API for spaMM
Mixed-Effect Models, Particularly Spatial Models

Global functions
.HLfit_body_augZXy Man page
.solve_IRLS_as_ZX Man page
.solve_IRLS_as_spprec Man page
AIC Man page
AIC.HLfit Man page Source code
AR1 Man page Source code
AUGI0_ZX_sparsePrecision Source code
Bartlett_robust Source code
Beta Man page Source code
Beta-distribution-random-effects Man page
CAR Man page
CHOL Source code
CMP_aic Source code
CMP_calc_dlW_deta_locfn Source code
CMP_dev.resid Source code
CMP_dev_resids Source code
CMP_linkfun Source code
CMP_linkfuni Source code
CMP_linkinv Source code
CMP_linkinvi Source code
CMP_mu.eta Source code
CMP_simfun Source code
CMP_use_asympto Source code
CMP_variance Source code
COMP_Pr_moments Source code
COMP_Z Source code
COMP_Z_integrand Source code
COMP_Z_lfacn Source code
COMP_Z_moment Source code
COMP_Z_n Source code
COMP_Z_n2 Source code
COMP_Z_n3 Source code
COMP_Z_ratio Source code
COMP_Z_sum Source code
COMP_dnu_objfn Source code
COMP_maxn Source code
COMP_simulate Source code
COMPoisson Man page Source code
Cauchy Man page Source code
CauchyCorr Man page Source code
Corr Man page Source code
DEPARSE Source code
Dim.corMatern Source code
Dist.chord.mat Source code
Dist.earth.mat Source code
Dvec_times_Matrix Source code
Dvec_times_Matrix_lower_block Source code
Dvec_times_m_Matrix Source code
Dvec_times_m_Matrix_upper_block Source code
Dvec_times_matrix Source code
Earth Man page
EarthChord Man page
Gamma Man page
HLCor Man page Source code
HLCor.obj Man page
HLCor_body Man page Source code
HL_process.args Source code
HL_strictify Source code
HLfit Man page Source code
HLfit.obj Man page
HLfit_body Man page
HLfit_body_augZXy Source code
HLfit_finalize_init_lambda Source code
HLframes Source code
Initialize Man page
Initialize.corMatern Man page Source code
LRT Man page Source code
LevenbergM Man page
Loaloa Man page
MLmess Source code
MSFDR Man page Source code
Matern Man page Source code
Matern.corr Man page
MaternCorr Man page
MaternCorr.default Man page Source code
Matrix_times_Dvec Source code
NB_shapeFn Source code
NB_shapeInv Source code
Nmatrix Man page
PLS-internals Man page
Poisson Man page Source code
Predictor Man page Source code
REMLmess Source code
RT Source code
RcppChol Source code
Rcpp_COMP_Z Source code
Rcpp_chol_R Source code
Rcpp_d2hdv2 Source code
Rcpp_dense_cbind_mat_mat Source code
Rcpp_dense_cbind_mat_vec Source code
Rcpp_sweepZ1W Source code
SAR_WWt Man page
Sig_times_b Source code
Sigsolve_sparsePrecision Source code
TNB_dev_integrand Source code
Tnegbin Man page Source code
Tpoisson Man page Source code
ULI Man page Source code
VarCorr Source code
Variogram Man page
Variogram.corMatern Man page Source code
ZWZt Source code
ZWZtbase Source code
ZWZtwrapper Source code
ZtWZ Source code
ZtWZwrapper Source code
adhoc_cbind_dgC_0 Source code
adhoc_cbind_dtC_sXaug_pxy_o Source code
adhoc_rbind_I_ZAL Source code
adjacency Man page Source code
adjlg Man page
adjlgMat Man page
anova Man page
anova.HLfit Man page Source code
arabidopsis Man page
asNoCorrFormula Source code
as_call_family Source code
as_dtCMatrix_cholL Source code
as_precision Man page Source code
as_predictor Source code
aschar_adhoc Source code
assignWrapper Source code
assign_beta_cov_info Source code
assign_canonLink_G_LMMbool Source code
assign_cov_matrices__from_covStruct Source code
assign_geoinfo_and_LMatrices_but_ranCoefs Source code
autoregressive Man page
bessel_lnKnu Source code
bessel_lnKnu_e Source code
binomialize Man page Source code
blackcap Man page
bloc_lambda Source code
calcD2hDv2 Source code
calcPHI Source code
calcPredVar Source code
calcRanefPars Source code
calcResidVar Source code
calcUniqueGeo Source code
calcZWZt_mat_or_diag Source code
calc_APHLs_by_augZXy_or_sXaug Source code
calc_APHLs_from_ZX Source code
calc_AR1_sparse_Q_ranges Source code
calc_AR1_t_chol_Q_block Source code
calc_CARdispGammaGLM Source code
calc_Evar Source code
calc_H_global_scale Source code
calc_LowUp_trRancoef Source code
calc_Md2hdvb2_info_spprec Source code
calc_Md2hdvb2_info_spprec_by_QR Source code
calc_Md2hdvb2_info_spprec_by_r22 Source code
calc_Qt_pwy_o Source code
calc_XZ_0I Source code
calc_ZAlist Source code
calc_Zlist Source code
calc_ZtWX Source code
calc_beta_cov_info_others Source code
calc_beta_cov_info_spprec Source code
calc_cAIC_pd Source code
calc_cAIC_pd_spprec Source code
calc_clik Source code
calc_corr_from_dist Source code
calc_cov_from_ranCoef Source code
calc_cov_from_trRancoef Source code
calc_d2mudeta2 Source code
calc_dataordered_levels Source code
calc_dispGammaGLM Source code
calc_dlW_deta Source code
calc_dvdloglamMat_new Source code
calc_dvdlogphiMat_new Source code
calc_etaGLMblob Source code
calc_fam_corrected_guess Source code
calc_fullrho Source code
calc_initial_init_lambda Source code
calc_inits Source code
calc_inits_ARphi Source code
calc_inits_Auto_rho Source code
calc_inits_cauchy Source code
calc_inits_dispPars Source code
calc_inits_geostat_rho Source code
calc_inits_nu Source code
calc_inits_ranCoefs Source code
calc_invL_coeffs Source code
calc_invL_from_trRancoef Source code
calc_invV.dV_info Source code
calc_invV_factors Source code
calc_inv_beta_cov Source code
calc_latentL Source code
calc_lhs_invV.dVdlam Source code
calc_logdisp_cov Source code
calc_loglamInfo Source code
calc_moreargs Source code
calc_newFrames_fixed Source code
calc_newFrames_ranef Source code
calc_newZACvar Source code
calc_new_X_ZAC Source code
calc_newpredvars Source code
calc_optim_args Source code
calc_plot_dims Source code
calc_r22 Source code
calc_range_info Source code
calc_rankinfo Source code
calc_raw_ZA Source code
calc_sXaug_Re Source code
calc_sliceVar Source code
calc_spprec_hatval_ZX_by_QR Source code
calc_spprec_hatval_ZX_by_r22 Source code
calc_sscaled_new Source code
calc_sub_diagmat_cov_newLv_oldv Source code
calc_wAugX Source code
calc_w_resid Source code
calc_weight_X Source code
calc_zAug_not_LMM Source code
canonizeRanPars Source code
cbind_dgC_dgC Source code
checkDistMatrix Source code
checkRandLink Source code
checkRandLinkS Source code
checkRespFam Source code
check_binomial_formula Source code
check_conflict_init_fixed Source code
check_conv_glm_reinit Source code
check_corrMatrix Source code
check_nb_cores Source code
check_subset_corrMatrix Source code
choose_QRmethod Source code
coef Man page
coef.corMatern Man page Source code
coef<- Man page
coef<-.corMatern Man page
compare_model_structures Source code
compute_ZAL Source code
compute_ZAXlist Source code
confint Man page
confint.HLfit Man page Source code
corFactor Man page
corFactor.corMatern Man page Source code
corMatern Man page Source code
corMatrix Man page
corMatrix.corMatern Man page Source code
corrHLfit Man page Source code
corrHLfit_body Man page Source code
corrHLfit_future Source code
corrMM.LRT Man page Source code
corrMatrix Man page Source code
corr_family Man page
corr_notEQL_lambda Source code
covStruct Man page
crack Man page
crossprod Source code
crossprodCpp Source code
dCOMP Source code
damping_to_solve Source code
def_AUGI0_ZX_sparsePrecision Man page Source code
def_AUGI0_ZX_sparsePrecision_scaled Man page
def_call_corrHLfit_body Source code
def_call_fitme_body Source code
def_sXaug_EigenDense_QRP_Chol_scaled Man page Source code
def_sXaug_Matrix_QRP_CHM_scaled Man page Source code
designL.from.Corr Man page
determine_LevenbergM Source code
determine_augZXy Source code
determine_sparse_X Source code
determine_spprec Source code
dev_resids Man page Source code
deviance Man page
deviance.HLfit Man page Source code
diagfast Source code
dim.precision Man page Source code
display_raw_lambdas Source code
do_TRACE Source code
do_damped_WLS Source code
do_damped_WLS_spprec Source code
etaFix Man page
eval.update.call Source code
evalWrapper Source code
eval_as_mat_arg Source code
eval_corrEst_args Source code
eval_gain_LevM_etaGLM Source code
eval_gain_LevM_spaMM_GLM Source code
eval_init_lambda_guess Source code
eval_v_h_bounds Source code
evenbergMsolveCpp Source code
evenbergMsolve_Matrix Source code
evenbergMstepCallingCpp Source code
expand_GeoMatrices Source code
explicit_0_term Source code
extractAIC Man page
extractAIC.HLfit Man page Source code
extract_check_coords Source code
extract_check_coords_within Source code
extractors Man page
family Man page
family.HLfit Man page Source code
fill_rhs_invV.dVdlam Source code
filled.mapMM Man page
findOffset Source code
findSpatial Source code
find_validname Source code
findbarsMM 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
fixFormulaObject Source code
fixed Man page
fixedLRT Man page Source code
fixef Man page
fixef.HLfit Man page Source code
force_solve Source code
formula Man page
formula.HLfit Man page Source code
freight Man page Man page
generateInitPhi Source code
geometric Man page
getCall.HLfit Man page Source code
getCovariate Man page
getCovariate.corMatern Man page Source code
getDistMat Man page Source code
getHLfit Source code
getPar Man page Source code
getValidData Source code
get_BinomialDen Source code
get_CorrEst_and_RanFix Source code
get_HLCorcall Man page Source code
get_RLRTSim_args Man page Source code
get_R_aug_ZXy Source code
get_WLS_ginv Source code
get_XZ_0I Source code
get_ZALMatrix Man page Source code
get_absdiagR Source code
get_adjMatrix_from_covStruct Source code
get_any_IC Man page Source code
get_beta_cov_any_version Source code
get_beta_cov_info Source code
get_beta_w_cov Source code
get_boot_response Man page Source code
get_cP_stuff Source code
get_clik_fn Source code
get_compact_cov_mats Source code
get_coordinates Source code
get_corr_prec_from_covStruct Source code
get_dist_nested_or_not Source code
get_family_par Source code
get_fixefVar Man page Source code
get_fixef_off_terms Source code
get_from_MME Man page
get_from_MME.AUGI0_ZX_sparsePrecision Man page Source code
get_from_MME.AUGI0_ZX_sparsePrecision_scaled Man page
get_from_MME.default Man page Source code
get_from_MME.sXaug_EigenDense_QRP_Chol_scaled Man page Source code
get_from_MME.sXaug_Matrix_QRP_CHM_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_geo_info Source code
get_glm_phi Source code
get_hatvalues_FM Source code
get_hatvalues_MM Source code
get_info_crits Source code
get_init_phi Source code
get_inits_by_glm Source code
get_intervals Man page Source code
get_invColdoldList Source code
get_invL_HLfit Source code
get_logdispObject Source code
get_matrix Man page Source code
get_methods_disp Source code
get_predCov_var_fix Man page Source code
get_predVar Man page Source code
get_ranPars Man page Source code
get_rankinfo Man page Source code
get_residVar Man page Source code
get_respVar Man page Source code
get_sub_corr_info Source code
get_valid_beta_coefs Source code
glm_reformat Source code
gmp_solve Source code
gmp_traceAB Source code
good-practice Man page
how Man page
how.HLfit Man page Source code
how.default Man page Source code
intervals Man page
inverse.Gamma Man page
is_separated Man page
lambda_table_fn Source code
landMask Man page
legend_lambda Source code
leverages Source code
leveragesWrap Source code
lmwithQR Source code
lmwithQRP Source code
lmwith_sparse_LDLp Source code
lmwith_sparse_LLp Source code
lmwith_sparse_QRp Source code
logDet Man page
logDet.corMatern Man page Source code
logLik Man page
logLik.HLfit Man page Source code
logLik.HLfitlist Man page Source code
loglfn_ranU Source code
longdepFn Source code
longdepInv Source code
m_Matrix_llblock_times_Dvec Source code
m_Matrix_times_Dvec Source code
makeCovEst1 Source code
makeInteraction Source code
makeLowerUpper Source code
makeTicks Man page Source code
make_Xscal Source code
make_beta_table Source code
make_corr_list Source code
make_lambda_object Source code
make_long_lambda Source code
make_new_corr_lists Source code
make_scaled_dist Man page Source code
makelong Source code
makenewname Source code
mapMM Man page Source code
mat_sqrt Man page Source code
match_coords_in_tUniqueGeo Source code
match_old_new_levels Source code
minimalErrorHandler Source code
model.matrix.HLfit Man page Source code
modify_list Source code
more_init_optim Source code
muetafn Source code
multi Man page Source code
multinomial Man page
negbin Man page Source code
new_locoptim Source code
new_phifit_init_corrPars Source code
newetaFix Source code
niceLabels Man page Source code
nit_optim_lambda_ranCoefs Source code
nit_optim_phi Source code
nit_precision_info Source code
nit_resp_z_corrections_new Source code
nitialize_v_h Source code
noRanef Source code
nobs Man page
nobs.HLfit Man page Source code
nonzeros Source code
nothing_to_fit Source code
ntervalStep_ZX Source code
ntervalStep_glm Source code
ntervalStep_spprec Source code
nuFn Source code
nuInv Source code
objfn_locoptim Source code
oceanmask Man page
ogAbsDetCpp Source code
ogAbsDetWrap Source code
onLoad Source code
optim_by_bobyqa Source code
optim_by_nloptr Source code
overcat Man page Source code
parseBars Source code
pedigree Man page
phiHGLM Man page
plot Man page
plot.HLfit Man page
plotScale Source code
point_predict Source code
post_process_LMatrices Source code
post_process_X Source code
post_process_ZALlist Source code
post_process_family Source code
post_process_fixed Source code
post_process_parlist Source code
post_process_resid_corrPars Source code
predict Man page
predict.HLfit Man page Source code
predict_body Source code
preprocess Source code
preprocess_HLmethod Source code
preprocess_SEMargs Source code
preprocess_control.dist Source code
preprocess_covStruct Source code
preprocess_data Source code
preprocess_fix_corr Man page Source code
preprocess_valuesforNAs Source code
prettify_family Source code
prettify_num Source code
print Man page
print.HLfit Man page Source code
print.HLfitlist Man page Source code
print.arglist Man page Source code
print.corr_family Man page Source code
print.fixedLRT Man page Source code
print.predictions Man page Source code
print.predictor Man page Source code
print.ranef Man page Source code
print.vcov.HLfit Man page Source code
print_adj_ests Source code
print_lambda_table Source code
probitgemWrap Source code
process_HLfit_corrPars Source code
process_corr_info_spprec Source code
process_ranCoefs Source code
process_resglm_list Source code
prompt Source code
provide_AR_factorization Source code
provide_assignment_qrXa_or_r22 Source code
provide_rho_mapping Source code
r_resid_var Source code
ranCoefs Man page
ranCoefsFn Source code
ranCoefsInv Source code
ranFix Man page
ranPars Man page
ranef Man page
ranef.HLfit Man page Source code
rankTrim Source code
rankinfo Man page Source code
re_form_col_indices Source code
recalc Man page
recalc.corMatern Man page Source code
reformat_LevenbergM Source code
reformat_Qmat_info Source code
reformat_init_lambda_with_NAs Source code
reformat_lFix Source code
reformat_resid_model Source code
reformat_verbose Source code
regularized_eigen Source code
remove_from_cP Source code
remove_from_parlist Man page Source code
residuals Man page
residuals.HLfit Man page Source code
resize_lambda Source code
rho.mapping Man page
rhoFn Source code
rhoInv Source code
rmNaN Source code
rmNaN_fn Source code
rnbinom Source code
rpois Source code
sXaug_EigenDense_QRP_Chol_scaled Source code
sXaug_Matrix_QRP_CHM_scaled Source code
s_identity Source code
s_link_canonical Source code
safesolve_qr_vector Source code
salamander Man page
saveSize Source code
scale Source code
scotlip Man page
seaMask Man page
seeds Man page
selfAdjointSolverCpp Source code
separation Man page
separator Source code
set_pars_stuff Source code
simulate Man page
simulate.HLfit Man page Source code
simulate.HLfitlist Man page Source code
slashTerms Source code
solve_IRLS_as_ZX Source code
solve_IRLS_as_spprec Source code
spMMexpandSlash Source code
spaMM Man page
spaMM-S3 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_boot Man page
spaMM_glm Man page Source code
spaMM_glm.fit Man page Source code
spaMM_lm.wfit Source code
spaMMplot2D Man page Source code
sparse_precision Man page
sphFn Source code
sphInv Source code
stripFormula Source code
stripHLfit Man page Source code
stripOffset Source code
stripOffset_ Source code
stripRanefs Source code
stripRanefs_ Source code
subbarsMM Source code
subcol_wAttr Source code
subset_prec Man page Source code
summary Man page
summary.HLfit Man page
summary.HLfitlist Man page Source code
summary.fixedLRT Man page Source code
sym_eigen Man page
tcrossprod Source code
tcrossprodCpp Source code
terms Man page
terms.HLfit Man page Source code
test_augZXy Source code
thetaMuDerivs Source code
timerraw Source code
traceAB Source code
traceDB Source code
tryCatch_W_E Source code
u_h_v_h_from_v_h Source code
unlist_with_attributes Source code
unscale Source code
update Man page
update.HLCor Man page
update.HLfit Man page Source code
updateW_ranefS Source code
updateWranef Source code
update_formula Source code
update_port_fit_values Source code
vcov Man page
vcov.HLfit Man page Source code
wafers Man page
warn_intervalStep Source code
welding Man page
worldcountries Man page
wrap_Ltri_t_chol Source code
wrap_Utri_chol Source code
xtol_abs_fn Source code
spaMM documentation built on Nov. 20, 2018, 1:04 a.m.