spaMM
Mixed-Effect Models, with or without Spatial Random Effects

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Search the spaMM package
Functions
1529
Source code
177
Man pages
115
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spaMM: Mixed-Effect Models, with or without Spatial Random Effects
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API

API for spaMM
Mixed-Effect Models, with or without Spatial Random Effects

Global functions
%*%,Kronfacto,Matrix-method Man page
%*%,Kronfacto,matrix-method Man page
%*%,Kronfacto,numeric-method Man page
%*%,ZAXlist,Matrix-method Man page
%*%,ZAXlist,matrix-method Man page
%*%,ZAXlist,numeric-method Man page
%*%,numeric,ZAXlist-method Man page Man page
%*%-methods Man page
..CMP_mu2lambda Source code
..calcPHI Source code
..calc_H_w.resid Source code
..calc_ZtWX Source code
..calc_d2hdv2_info Source code
..calc_dlW_deta Source code
..calc_normalized_ZA Source code
..calc_normalized_ZA_with_subsetting Source code
..get_Q_CHMfactor__assign_template__perm_ZA Source code
..get_bare_fnname Source code
..get_fittedPars Source code
..get_locdata Source code
..n_names2expr Source code
..slice_n_predict_body Source code
..trDiagonal Source code
.AR1_assign_geoinfo_and_LMatrices_but_ranCoefs Source code
.AUGI0_ZX_spprec Source code
.BLOB Source code
.Bartlett_robust Source code
.CHM2uhatval Source code
.CHM_eigrange Source code
.CMP_aic Source code
.CMP_asympto_EX Source code
.CMP_asympto_Var Source code
.CMP_asympto_k3 Source code
.CMP_asympto_k4 Source code
.CMP_attr_y Source code
.CMP_calc_dlW_deta_locfn Source code
.CMP_clik_fn Source code
.CMP_dev.resid Source code
.CMP_dev_resids Source code
.CMP_lambda2mu Source code
.CMP_lambda2mui Source code
.CMP_loglambda_linkfun Source code
.CMP_loglambda_linkinv Source code
.CMP_mu2lambda Source code
.CMP_muetaenv Source code
.CMP_series_EX Source code
.CMP_series_EX2 Source code
.CMP_series_EX3 Source code
.CMP_series_EX4 Source code
.CMP_simfun Source code
.CMP_thetaMuDerivs_2 Source code
.CMP_thetaMuDerivs_3 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_n4 Source code
.COMP_Z_ratio Source code
.COMP_Z_sum Source code
.COMP_add_Md_logcLdeta_terms Source code
.COMP_dnu_objfn Source code
.COMP_maxn Source code
.COMP_simulate Source code
.C_calc_cov_from_ranCoef Source code
.C_dispInv Source code
.C_makelong Source code
.C_makelong2 Source code
.CauchyCorr_hasSlotx Source code
.Corr Source code
.D2detadmuDeta2 Source code
.D2muDeta2 Source code
.D3muDeta3 Source code
.DEPARSE Source code
.D_dlWdmu_Deta Source code
.DdetadmuDeta Source code
.Dim.corMatern Source code
.Dist.chord.mat Source code
.DlogM_Tnegbin_mpfr 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
.FishFn Source code
.Gamma2LLF Source code
.GetValidData_info Source code
.HLfit_body_augZXy Man page Source code
.HLfit_finalize_init_lambda Source code
.IMRFcrossfactor Source code
.Kronfacto_mMat_crossprod Source code
.Kronfacto_num_crossprod Source code
.Kronfacto_num_prod Source code
.LRT Source code
.LevenbergMsolveCpp Source code
.LevenbergMsolve_Matrix Source code
.LevenbergMstepCallingCpp Source code
.LogAbsDetCpp Source code
.LogAbsDetWrap Source code
.Lunique_info_from_Q_CHM Source code
.MLmess Source code
.Matcrossprod Source code
.MaternCorr_hasSlotx Source code
.Matrix_tcrossprod Source code
.Matrix_times_Dvec Source code
.NB_shapeFn Man page
.NB_shapeInv Man page
.REMLmess Source code
.RcppChol Source code
.RcppMatrixCb2 Source code
.Rcpp_COMP_Z Source code
.Rcpp_COMP_Z_asympto Source code
.Rcpp_Csum Source code
.Rcpp_adhoc_shermanM_sp Source code
.Rcpp_adhoc_shermanMstep_sp Source code
.Rcpp_backsolve Source code
.Rcpp_backsolve_M_M Source code
.Rcpp_chol2solve Source code
.Rcpp_chol_R Source code
.Rcpp_crossprod Source code
.Rcpp_d2hdv2 Source code
.Rcpp_dense_cbind_mat_mat Source code
.Rcpp_dense_cbind_mat_vec Source code
.Rcpp_sweepZ1W Source code
.TRACE_fn Source code
.ULI Source code
.Utri_chol_by_qr Source code
.WLS_mat_XtWX Source code
.WLS_substitute Source code
.WLS_substitute_spprec Source code
.Wendland Source code
.XDtemplate Source code
.ZAX_mMat_crossprod Source code
.ZAX_mMat_prod Source code
.ZAX_num_crossprod Source code
.ZAX_num_prod Source code
.ZAX_tcrossprod Source code
.ZAXlist_times_Dvec Source code
.ZA_update Source code
.ZWZt Man page Source code
.ZWZtwrapper Source code
.ZtWZ Source code
.ZtWZwrapper Source code
.ZxA_with_attrs Source code
.ad_hoc_cbind Source code
.ad_hoc_grXhessians_transf Source code
.ad_hoc_jac_transf Source code
.ad_hoc_solve_d2hdv2_Bvec Source code
.ad_hoc_trRanpars Source code
.addPhiGLMwarning Source code
.add_Md_logcLdeta_terms Source code
.add_ZAfix_info Source code
.add_boot_results Source code
.add_cov_matrices__from_mv_global Source code
.add_famPars_outer Source code
.add_fitobject_envir Source code
.add_loopout_vars Source code
.add_phi_returns Source code
.add_ranef_returns Source code
.add_residVar Source code
.add_unscaled_X.pv_fixef Source code
.add_varCorr_phi_lines Source code
.addrightcols_Z Source code
.adhoc_cbind_dgC_0 Source code
.adhoc_cbind_dgC_sXaug_pxy_o Source code
.adhoc_rbind_I_dgC Source code
.adhoc_rbind_dgC_dvec Source code
.adhoc_rbind_dtC_dvec Source code
.all.subsets Source code
.allNULL Source code
.anova.glm Source code
.anova_fallback Source code
.anyNULL Source code
.any_gaussian_inverse Source code
.asNoCorrFormula Source code
.as_call_family Source code
.as_char_bars Source code
.as_ddi_dgC Source code
.as_dtCMatrix_cholL Source code
.as_factor Source code
.as_mat_wAttr Source code
.as_spMat_wAttr Source code
.aschar_adhoc Source code
.assignWrapper Source code
.assign_AMatrices_IMRF Source code
.assign_AMatrices_corrFamily Source code
.assign_ZAfix Source code
.assign_corr_types_families Source code
.assign_cov_matrices__from_covStruct Source code
.assign_geoinfo_and_LMatrices_but_ranCoefs Source code
.assign_newLv_for_newlevels_corrMatrix Source code
.assign_newLv_for_newlevels_fullcorrMatrix Source code
.augZXy_obj Source code
.back2hyperpars Source code
.backsolve Source code
.bdiag_Amatrix Source code
.bdiag_dsC Source code
.bdiag_dtC Source code
.betabin_add_Md_logcLdeta_terms Source code
.binom_add_Md_logcLdeta_terms Source code
.binomial2LLF Source code
.binomial_corr_eta Source code
.binomial_raw_linkinv Source code
.bloc_lambda Source code
.boot_single_par Source code
.bracket Source code
.broom_corrMatrices Source code
.calcD2hDv2 Source code
.calcPHIs Source code
.calcPredVar Source code
.calcRanefPars Source code
.calcResidVar Source code
.calcUniqueGeo Source code
.calcZWZt_mat_or_diag Source code
.calc_AMatrix_IMRF Source code
.calc_APHLs_XLM Source code
.calc_APHLs_by_augZXy_or_sXaug Source code
.calc_APHLs_from_ZX Source code
.calc_APHLs_from_params Source code
.calc_AR1_sparse_Q_ranges Source code
.calc_AR1_t_chol_Q_block Source code
.calc_Binomial_Den Source code
.calc_CARdispGammaGLM Man page Source code
.calc_Evar Source code
.calc_GLMweights Source code
.calc_G_dG Source code
.calc_Gmat Source code
.calc_H_dH Source code
.calc_H_global_scale Source code
.calc_H_w.resid Source code
.calc_IMRF_Qmat Source code
.calc_LowUp_trRancoef Source code
.calc_Lunique_for_correl_algos 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_Var_given_fixef Source code
.calc_XZ_0I Source code
.calc_X_lamres Source code
.calc_Xscal_newscaled Source code
.calc_ZACw Source code
.calc_ZAlist Source code
.calc_ZAlist_newdata Source code
.calc_ZAlist_newdata_mv Source code
.calc_Z_LHS_model_matrix Source code
.calc_Z_lev_lambda Source code
.calc_Z_lev_phi Source code
.calc_Zmatrix Source code
.calc_ZtWX Source code
.calc_beta_cov_info_from_sXaug Source code
.calc_beta_cov_info_others Source code
.calc_beta_cov_info_spprec Source code
.calc_cAIC_pd_from_sXaug Source code
.calc_cAIC_pd_others Source code
.calc_cAIC_pd_spprec Source code
.calc_clik Source code
.calc_corrMatrix_precisionFactor__assign_Lunique Source code
.calc_corr_from_dist Source code
.calc_cov_from_ranCoef Source code
.calc_cov_from_trRancoef Source code
.calc_d2hdv2_info Source code
.calc_d2mudeta2 Source code
.calc_denseness Source code
.calc_dfs Source code
.calc_dispGammaGLM Man page
.calc_dlW_deta Source code
.calc_dlogL_blob Source code
.calc_dvdloglamMat_new Source code
.calc_dvdlogphiMat_new Source code
.calc_etaGLMblob Source code
.calc_etaLLMblob Source code
.calc_fam_corrected_guess Source code
.calc_fixef_lowup Source code
.calc_full_fixef Source code
.calc_fullrho Source code
.calc_grad_side_arg Source code
.calc_grad_thr Source code
.calc_hatval_Z_by_subsetinv Source code
.calc_hatval_Z_u_h_cols_on_left Source code
.calc_init.optim_family_par 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_IMRF Source code
.calc_inits_by_xLM Source code
.calc_inits_cauchy Source code
.calc_inits_corrFamily Source code
.calc_inits_dispPars Source code
.calc_inits_geostat_rho Source code
.calc_inits_hyper 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_inv_d2hdv2_QRP_CHM Source code
.calc_inv_d2hdv2_QRP_CHM_signs Source code
.calc_inv_d2hdv2_decorr Source code
.calc_inv_d2hdv2_decorr_nonSPD Source code
.calc_iter_mean_dispFix Source code
.calc_iter_mean_dispVar Source code
.calc_latentL Source code
.calc_lhs_InvSigma_rhs Source code
.calc_lhs_invV.dVdlam Source code
.calc_lhs_inv_MD2hdv2_rhs Source code
.calc_logdispObject Source code
.calc_logdisp_cov Source code
.calc_logdisp_cov_mv Source code
.calc_loglamInfo Source code
.calc_logphiInfo Source code
.calc_m_grad_obj Source code
.calc_moreargs Source code
.calc_need_Cnn Source code
.calc_neg_d2f_dv_dloglam Source code
.calc_newZACvar Source code
.calc_new_X_ZAC Source code
.calc_new_X_ZAC_mv Source code
.calc_newpredvars Source code
.calc_normalized_ZAlist Source code
.calc_numderivs_LMLT Source code
.calc_optim_args Source code
.calc_optim_args_mv Source code
.calc_p_bv_adjust_nonstdREML Source code
.calc_p_rdisp Source code
.calc_pd_product Source code
.calc_plot_dims Source code
.calc_r12 Source code
.calc_r22_postfit Source code
.calc_range_info Source code
.calc_rankinfo Source code
.calc_raw_ZA Source code
.calc_rhs_m_SCALED_grad_as_szAug Source code
.calc_rhs_m_grad_as_szAug Source code
.calc_sXaug_Re Source code
.calc_sXaug_Re_spprec Source code
.calc_sliceVar Source code
.calc_splitord Source code
.calc_spprec_hatval_ZX_by_QR Source code
.calc_spprec_hatval_ZX_by_r22 Source code
.calc_sscaled_new Source code
.calc_std_leverages Source code
.calc_sub_diagmat_cov_newLv_oldv Source code
.calc_sum_pwt_Q_y_o_2 Source code
.calc_summand_gainratio Source code
.calc_summand_gainratio_spprec Source code
.calc_summingMat_hyper Source code
.calc_t_Q_scaled Source code
.calc_terms_heuristic_denseness Source code
.calc_vec_normIMRF Source code
.calc_wAugX Source code
.calc_w_resid Source code
.calc_weight_X Source code
.calc_z1 Source code
.calc_z1_obs Source code
.calc_z2 Source code
.calc_zAug_not_LMM Source code
.canonizeNames Source code
.canonizeRanPars Source code
.canonize_disp_env Source code
.canonize_disp_envs Source code
.cat_break_info Source code
.cbind_dgC_dgC Source code
.checkDistMatrix Source code
.checkRandLink Source code
.checkRandLinkS Source code
.checkRespFam Source code
.check_Earth_coords Source code
.check_args_corrHLfit Source code
.check_args_fitme Source code
.check_binomial_formula Source code
.check_bootreps Source code
.check_call_on_core Source code
.check_conflict_init_fixed Source code
.check_conv_dispGammaGLM_reinit Source code
.check_corrMatrix Source code
.check_fix_user_AMatrices Source code
.check_identifiability_LMM Source code
.check_identifiability_LMM_mv Source code
.check_init.HLfit Source code
.check_inverse_pred Source code
.check_mv_in_submodels Source code
.check_nb_cores Source code
.check_numDeriv_task Source code
.check_outer_at_bound Source code
.check_phi_Fix Source code
.check_rownames_corrMatrix Source code
.check_simulate_pw Source code
.check_stepwise_sol Source code
.check_suspect_rho Source code
.check_time_G_diagnosis Source code
.check_y Source code
.chlFn Source code
.choose_QRmethod Source code
.close_cores Source code
.compare_model_structures Source code
.compare_phimodels_structures Source code
.compute_ZAL Source code
.compute_ZAXlist Source code
.condcorr2canonARpar Source code
.confint_LRT Source code
.confint_LRT_single_par Source code
.confint_boot Source code
.constr_ranCoefsFn Source code
.constr_ranCoefsInv Source code
.corrFn Source code
.corr_notEQL_lambda Source code
.correct_ZA_mv_ranCoefs Source code
.correct_newZAlist_mv_ranCoefs Source code
.corrfamily2Matrix Source code
.corrfamily_permute Source code
.cosy_names_lambdas Source code
.crossprod Man page Source code
.crossprodCpp_d Source code
.crossprod_factor_inv_Md2hdv2_rhs Source code
.crossprod_not_dge Source code
.dCOMP Source code
.damping_to_solve Source code
.debug_COMP_Z_integrand Source code
.declare_new_Lv_env Source code
.def_Kronfacto Source code
.def_off_fn Source code
.def_u_h_v_h_from_v_h Source code
.def_updateW_ranefS Source code
.define_corrFamily_from_map Source code
.denullify Source code
.designX_prod_mv Source code
.determine_sparse_X Source code
.determine_sparse_X_mv Source code
.dev_resids Source code
.df.null Source code
.dfs_ranCoefs Source code
.dgCcrossprod Source code
.dgCprod Source code
.dgCtcrossprod Source code
.diagfast Source code
.diagnose_bootreps_pbs Source code
.diagnose_coeff_not_moving Source code
.diagnose_conv_problem_LevM Source code
.diagnose_lev_lambda Source code
.dispFn Man page
.dispInv Man page
.display_raw_lambdas Source code
.dlW_Hexp__dmu Source code
.dlog_HratioDeta Source code
.do_damped_WLS Source code
.do_damped_WLS_glm Source code
.do_damped_WLS_llm Source code
.do_damped_WLS_spprec Source code
.dopar Source code
.drop1.lm Source code
.drop1_fallback Source code
.dsCsum Source code
.dyad_Z2A Source code
.eigen_sym Source code
.eta_linkfun Source code
.eval.update.call Source code
.evalWrapper Man page Source code
.eval_X_scaled_H_unscaled_logdet_r22_SPD Source code
.eval_as_mat_arg Source code
.eval_as_mat_arg.HLfit Source code
.eval_both_fits Source code
.eval_check_vec_n_u_h Source code
.eval_conv.corr Source code
.eval_conv.lambda Source code
.eval_conv.phi Source code
.eval_gain_clik_LevM Source code
.eval_gain_dev_LevM Source code
.eval_init_lambda_guess Source code
.eval_qrXa Source code
.eval_replicate2 Man page Source code
.eval_v_h_bounds Source code
.expandDoubleVert Source code
.expand_GeoMatrices Source code
.expand_grouping Source code
.expand_hyper Source code
.expand_multIMRF Source code
.explicit_0_term Source code
.extract_check_coords Source code
.extract_check_coords_within Source code
.factor_inv_Md2hdv2_times_rhs Source code
.fill_init_lambda Source code
.fill_parvec Source code
.fill_rhs_invV.dVdlam Source code
.find_validname Source code
.fix_LowUp Source code
.force_solve Source code
.foreach_PSOCK_nofuture Source code
.foreach_serial_bar Source code
.foreach_snow_bar Source code
.foreach_try_progressr Source code
.format_eta Source code
.future_apply Source code
.fv_linkinv Source code
.gaussian2LLF Source code
.getHLfit Source code
.getPar Source code
.get_BinomialDen Source code
.get_CorrEst_and_RanFix Source code
.get_H_w.resid Source code
.get_LMatrix Source code
.get_LRTSim_args Source code
.get_MME_method Source code
.get_Q_CHMfactor__assign_template__perm_ZA Source code
.get_RLRTSim_args Source code
.get_R_aug_ZXy Source code
.get_WLS_ginv Source code
.get_XZ_0I Source code
.get_Y Source code
.get_ZAfix Source code
.get_absdiagR Source code
.get_absdiagR_blocks Source code
.get_adjMatrix_from_covStruct Source code
.get_bare_fnname.HLfit Source code
.get_beta_cov_any_version Source code
.get_beta_cov_info Source code
.get_beta_v_cov Source code
.get_bobyqa_controls Source code
.get_cP_stuff Source code
.get_clik_fn Source code
.get_compact_cov_mats Source code
.get_control_dist Source code
.get_coordinates Source code
.get_corr_prec_from_covStruct Source code
.get_cov_info_geostat Source code
.get_covbeta Source code
.get_disp_effect_on_newZACw Source code
.get_dist_nested_or_not Source code
.get_family_par Source code
.get_family_parlist Source code
.get_fittedPars Source code
.get_fixed_adjacency_info Source code
.get_fixef_WLS_ginv Source code
.get_from_data_attrs Source code
.get_from_ranef_info Source code
.get_from_terms_info 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_beta Source code
.get_init_in_Xbeta_image Source code
.get_inits_by_xLM Source code
.get_invColdoldList Source code
.get_invL_HLfit Source code
.get_lambdas_notrC_from_hlfit Source code
.get_levels_type Source code
.get_locdata Source code
.get_logdispObject Source code
.get_long_chol_Q_phantom_map Source code
.get_long_precmat_phantom_map Source code
.get_methods_disp Source code
.get_moreargs Source code
.get_nestednames_ZA Source code
.get_newX_info Source code
.get_new_AMatrices Source code
.get_new_X_ZAC_blob Source code
.get_new_damping Source code
.get_newfixef_info Source code
.get_newinold Source code
.get_nlminb_controls Source code
.get_nloptr_controls Source code
.get_objLik Source code
.get_obsInfo Source code
.get_old_info_uniqueGeo Source code
.get_oldlevels Source code
.get_outer_inits_from_fit Source code
.get_phantom_map Source code
.get_phiW Source code
.get_phi_fit Source code
.get_phi_object Source code
.get_phifam Source code
.get_phiform Source code
.get_rC_inits_from_hlfit Source code
.get_rC_longLv_phantom_map Source code
.get_ranPars_notPhi Source code
.get_ranef_resid_Pars Source code
.get_rdisPars_LowUp Source code
.get_refit_args Source code
.get_rho_from_SEM_output Source code
.get_rownames_corrMatrix Source code
.get_t_chol_Q_AR1 Source code
.get_tcrossfac_beta_v_cov Source code
.get_tcrossfac_beta_w_cov Source code
.get_type3_contrasts Source code
.get_u_h Source code
.get_v_condcov Source code
.get_valid_beta_coefs Source code
.gmp.kronecker2D Source code
.gmp_solve Source code
.gmp_traceAB Source code
.guess_Rnest Source code
.guess_new_BinomialDen Source code
.hack.model.frame Source code
.hatvals2std_lev Source code
.inRstudio Source code
.init_AUGI0_ZX Source code
.init_AUGI0_ZX_envir_spprec_info Source code
.init_assign_geoinfo Source code
.init_optim_lambda_ranCoefs Source code
.init_optim_phi Source code
.init_promises_decorr Source code
.init_promises_spprec Source code
.init_promises_spprec_compos_corrMatrix Source code
.init_rdisPars Source code
.init_spprec Source code
.initialize_corrFamily Source code
.initialize_v_h Source code
.integrate_marg Source code
.integrate_marg_lowup Source code
.intervalStep_ZX Source code
.intervalStep_glm Source code
.intervalStep_llm Source code
.intervalStep_spprec Source code
.invL_G.P Source code
.inv_L_G_ZtsqrW Source code
.inv_Lmatrix Source code
.is.multi Source code
.is_2_in_1 Source code
.is_LM Source code
.is_evaluated Source code
.is_identity Source code
.is_link_canonical Source code
.is_marginal Source code
.is_nested_family Source code
.is_promise Source code
.is_spprec Man page
.is_spprec_fit Man page Source code
.is_unit Source code
.kappaFn Source code
.kappaInv Source code
.kappa_inits_from_spde_prior Source code
.kappa_range_factor Source code
.lambda_table_fn Source code
.legend_lambda Source code
.leverages Source code
.leveragesWrap Source code
.lhs_rhs_bars Source code
.llm_step_solver Source code
.lmwithQR Source code
.lmwithQRP Source code
.lmwith_sparse_LDLp Source code
.lmwith_sparse_LLp Source code
.lmwith_sparse_QRp Source code
.loc_pot_tol Source code
.locate_in_tv Source code
.logit Source code
.loglfn_ranU Source code
.longdepFn Source code
.longdepInv Source code
.loop_while_TRUE Source code
.lower_tri_tcrossfactorize Source code
.lu_doo Source code
.mMatrix_bigq Source code
.m_Matrix_times_Dvec Source code
.makeCovEst1 Source code
.makeInteraction Source code
.makeLowUp_stuff_mv Source code
.makeLowerUpper Source code
.make_Cor_template_diallel 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_new_corr_lists_IMRFs Source code
.make_new_corr_mats_NOT_ranCoef Source code
.make_new_corr_mats_rhs_composite Source code
.make_new_corr_mats_simple_ranCoef Source code
.makelong Source code
.makelong_bigq Source code
.makelong_kronprod Source code
.makenewname Source code
.map_rd_mv Source code
.match_old_new_levels Source code
.maxit.mean Source code
.merge_Xs Source code
.merge_ZAlists Source code
.merge_ZZlists Source code
.merge_Zlists Source code
.merge_fixed Source code
.merge_hyper_infos Source code
.merge_lambdas_mv Source code
.merge_mv_list Source code
.merge_mv_parlist Source code
.merge_processed Source code
.merge_rand_families Source code
.minKappa Source code
.minimalErrorHandler Source code
.model.frame Source code
.modify_list Man page
.more_init_optim Source code
.mu_U2fv Source code
.muetafn Source code
.muetafn_LLgeneric Source code
.muetafn_expInfo Source code
.mvize Source code
.mvrnorm Source code
.naresid.exclude Source code
.ncol Source code
.need_obsAlgo Source code
.negbin1_p0 Source code
.negbin2_p0 Source code
.new_locoptim Source code
.new_phifit_init_corrPars Source code
.newetaFix Source code
.noRanef Source code
.nonzeros Source code
.normalize_IMRF Source code
.normalize_IMRF_ZA Source code
.nothing_to_fit Source code
.nuFn Man page Source code
.nuInv Man page Source code
.null.deviance Source code
.nuln_plus_bessel_lnKnu Source code
.numInfo_objfn Source code
.num_ZAX_prod Source code
.objfn_locoptim Source code
.old_NCOL Source code
.old_hack_trTemplate Source code
.oldcbind_dgC_dgC Source code
.onLoad Source code
.optim_by_bobyqa Source code
.optim_by_nloptr Source code
.options.processed Source code
.overcat_phifit_progress Source code
.p_corr_inner_rC Source code
.param.inla_dgT2dgC Source code
.pasteCols Source code
.plotScale Source code
.point_predict Source code
.poisson_raw_linkinv Source code
.post_process_X Source code
.post_process_family_it Source code
.post_process_hlcorcall Source code
.post_process_resid_corrPars Source code
.post_process_respfamilies Source code
.post_process_v_h_LMatrices Source code
.post_process_warningEnv Source code
.pot4improv Source code
.precision2cov Source code
.precisionFactorize Source code
.predict_body Source code
.predict_marg Source code
.preprocess Source code
.preprocess_HL_REMLformula Source code
.preprocess_HLmethod Source code
.preprocess_LevM Source code
.preprocess_SEMargs Source code
.preprocess_X_XRe_off Source code
.preprocess_arglists Source code
.preprocess_augZXy Source code
.preprocess_control.dist Source code
.preprocess_corrFamily Source code
.preprocess_corrHLfit Source code
.preprocess_covStruct Source code
.preprocess_data Source code
.preprocess_fitme Source code
.preprocess_fixed Source code
.preprocess_formula Source code
.preprocess_hyper Source code
.preprocess_init.HLfit Source code
.preprocess_phi_model Source code
.preprocess_pw Source code
.preprocess_resid Source code
.preprocess_scope Source code
.preprocess_spaMM_tol Source code
.preprocess_valuesforNAs Source code
.pretest_fn_on_cores Source code
.prettify_family Source code
.prettify_list Source code
.prettify_method Source code
.prettify_num Source code
.pretty_summ_lambda Source code
.print_adj_ests Source code
.print_lambda_table Source code
.probitgemWrap Source code
.process_HLfit_corrPars Source code
.process_IMRF_bar Source code
.process_LMatrices Source code
.process_MaternIMRFa_bar Source code
.process_ZAL Source code
.process_bars Source code
.process_bars_mv Source code
.process_betaFix Source code
.process_corr_info_spprec Source code
.process_ranCoefs Source code
.process_ranef_case Source code
.process_resglm_list Source code
.prompt Source code
.provide_AR_factorization_info Source code
.provide_BLOB_factor_inv_Md2hdv2 Source code
.provide_BLOB_hatval_Z_ Source code
.provide_CHMfactor Source code
.provide_rho_mapping Source code
.pure_R_COMP_Z_asympto Source code
.pw_famparm Source code
.rC_inv_chol_cpp Source code
.r_resid_var Source code
.r_resid_var_over_cols Source code
.ranCoefsFn Source code
.ranCoefsInv Source code
.rankTrim Source code
.rankinfo Source code
.rcDispFn Source code
.rcDispInv Source code
.re_form_col_indices Source code
.redef_Cf_4_nested_ranef Source code
.reformat_Qmat_info Source code
.reformat_adjMatrix Source code
.reformat_corrPars Source code
.reformat_info_uniqueGeo Source code
.reformat_init_lambda_with_NAs Source code
.reformat_lambda Source code
.reformat_parlist Source code
.reformat_phi Source code
.reformat_ranPars Source code
.reformat_resid_model Source code
.reformat_verbose Source code
.reformat_with_attributes Source code
.reformat_with_attributes_mv Source code
.relist_rep Source code
.remove_from_cP Source code
.rename_lambda Source code
.rename_ranPars Source code
.residuals_bare Source code
.resize_lambda Source code
.rhoFn Man page Source code
.rhoInv Man page Source code
.rhs2factor Source code
.rmNaN Source code
.rmNaN_fn Source code
.rm_Xi_ncol_geq_1 Source code
.rnbinom Source code
.rnbinom_warn Source code
.rpois Source code
.sXaug_EigenDense_QRP_Chol_scaled Source code
.sXaug_Matrix_CHM_H_scaled Source code
.sXaug_Matrix_QRP_CHM_scaled Source code
.safe_ZtWZwrapper Source code
.safe_condnum Source code
.safe_eval_dispval Source code
.safe_glm Source code
.safe_llm Source code
.safe_opt Man page Source code
.safe_true Source code
.safesolve_qr_vector Source code
.sanitize_eta Source code
.sanitize_eta_log_link Source code
.sanitize_phi_est Source code
.sapply Source code
.sapply_anyNA Source code
.sapply_null_or_NA Source code
.scale Source code
.selfAdjointSolverCpp Source code
.seq_levelrange Source code
.setCluster Man page Man page Source code
.setNbThreads Source code
.set_augX_methods Source code
.set_cluster_type Source code
.set_pars_stuff Source code
.set_progrbar Source code
.setattr_G_LMMbool Source code
.shermanM_de Source code
.shermanMstep_de Source code
.silent_M_E Source code
.silent_W_E Source code
.simulate_ranef Source code
.smooth_regul Source code
.solve_IRLS_as_ZX Man page Source code
.solve_IRLS_as_spprec Man page Source code
.solve_crossr22 Source code
.spaMM_lm.wfit Source code
.spaMM_spde.make.A Source code
.sparse_cwiseprod Source code
.sparse_expand_GeoMatrices Source code
.sphFn Source code
.spprec2spcorr Source code
.statsfam2LLF Source code
.std_dev_resids Source code
.stripOffset Man page
.stripRanefs Man page
.structure_list Source code
.stub Source code
.subcol_wAttr Source code
.subrange Source code
.subset_corrFamily Source code
.subset_corrMatrix Source code
.sum_pwt_Q_y_o_2 Source code
.summary_phi_object Source code
.sym_checked Source code
.table_glm_phi Source code
.tcrossprod Man page Source code
.tcrossprodCpp Source code
.test_and_find_sep Source code
.test_augZXy Source code
.thetaMuDerivs Source code
.timerraw Source code
.to_grid_coord Source code
.to_respScale_var Source code
.tr2cov Source code
.traceAB Source code
.traceDB Source code
.tryCatch_W_E Source code
.u_h_v_h_from_v_h Source code
.ugly_na.action_mv Source code
.uniqueGeo_from_ulevels Source code
.unlist Source code
.unloads4spaMM Man page Source code
.unscale Source code
.updateW_ranefS Source code
.updateWranef Source code
.update_APHLs Source code
.update_R_in_place Source code
.update_ZAlist Source code
.update_control Source code
.update_cov_no_nn Source code
.update_data Source code
.update_formula_shared_ranefs Source code
.update_main_terms_info Source code
.update_newuniqueGeo Source code
.update_phifitarglist Source code
.update_port_fit_values Source code
.update_port_fit_values_residModel Source code
.update_ranef_info Source code
.updates_from_w.resid Source code
.upper_tri_tcrossfactorize Source code
.vecdisneeded Source code
.verbose_warnings Source code
.warn_ests_at_bound Source code
.warn_pw_mismatch Source code
.warn_size_mismatch Source code
.which_i_llblock Source code
.wrap_IRLS Source code
.wrap_Ltri_t_chol Man page Source code
.wrap_MakeADFun Source code
.wrap_Utri_chol Source code
.wrap_calcPredVar Source code
.wrap_calc_famdisp_lowup Source code
.wrap_compute_ZALlist4simulate Source code
.wrap_determine_spprec Source code
.wrap_do_damped_WLS_outer Source code
.wrap_precisionFactorize_ranCoefs Source code
.wrap_registerDoParallel Source code
.wrap_registerDoSNOW Source code
.wrap_register_doFuture Source code
.wrap_solve_logdispinfo Source code
.wrap_solve_warn Source code
.wrap_v_h_IRLS Source code
.wrap_wrap_SEM Source code
.wrap_wrap_v_h_IRLS Source code
.xtol_abs_fn Source code
AIC Man page
AIC.HLfit Man page Source code
AR1 Man page Source code
ARMA Man page Source code
ARp Man page Source code
Beta Man page Source code
Beta-distribution-random-effects Man page
CAR Man page
COMPoisson Man page Source code
Cauchy Man page Source code
CauchyCorr Man page
CauchyCorr.default Man page Source code
CauchyCorr.dgCMatrix Man page
CauchyCorr.dsCMatrix Man page
Corr Man page Source code
DHARMa Man page
DoF Man page Source code
Earth Man page
EarthChord Man page
Gamma Man page
Gryphon Man page
Gryphon_A Man page
Gryphon_df Man page
Gryphon_pedigree Man page
GxE Man page
HLCor Man page Source code
HLCor.obj Man page
HLCor_body Man page Source code
HLfit Man page Source code
HLfit.obj Man page
HLfit_body Man page Source code
HLfit_body_old Man page Source code
IMRF Man page Source code
Initialize Man page
Initialize.corMatern Man page Source code
Kronfacto Man page
Kronfacto-class Man page
LL-family Man page
LMLTslots Man page
LMLTslots-class Man page
LR2R2 Man page Source code
LRT Man page Source code
Leuca Man page
LevenbergM Man page
Loaloa Man page
MSFDR Man page Source code
Matern Man page Source code
Matern.corr Man page
MaternCorr Man page
MaternCorr.default Man page
MaternCorr.dgCMatrix Man page
MaternCorr.dsCMatrix Man page
MaternIMRFa Man page Source code
Nmatrix Man page
PLS-internals Man page
Poisson Man page
Predictor Man page Source code
REMLformula Man page
RLRsim Man page
SAR_WWt Man page
Tnegbin Man page Source code
Tpoisson Man page Source code
ULI Man page
VarCorr Man page
VarCorr.HLfit Man page Source code
Variogram Man page
Variogram.corMatern Man page Source code
WinterWheat Man page
X.GCA Man page Source code
X.antisym Man page Source code
X2X Man page
ZAXlist Man page
ZAXlist-class Man page
`%*id%` Source code
`%ZA*gI%` Source code
`%id*%` Source code
`%id*id%` Source code
`.lower.tri<-` Source code
`.theta.mu.canonical` Source code
`.upper.tri<-` Source code
`DHARMa-on-HLfit` Man page
`HLCor.obj` Source code
`HLfit.obj` Source code
`[.precision` Source code
`filled.mapMM` Source code
`plot.HLfit` Source code
`summary.HLfit` Source code
adjacency Man page Source code
adjlg Man page
adjlgMat Man page
algebra Man page
anova Man page
anova.HLfit Man page Source code
anova.LMLT Man page Source code
antisym Man page Source code
arabidopsis Man page
as_LMLT Man page Source code
as_precision Man page Source code
autoregressive Man page
barstyle Man page
beta_resp Man page
beta_table Man page
betabin Man page
binomialize Man page Source code
blackcap Man page
class:Kronfacto Man page
class:LMLTslots Man page
class:ZAXlist Man page
class:missingOrNULL Man page
clinics Man page
coef Man page
coef.corMatern Man page Source code
coef<- Man page
coef<-.corMatern Man page
combinepar Man page Source code
composite-ranef Man page
confint Man page
confint.HLfit Man page Source code
control.HLfit Man page
convergence Man page
corFactor Man page
corFactor.corMatern Man page Source code
corMatern Man page Source code
corMatrix Man page
corMatrix.corMatern Man page Source code
corrFamily Man page Source code
corrFamily-definition Man page
corrFamily-design Man page
corrHLfit Man page Source code
corrHLfit_body Man page Source code
corrMM.LRT Man page Source code
corrMatrix Man page Source code
corrPars Man page
corr_family Man page
covStruct Man page
crack Man page
crossprod,Kronfacto,Matrix-method Man page
crossprod,Kronfacto,matrix-method Man page
crossprod,Kronfacto,numeric-method Man page
crossprod,ZAXlist,Matrix-method Man page
crossprod,ZAXlist,matrix-method Man page
crossprod,ZAXlist,numeric-method Man page
crossprod-methods Man page
def_AUGI0_ZX_spprec Man page Source code
def_sXaug_EigenDense_QRP_Chol_scaled Man page Source code
def_sXaug_Matrix_CHM_H_scaled Man page Source code
def_sXaug_Matrix_QRP_CHM_scaled Man page Source code
def_sXaug_Matrix_cholP_scaled Man page
dev_resids Man page Source code
deviance Man page
deviance.HLfit Man page Source code
df.residual Man page
df.residual.HLfit Man page Source code
diagnose_conv Man page
diallel Man page Source code
dim.Kronfacto Man page Source code
dim.precision Man page Source code
dimnames.bigq Man page Source code
div_info Man page Source code
dofuture Man page Source code
dopar Man page
drop1 Man page
drop1.HLfit Man page Source code
drop1.LMLT Man page Source code
etaFix Man page
eval_replicate Man page Source code
external-libraries Man page
extractAIC Man page
extractAIC.HLfit Man page Source code
extractors Man page
extreme_eig Man page Source code
family Man page
family.HLfit Man page Source code
filled.mapMM Man page
fitme Man page Source code
fitme_body Man page Source code
fitmv Man page Source code
fitmv_body Man page Source code
fitted Man page
fitted.HLfit Man page Source code
fitted.HLfitlist Man page Source code
fix_predVar Man page
fixed Man page
fixedLRT Man page Source code
fixef Man page
fixef.HLfit Man page Source code
formula Man page
formula.HLfit Man page Source code
formula_env Man page
freight Man page Man page
geometric Man page
getCall.HLfit Man page Source code
getCovariate Man page
getCovariate.corMatern Man page Source code
getDistMat Man page Source code
getPar Man page
get_HLCorcall Man page Source code
get_RLRTSim_args Man page Source code
get_RLRsim_args Man page Source code
get_ZALMatrix Man page Source code
get_any_IC Man page Source code
get_cPredVar Man page Source code
get_fittedPars Man page Source code
get_fixefVar Man page Source code
get_from_MME Man page
get_from_MME.AUGI0_ZX_spprec Man page Source code
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_CHM_H_scaled Man page Source code
get_from_MME.sXaug_Matrix_QRP_CHM_scaled Man page Source code
get_from_MME.sXaug_Matrix_cholP_scaled Man page
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_inits_from_fit Man page Source code
get_intervals Man page Source code
get_matrix Man page 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
glht Man page
glm.nodev.fit Man page
good-practice Man page
gridIMRF Man page Source code
hatvalues Man page
hatvalues.HLfit Man page Source code
how Man page
how.HLfit Man page Source code
how.HLfitlist Man page Source code
how.default Man page Source code
hyper Man page
inits Man page
inla.spde2.matern Man page
inla.spde2.pcmatern Man page
intervals Man page
inverse.Gamma Man page
is_separated Man page
is_separated.formula Man page Source code
keepInREML Man page
landMask Man page
lev2bool Man page Source code
llm.fit Man page
lmerTest Man page
logDet Man page
logDet.corMatern Man page Source code
logLik Man page
logLik.HLfit Man page Source code
logLik.HLfitlist Man page Source code
makeTicks Man page Source code
make_scaled_dist Man page
mapMM Man page
map_ranef Man page Source code
mat_sqrt Man page Source code
method Man page
missingOrNULL Man page
missingOrNULL-class Man page
model.frame.HLfit Man page Source code
model.matrix.HLfit Man page Source code
model.matrix.LMLTslots Man page Source code
model.offset.HLfit Man page Source code
multIMRF Man page
multcomp Man page
multi Man page Source code
multinomial Man page
mv Man page
negbin Man page
negbin1 Man page
negbin2 Man page
niceLabels Man page
nobs Man page
nobs.HLfit Man page Source code
numInfo Man page Source code
obsInfo Man page
oceanmask Man page
overcat Man page Source code
pdep_effects Man page Source code
pedigree Man page
phi-resid.model Man page
plot Man page
plot.HLfit Man page
plot_effects Man page Source code
post-fit Man page
predVar Man page
predict Man page
predict.HLfit 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.bootci4print Man page Source code
print.corr_family Man page
print.fixedLRT Man page Source code
print.predictions Man page
print.predictor Man page
print.ranef Man page Source code
print.singeigs Man page Source code
print.spcall Man page
print.vcov.HLfit Man page Source code
prior.weights Man page
projpath Man page
pseudoR2 Man page Source code
ranCoefs Man page
ranFix Man page
ranGCA Man page Source code
ranPars Man page
random-effects Man page
ranef Man page
ranef.HLfit Man page Source code
rankinfo Man page
recalc Man page
recalc.corMatern Man page Source code
recond Man page
refit Man page
register_cF Man page Source code
regularize Man page Source code
remove_from_parlist Man page Source code
resid.model Man page
residVar Man page Source code
residuals Man page
residuals.HLfit Man page Source code
respName Man page
response Man page Source code
rho.mapping Man page
salamander Man page
scotlip Man page
seaMask Man page
seeds Man page
separation Man page
setNbThreads Man page
simulate Man page
simulate.HLfit Man page Source code
simulate.HLfitlist Man page Source code
simulate4boot Man page Source code
simulate_ranef Man page Source code
small_spde Man page
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
spaMM.options Man page Source code
spaMM2boot Man page Source code
spaMM_Gamma Man page
spaMM_boot Man page Source code
spaMM_glm Man page Source code
spaMM_glm.fit Man page
spaMMplot2D Man page
sparse_precision Man page
str.inla.spde2 Man page Source code
stripHLfit Man page Source code
subset_prec Man page
summary Man page
summary.HLfit Man page
summary.HLfitlist Man page Source code
summary.fixedLRT Man page Source code
t.ZAXlist Man page Source code
tcrossprod,ZAXlist,missingOrNULL-method Man page
tcrossprod-methods Man page
terms Man page
terms.HLfit Man page Source code
unregister_cF Man page Source code
update.HLfit Man page Source code
update.formula Man page
update_formulas Man page Source code
update_resp Man page Source code
vcov Man page
vcov.HLfit Man page Source code
verbose Man page
wafers Man page
weights Man page
weights.HLfit Man page Source code
welding Man page
worldcountries Man page
wrap_parallel Man page
spaMM documentation built on June 22, 2024, 9:48 a.m.

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