit	summary.HL
print.HLfitlist	summary.HL
print.predictor	spaMM-S3
print.ranef	extractors
print.singeigs	numInfo
print.spaMM_predictions	spaMM-S3
print.vcov.HLfit	spaMM-S3
prior.weights	HLfit
projpath	spaMM-internal
pseudoR2	R2
ranCoefs	fixed
ranCoefs_for_diag	WinterWheat
random-effects	random-effects
ranef	extractors
ranef.HLfit	extractors
ranFix	fixed
ranGCA	diallel
rankinfo	rankinfo
ranPars	fixed
recalc	spaMM-internal
recalc.corMatern	corMatern
recond	spaMM-internal
recover_data.HLfit	spaMM-S3
refit	update
register_cF	register_cF
regularize	extreme_eig
REMLformula	HLfit
remove_from_parlist	get_fittedPars
reshape2long	pois4mlogit
resid.model	resid.model
residuals	residuals.HLfit
residuals.HLfit	residuals.HLfit
residVar	residVar
respName	update
response	extractors
rho.mapping	make.scaled.dist
RLRsim	post-fit
salamander	salamander
SAR_WWt	corr_family
scotlip	scotlip
seaMask	seaMask
seeds	seeds
separation	is_separated
setNbThreads	setNbThreads
simulate	simulate
simulate.HLfit	simulate
simulate.HLfitlist	simulate
simulate4boot	simulate
simulate_ranef	simulate
small_spde	IMRF
spaMM	spaMM
spaMM-conventions	spaMM-conventions
spaMM-S3	spaMM-S3
spaMM.colors	spaMMcolors
spaMM.filled.contour	spaMM.filled.contour
spaMM.getOption	options
spaMM.options	options
spaMM2boot	spaMM_boot
spaMMplot2D	mapMM
spaMM_boot	spaMM_boot
spaMM_Gamma	spaMM-internal
spaMM_glm	GLM.fit
spaMM_glm.fit	GLM.fit
sparse_precision	algebra
str.inla.spde2	IMRF
stripHLfit	stripHLfit
summary	summary.HL
summary.fixedLRT	summary.HL
summary.HLfit	summary.HL
summary.HLfitlist	summary.HL
t.ZAXlist	ZAXlist
tcrossprod,ZAXlist,missingOrNULL-method	ZAXlist
tcrossprod-methods	ZAXlist
terms	extractors
terms.HLfit	extractors
Tnegbin	negbin
Tpoisson	poisson
unregister_cF	register_cF
update.formula	update
update.HLfit	update
update_formulas	update
update_resp	update
VarCorr	vcov
VarCorr.HLfit	vcov
Variogram	spaMM-internal
Variogram.corMatern	corMatern
vcov	vcov
vcov.HLfit	vcov
verbose	verbose
wafers	wafers
weights	extractors
weights.HLfit	extractors
welding	welding
WinterWheat	WinterWheat
worldcountries	seaMask
wrap_parallel	wrap_parallel
X.antisym	diallel_fixed
X.GCA	diallel_fixed
X2X	fitmv
ZAXlist	ZAXlist
ZAXlist-class	ZAXlist
`DHARMa-on-HLfit`	plot.HL
