Index

A

absorb_repara() (mssm.src.python.terms.f method) adjust_CI() (in module mssm.src.python.utils)

adjust_pen_drop() (in module mssm.src.python.penalties) apply_eigen_perm() (in module mssm.src.python.gamm_solvers) approx_smooth_p_values() (in module mssm.src.python.utils)

B

B_spline_basis() (in module mssm.src.python.smooths) back_track_alpha() (in module mssm.src.python.gamm_solvers) bbase() (in module mssm.src.python.smooths) Binomial (class in mssm.src.python.exp_fam) build_ir_smooth_series() (in module mssm.src.python.terms) build_linear_term() (in module mssm.src.python.terms) build_matrix() (mssm.src.python.terms.f method) (mssm.src.python.terms.fs method) (mssm.src.python.terms.GammTerm method) (mssm.src.python.terms.i method) (mssm.src.python.terms.irf method) (mssm.src.python.terms.l method) (mssm.src.python.terms.ri method) (mssm.src.python.terms.rs method)

build_model_matrix() (in module mssm.src.python.formula) build_penalties() (in module mssm.src.python.formula) build_penalty() (mssm.src.python.terms.f method) (mssm.src.python.terms.fs method) (mssm.src.python.terms.GammTerm method) (mssm.src.python.terms.irf method) (mssm.src.python.terms.ri method) (mssm.src.python.terms.rs method) build_sparse_matrix_from_formula() (in module mssm.src.python.formula)

C

C (mssm.src.python.custom_types.Reparameterization attribute) calculate_edf() (in module mssm.src.python.gamm_solvers) calculate_term_edf() (in module mssm.src.python.gamm_solvers) check_drop_valid_gammlss() (in module mssm.src.python.gamm_solvers) check_drop_valid_gensmooth() (in module mssm.src.python.gamm_solvers) clear_cache() (in module mssm.src.python.file_loading) clust_series (mssm.src.python.custom_types.LambdaTerm attribute) clust_weights (mssm.src.python.custom_types.LambdaTerm attribute) code (mssm.src.python.custom_types.Fit_info attribute) COEFFICIENTS (mssm.src.python.custom_types.PenType attribute) compare_CDL() (in module mssm.src.python.compare) compute_B() (in module mssm.src.python.matrix_solvers) compute_bias_corrected_edf() (in module mssm.src.python.utils) compute_block_B_shared() (in module mssm.src.python.matrix_solvers) compute_block_B_shared_cluster() (in module mssm.src.python.matrix_solvers) compute_block_linv_shared() (in module mssm.src.python.matrix_solvers) compute_eigen_perm() (in module mssm.src.python.gamm_solvers) compute_lgdetD_bsb() (in module mssm.src.python.gamm_solvers) compute_Linv() (in module mssm.src.python.matrix_solvers) compute_reml_candidate_GAMM() (in module mssm.src.python.utils) compute_REML_candidate_GSMM() (in module mssm.src.python.utils) compute_S_emb_pinv_det() (in module mssm.src.python.gamm_solvers) compute_Vb_corr_WPS() (in module mssm.src.python.utils) compute_Vp_WPS() (in module mssm.src.python.utils) computeAr1Chol() (in module mssm.src.python.utils) computeH() (in module mssm.src.python.compact_rep) computeHSR1() (in module mssm.src.python.compact_rep) computetrVS3() (in module mssm.src.python.gamm_solvers) computeV() (in module mssm.src.python.compact_rep)

computeVSR1() (in module mssm.src.python.compact_rep) Constraint (class in mssm.src.python.custom_types) constructor() (mssm.src.python.penalties.DifferencePenalty method) (mssm.src.python.penalties.IdentityPenalty method) (mssm.src.python.penalties.Penalty method) ConstType (class in mssm.src.python.custom_types) convolve_event() (in module mssm.src.python.smooths) correct_coef_step() (in module mssm.src.python.gamm_solvers) correct_coef_step_gammlss() (in module mssm.src.python.gamm_solvers) correct_coef_step_gen_smooth() (in module mssm.src.python.gamm_solvers) correct_lambda_step() (in module mssm.src.python.gamm_solvers) correct_lambda_step_gamlss() (in module mssm.src.python.gamm_solvers) correct_lambda_step_gen_smooth() (in module mssm.src.python.gamm_solvers) correct_VB() (in module mssm.src.python.utils) cpp_backsolve_tr() (in module mssm.src.python.matrix_solvers) cpp_chol() (in module mssm.src.python.matrix_solvers) cpp_cholP() (in module mssm.src.python.matrix_solvers) cpp_dqrr() (in module mssm.src.python.matrix_solvers) cpp_qr() (in module mssm.src.python.matrix_solvers) cpp_qrr() (in module mssm.src.python.matrix_solvers) cpp_solve_am() (in module mssm.src.python.matrix_solvers) cpp_solve_coef() (in module mssm.src.python.matrix_solvers) cpp_solve_coef_pqr() (in module mssm.src.python.matrix_solvers) cpp_solve_coefXX() (in module mssm.src.python.matrix_solvers) cpp_solve_L() (in module mssm.src.python.matrix_solvers) cpp_solve_LXX() (in module mssm.src.python.matrix_solvers) cpp_solve_qr() (in module mssm.src.python.matrix_solvers) cpp_solve_tr() (in module mssm.src.python.matrix_solvers) cpp_symqr() (in module mssm.src.python.matrix_solvers) CUSTOM (mssm.src.python.custom_types.PenType attribute)

D

D() (mssm.src.python.exp_fam.Binomial method) (mssm.src.python.exp_fam.Family method) (mssm.src.python.exp_fam.Gamma method) (mssm.src.python.exp_fam.Gaussian method) (mssm.src.python.exp_fam.InvGauss method) (mssm.src.python.exp_fam.Poisson method) D_J_emb (mssm.src.python.custom_types.LambdaTerm attribute) deriv_transform_eta_beta() (in module mssm.src.python.gamm_solvers) deriv_transform_mu_eta() (in module mssm.src.python.gamm_solvers) DERIVATIVE (mssm.src.python.custom_types.PenType attribute) deviance() (mssm.src.python.exp_fam.Binomial method) (mssm.src.python.exp_fam.Family method) (mssm.src.python.exp_fam.Gamma method) (mssm.src.python.exp_fam.Gaussian method) (mssm.src.python.exp_fam.InvGauss method) (mssm.src.python.exp_fam.Poisson method) DIFF (mssm.src.python.custom_types.ConstType attribute) DIFFERENCE (mssm.src.python.custom_types.PenType attribute) DifferencePenalty (class in mssm.src.python.penalties) dist_param (mssm.src.python.custom_types.LambdaTerm attribute) DISTANCE (mssm.src.python.custom_types.PenType attribute)

DROP (mssm.src.python.custom_types.ConstType attribute) drop_terms_S() (in module mssm.src.python.gamm_solvers) drop_terms_X() (in module mssm.src.python.gamm_solvers) dropped (mssm.src.python.custom_types.Fit_info attribute) Drp (mssm.src.python.custom_types.Reparameterization attribute) DummyRhoPrior (class in mssm.src.python.utils) dVy1() (mssm.src.python.exp_fam.Binomial method) (mssm.src.python.exp_fam.Family method) (mssm.src.python.exp_fam.Gamma method) (mssm.src.python.exp_fam.Gaussian method) (mssm.src.python.exp_fam.InvGauss method) (mssm.src.python.exp_fam.Poisson method) dy1() (mssm.src.python.exp_fam.Identity method) (mssm.src.python.exp_fam.Link method) (mssm.src.python.exp_fam.LOG method) (mssm.src.python.exp_fam.LOGb method) (mssm.src.python.exp_fam.Logit method) dy2() (mssm.src.python.exp_fam.Identity method) (mssm.src.python.exp_fam.Link method) (mssm.src.python.exp_fam.LOG method) (mssm.src.python.exp_fam.LOGb method) (mssm.src.python.exp_fam.Logit method)

E

embed_in_S_sparse() (in module mssm.src.python.penalties) embed_in_Sj_sparse() (in module mssm.src.python.penalties) embed_shared_penalties() (in module mssm.src.python.penalties) encode_data() (mssm.src.python.formula.Formula method)

eps (mssm.src.python.custom_types.Fit_info attribute) est_condition() (in module mssm.src.python.matrix_solvers) est_scale() (in module mssm.src.python.exp_fam) estimateVp() (in module mssm.src.python.utils) extend_lambda_step() (in module mssm.src.python.gamm_solvers)

F

f (class in mssm.src.python.terms) f() (mssm.src.python.exp_fam.Identity method) (mssm.src.python.exp_fam.Link method) (mssm.src.python.exp_fam.LOG method) (mssm.src.python.exp_fam.LOGb method) (mssm.src.python.exp_fam.Logit method) FACTOR (mssm.src.python.custom_types.VarType attribute) Family (class in mssm.src.python.exp_fam) fi() (mssm.src.python.exp_fam.Identity method) (mssm.src.python.exp_fam.Link method) (mssm.src.python.exp_fam.LOG method) (mssm.src.python.exp_fam.LOGb method) (mssm.src.python.exp_fam.Logit method)

fit() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) Fit_info (class in mssm.src.python.custom_types) form_cross_prod_mp() (in module mssm.src.python.gamm_solvers) form_eta_mp() (in module mssm.src.python.gamm_solvers) Formula (class in mssm.src.python.formula) frozen (mssm.src.python.custom_types.LambdaTerm attribute) fs (class in mssm.src.python.terms)

G

GAMLSSFamily (class in mssm.src.python.exp_fam) GAMLSSGSMMFamily (class in mssm.src.python.utils) GAMM (class in mssm.models) Gamma (class in mssm.src.python.exp_fam) GAMMALS (class in mssm.src.python.exp_fam) GAMMLSS (class in mssm.models) GammTerm (class in mssm.src.python.terms) GAUMLSS (class in mssm.src.python.exp_fam) Gaussian (class in mssm.src.python.exp_fam) gd_coef_smooth() (in module mssm.src.python.gamm_solvers) get_baseline_hazard() (mssm.src.python.exp_fam.PropHaz method) get_coding_factors() (mssm.src.python.formula.Formula method) get_coef_info() (mssm.src.python.terms.f method) (mssm.src.python.terms.fs method) (mssm.src.python.terms.GammTerm method) (mssm.src.python.terms.i method) (mssm.src.python.terms.irf method) (mssm.src.python.terms.l method) (mssm.src.python.terms.ri method) (mssm.src.python.terms.rs method) get_data() (mssm.src.python.formula.Formula method) get_depvar() (mssm.src.python.formula.Formula method) get_factor_codings() (mssm.src.python.formula.Formula method) get_factor_levels() (mssm.src.python.formula.Formula method) get_has_intercept() (mssm.src.python.formula.Formula method) get_ir_smooth_term_idx() (mssm.src.python.formula.Formula method) get_lhs() (mssm.src.python.formula.Formula method) get_linear_coef_info() (in module mssm.src.python.terms) get_linear_term_idx() (mssm.src.python.formula.Formula method) get_llk() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) get_mmat() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method)

get_n_coef() (mssm.src.python.formula.Formula method) get_notNA() (mssm.src.python.formula.Formula method) get_pars() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) get_random_term_idx() (mssm.src.python.formula.Formula method) get_reml() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) get_resid() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) (mssm.src.python.exp_fam.GAMLSSFamily method) (mssm.src.python.exp_fam.GAMMALS method) (mssm.src.python.exp_fam.GAUMLSS method) (mssm.src.python.exp_fam.GSMMFamily method) (mssm.src.python.exp_fam.MULNOMLSS method) (mssm.src.python.exp_fam.PropHaz method) get_smooth_term_idx() (mssm.src.python.formula.Formula method) get_subgroup_variables() (mssm.src.python.formula.Formula method) get_survival() (mssm.src.python.exp_fam.PropHaz method) get_term_names() (mssm.src.python.formula.Formula method) get_terms() (mssm.src.python.formula.Formula method) get_var_map() (mssm.src.python.formula.Formula method) get_var_maxs() (mssm.src.python.formula.Formula method) get_var_mins() (mssm.src.python.formula.Formula method) get_var_mins_maxs() (mssm.src.python.formula.Formula method) get_var_types() (mssm.src.python.formula.Formula method) grad_lambda() (in module mssm.src.python.gamm_solvers) gradient() (mssm.src.python.exp_fam.GSMMFamily method) (mssm.src.python.exp_fam.PropHaz method) (mssm.src.python.utils.GAMLSSGSMMFamily method) GSMM (class in mssm.models) GSMMFamily (class in mssm.src.python.exp_fam)

H

handle_drop_gammlss() (in module mssm.src.python.gamm_solvers) handle_drop_gsmm() (in module mssm.src.python.gamm_solvers) has_ir_terms() (mssm.src.python.formula.Formula method)

hessian() (mssm.src.python.exp_fam.GSMMFamily method) (mssm.src.python.exp_fam.PropHaz method) (mssm.src.python.utils.GAMLSSGSMMFamily method)

I

i (class in mssm.src.python.terms) identify_drop() (in module mssm.src.python.gamm_solvers) Identity (class in mssm.src.python.exp_fam) IDENTITY (mssm.src.python.custom_types.PenType attribute) IdentityPenalty (class in mssm.src.python.penalties) init_coef() (mssm.src.python.exp_fam.GAMLSSFamily method) (mssm.src.python.exp_fam.GAMMALS method) (mssm.src.python.exp_fam.GAUMLSS method) (mssm.src.python.exp_fam.GSMMFamily method) (mssm.src.python.exp_fam.PropHaz method) init_lambda() (mssm.src.python.exp_fam.GAMLSSFamily method) (mssm.src.python.exp_fam.GSMMFamily method)

init_mu() (mssm.src.python.exp_fam.Binomial method) (mssm.src.python.exp_fam.Family method) (mssm.src.python.exp_fam.Poisson method) init_step_gam() (in module mssm.src.python.gamm_solvers) initialize_extension() (in module mssm.src.python.gamm_solvers) InvGauss (class in mssm.src.python.exp_fam) irf (class in mssm.src.python.terms) IRrp (mssm.src.python.custom_types.Reparameterization attribute) IRSMOOTH (mssm.src.python.custom_types.TermType attribute) iter (mssm.src.python.custom_types.Fit_info attribute)

K

K2 (mssm.src.python.custom_types.Fit_info attribute)

keep_eta() (in module mssm.src.python.gamm_solvers) keep_XTX() (in module mssm.src.python.gamm_solvers)

L

l (class in mssm.src.python.terms) lam (mssm.src.python.custom_types.LambdaTerm attribute) lambda_updates (mssm.src.python.custom_types.Fit_info attribute) LambdaTerm (class in mssm.src.python.custom_types) lhs (class in mssm.src.python.formula) li() (in module mssm.src.python.terms) LINEAR (mssm.src.python.custom_types.TermType attribute) Link (class in mssm.src.python.exp_fam) llk() (mssm.src.python.exp_fam.Binomial method) (mssm.src.python.exp_fam.Family method) (mssm.src.python.exp_fam.GAMLSSFamily method) (mssm.src.python.exp_fam.Gamma method) (mssm.src.python.exp_fam.GAMMALS method) (mssm.src.python.exp_fam.GAUMLSS method) (mssm.src.python.exp_fam.Gaussian method) (mssm.src.python.exp_fam.GSMMFamily method) (mssm.src.python.exp_fam.InvGauss method) (mssm.src.python.exp_fam.MULNOMLSS method) (mssm.src.python.exp_fam.Poisson method) (mssm.src.python.exp_fam.PropHaz method) (mssm.src.python.utils.GAMLSSGSMMFamily method)

LOG (class in mssm.src.python.exp_fam) LOGb (class in mssm.src.python.exp_fam) Logit (class in mssm.src.python.exp_fam) logpdf() (mssm.src.python.utils.DummyRhoPrior method) (mssm.src.python.utils.RhoPrior method) lp() (mssm.src.python.exp_fam.Binomial method) (mssm.src.python.exp_fam.Family method) (mssm.src.python.exp_fam.GAMLSSFamily method) (mssm.src.python.exp_fam.Gamma method) (mssm.src.python.exp_fam.GAMMALS method) (mssm.src.python.exp_fam.GAUMLSS method) (mssm.src.python.exp_fam.Gaussian method) (mssm.src.python.exp_fam.InvGauss method) (mssm.src.python.exp_fam.MULNOMLSS method) (mssm.src.python.exp_fam.Poisson method)

M

map_csc_to_eigen() (in module mssm.src.python.matrix_solvers) map_csr_to_eigen() (in module mssm.src.python.matrix_solvers) module mssm.models mssm.src.python.compact_rep mssm.src.python.compare mssm.src.python.custom_types mssm.src.python.exp_fam mssm.src.python.file_loading mssm.src.python.formula mssm.src.python.gamm_solvers mssm.src.python.matrix_solvers mssm.src.python.penalties mssm.src.python.repara mssm.src.python.smooths mssm.src.python.terms mssm.src.python.utils mssm.models module mssm.src.python.compact_rep module mssm.src.python.compare module

mssm.src.python.custom_types module mssm.src.python.exp_fam module mssm.src.python.file_loading module mssm.src.python.formula module mssm.src.python.gamm_solvers module mssm.src.python.matrix_solvers module mssm.src.python.penalties module mssm.src.python.repara module mssm.src.python.smooths module mssm.src.python.terms module mssm.src.python.utils module MULNOMLSS (class in mssm.src.python.exp_fam)

N

newton_coef_smooth() (in module mssm.src.python.gamm_solvers)

NULL (mssm.src.python.custom_types.PenType attribute) NUMERIC (mssm.src.python.custom_types.VarType attribute)

P

Penalty (class in mssm.src.python.penalties) PenType (class in mssm.src.python.custom_types) PIRLS_newton_weights() (in module mssm.src.python.gamm_solvers) PIRLS_pdat_weights() (in module mssm.src.python.gamm_solvers) Poisson (class in mssm.src.python.exp_fam) predict() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) predict_diff() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method)

print_parametric_terms() (in module mssm.src.python.utils) (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) print_smooth_terms() (in module mssm.src.python.utils) (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) PropHaz (class in mssm.src.python.exp_fam)

Q

QR (mssm.src.python.custom_types.ConstType attribute)

R

RANDINT (mssm.src.python.custom_types.TermType attribute) RANDSLOPE (mssm.src.python.custom_types.TermType attribute) rank (mssm.src.python.custom_types.LambdaTerm attribute) (mssm.src.python.custom_types.Reparameterization attribute) read_cor_cov_single() (in module mssm.src.python.file_loading) read_cov() (in module mssm.src.python.file_loading) read_cov_no_cor() (in module mssm.src.python.file_loading) read_dtype() (in module mssm.src.python.file_loading) read_eta() (in module mssm.src.python.gamm_solvers) read_mmat() (in module mssm.src.python.gamm_solvers) read_no_cor_cov_single() (in module mssm.src.python.file_loading) read_unique() (in module mssm.src.python.file_loading) read_unique_single() (in module mssm.src.python.file_loading) read_XTX() (in module mssm.src.python.gamm_solvers)

REML() (in module mssm.src.python.utils) rep_sj (mssm.src.python.custom_types.LambdaTerm attribute) reparam() (in module mssm.src.python.repara) REPARAM1 (mssm.src.python.custom_types.PenType attribute) reparam_model() (in module mssm.src.python.repara) Reparameterization (class in mssm.src.python.custom_types) restart_coef() (in module mssm.src.python.gamm_solvers) restart_coef_gammlss() (in module mssm.src.python.gamm_solvers) RhoPrior (class in mssm.src.python.utils) ri (class in mssm.src.python.terms) rms1 (mssm.src.python.custom_types.Reparameterization attribute) rms2 (mssm.src.python.custom_types.Reparameterization attribute) rp_idx (mssm.src.python.custom_types.LambdaTerm attribute) rs (class in mssm.src.python.terms)

S

S_J (mssm.src.python.custom_types.LambdaTerm attribute) S_J_emb (mssm.src.python.custom_types.LambdaTerm attribute) S_J_lam (mssm.src.python.custom_types.LambdaTerm attribute) sample_MVN() (in module mssm.src.python.utils) sample_post() (mssm.models.GAMM method) (mssm.models.GAMMLSS method) (mssm.models.GSMM method) scale (mssm.src.python.custom_types.Reparameterization attribute)

setup_cache() (in module mssm.src.python.file_loading) SMOOTH (mssm.src.python.custom_types.TermType attribute) solve_gamm_sparse() (in module mssm.src.python.gamm_solvers) solve_gamm_sparse2() (in module mssm.src.python.gamm_solvers) solve_gammlss_sparse() (in module mssm.src.python.gamm_solvers) solve_generalSmooth_sparse() (in module mssm.src.python.gamm_solvers) Srp (mssm.src.python.custom_types.Reparameterization attribute) start_index (mssm.src.python.custom_types.LambdaTerm attribute) step_fellner_schall_sparse() (in module mssm.src.python.gamm_solvers)

T

term (mssm.src.python.custom_types.LambdaTerm attribute) TermType (class in mssm.src.python.custom_types) test_SR1() (in module mssm.src.python.gamm_solvers) TP_basis_calc() (in module mssm.src.python.smooths)

TP_pen() (in module mssm.src.python.penalties) tpower() (in module mssm.src.python.smooths) translate_sparse() (in module mssm.src.python.matrix_solvers) type (mssm.src.python.custom_types.Constraint attribute) (mssm.src.python.custom_types.LambdaTerm attribute)

U

undo_extension_lambda_step() (in module mssm.src.python.gamm_solvers) update_coef() (in module mssm.src.python.gamm_solvers) update_coef_and_scale() (in module mssm.src.python.gamm_solvers) update_coef_gammlss() (in module mssm.src.python.gamm_solvers)

update_coef_gen_smooth() (in module mssm.src.python.gamm_solvers) update_PIRLS() (in module mssm.src.python.gamm_solvers) update_scale_edf() (in module mssm.src.python.gamm_solvers) updateVp() (in module mssm.src.python.utils)

V

V() (mssm.src.python.exp_fam.Binomial method) (mssm.src.python.exp_fam.Family method) (mssm.src.python.exp_fam.Gamma method) (mssm.src.python.exp_fam.Gaussian method) (mssm.src.python.exp_fam.InvGauss method) (mssm.src.python.exp_fam.Poisson method)

VarType (class in mssm.src.python.custom_types)

Z

Z (mssm.src.python.custom_types.Constraint attribute)