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
.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
AMatrices	random-effects
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
boxcox	transffit
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
distMatrix	corrMatrix
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
genX2X	genX2X
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
lower	optimBounds
LR2R2	R2
LRT	LRT
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
optimBounds	optimBounds
overcat	spaMM-internal
PAIRfn	PAIRfn
pdep_effects	plot_effect
pedigree	pedigree
phi-resid.model	phi-resid.model
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
rand.family	HLfit
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
transffit	transffit
unregister_cF	register_cF
update.formula	update
update.HLfit	update
update_formulas	update
update_resp	update
upper	optimBounds
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	genX2X
ZAXlist	ZAXlist
ZAXlist-class	ZAXlist
`DHARMa-on-HLfit`	plot.HL
