Index

Symbols

(a / 01-03 01-05, [1], [2] 01-06 01-07, [1] 01-08, [1] 01-09, [1], [2] 01-10, [1], [2], [3] 01-11, [1] 01-12 01-14 01-15, [1], [2], [3] 01-16, [1], [2], [3] 01-18 01-19 01-20 01-21, [1] 01-22, [1], [2], [3] 01-23, [1], [2] 01-24, [1] 01-25 01-26, [1], [2], [3] 01-27 01-28, [1], [2] 01-30 01-31, [1], [2] 02-01 02-02, [1] 02-03 02-04, [1] 02-05, [1] 02-06, [1] 02-07 02-08, [1] 02-09 02-11 02-12 02-13, [1] 02-14, [1], [2] 02-16 02-17, [1], [2] 02-18, [1] 02-20, [1], [2] 02-26, [1] 02-28 02-29 03-02 03-03 03-04, [1] 03-06, [1], [2] 03-08, [1] 03-09, [1] 03-10, [1] 03-11 03-12 03-13 03-15 03-17 03-18 03-19, [1] 03-20 03-21, [1] 03-22, [1] 03-23, [1] 03-24 03-25, [1] 03-26 03-27, [1], [2] 03-28, [1] 03-29, [1] 03-30 03-31 04-01 04-03, [1] 04-04, [1], [2] 04-05, [1] 04-06, [1], [2] 04-07, [1], [2] 04-08, [1], [2] 04-09, [1], [2], [3] 04-10, [1] 04-11, [1], [2], [3] 04-12, [1], [2] 04-13 04-14, [1] 04-15, [1] 04-16, [1], [2], [3] 04-17, [1], [2], [3] 04-18, [1], [2] 04-19, [1], [2] 04-20, [1], [2] 04-21, [1], [2], [3], [4] 04-22, [1], [2], [3] 04-23, [1], [2], [3] 04-24, [1], [2], [3] 04-25, [1], [2], [3] 04-26, [1], [2], [3] 04-27, [1], [2] 04-28, [1] 04-29, [1] 04-30, [1] 05-01, [1], [2], [3] 05-02, [1], [2], [3] 05-03, [1], [2] 05-04, [1], [2] 05-05, [1], [2], [3] 05-06, [1], [2] 05-07, [1], [2], [3] 05-08, [1] 05-09, [1], [2] 05-10 05-11 05-12, [1] 05-14 05-15, [1], [2] 05-16 05-18, [1] 05-19, [1] 05-20 05-21, [1], [2], [3], [4] 05-22, [1] 05-23, [1], [2] 05-24, [1] 05-25, [1] 05-27 05-29, [1] 05-30 05-31 06-01, [1] 06-02 06-03 06-04, [1] 06-05 06-06, [1], [2] 06-07, [1] 06-08, [1] 06-09, [1] 06-10, [1] 06-11 06-12, [1] 06-13, [1] 06-14, [1], [2] 06-15, [1] 06-17, [1], [2] 06-18, [1], [2] 06-20, [1] 06-21, [1], [2] 06-22, [1], [2], [3] 06-23, [1] 06-24, [1], [2], [3], [4] 06-25, [1] 06-26, [1], [2] 06-27, [1], [2], [3] 06-28, [1], [2] 06-29, [1] 06-30, [1], [2] 07-01, [1], [2] 07-02, [1], [2] 07-03 07-04, [1] 07-05, [1], [2], [3] 07-06, [1], [2] 07-07 07-08 07-09, [1] 07-10, [1], [2] 07-11, [1], [2] 07-13, [1], [2] 07-14, [1], [2] 07-15, [1], [2] 07-16

07-17 07-19, [1] 07-20, [1] 07-21, [1] 07-22, [1] 07-23, [1] 07-24, [1], [2] 07-25, [1], [2], [3] 07-26 07-27, [1] 07-28, [1] 07-29, [1], [2], [3] 07-30, [1] 07-31, [1] 08-01, [1] 08-02 08-03 08-04 08-06 08-07, [1] 08-08, [1], [2], [3] 08-09, [1], [2] 08-12, [1] 08-13, [1], [2] 08-14 08-15, [1], [2] 08-16 08-17 08-18, [1], [2] 08-19 08-20 08-21, [1], [2] 08-22, [1] 08-23, [1] 08-24, [1] 08-25 08-26 08-27, [1] 08-28 08-29 08-30, [1], [2] 08-31, [1] 09-01, [1] 09-02 09-03 09-09 09-11 09-12 09-13 09-14 09-15 09-16, [1] 09-17, [1] 09-18, [1] 09-19, [1] 09-20, [1] 09-21, [1], [2] 09-22, [1] 09-23, [1] 09-24, [1], [2] 09-25 09-26, [1] 09-27 09-28, [1] 09-29, [1] 09-30, [1], [2], [3] 1 10-01, [1] 10-02, [1] 10-04 10-05, [1] 10-06, [1], [2] 10-07 10-08 10-09, [1] 10-10 10-11, [1] 10-12, [1], [2] 10-13, [1], [2] 10-14, [1], [2], [3], [4] 10-15, [1], [2], [3] 10-16, [1], [2], [3] 10-17, [1] 10-18, [1], [2], [3] 10-19, [1] 10-20, [1], [2], [3], [4] 10-21, [1] 10-22, [1] 10-23 10-24, [1], [2], [3] 10-25, [1], [2] 10-26 10-27 10-28 10-29 10-30, [1] 10-31, [1] 11-01 11-02 11-03, [1], [2] 11-04 11-05, [1] 11-06, [1] 11-07, [1] 11-08 11-09 11-10 11-12, [1] 11-14, [1] 11-15, [1] 11-16, [1] 11-17, [1] 11-18 11-19 11-20, [1] 11-21 11-22, [1], [2] 11-23, [1] 11-24, [1] 11-25 11-26, [1] 11-27, [1] 11-28 11-29, [1] 11-30, [1] 12-01 12-02, [1] 12-03 12-04 12-05, [1], [2] 12-06 12-07 12-08 12-09, [1] 12-10, [1] 12-13, [1] 12-14, [1], [2] 12-15, [1] 12-16 12-17 12-18 12-19, [1] 12-20, [1] 12-21 12-22, [1], [2] 12-24 12-25 12-26 12-27 12-29, [1], [2], [3] 12-30, [1], [2], [3] 12-31 122 1: 2 2015, [1] 2016, [1] 2017, [1] 2018, [1] 2019, [1] 2020, [1] 2021, [1] 2022, [1] 2023, [1] 2024, [1] 2025, [1] 2026, [1] 2: 3: 4: 5: 6: 7:

A

a, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36] a^s a^theta a^u a_i, [1], [2] a_i(k) a_i(u a_l a_nnz a_nr a_u above, [1] abs_tol absolute, [1] abstract accept_after_max_steps add add_std_scale_all add_std_scale_none add_var_scale_all add_var_scale_none adding additions adjusted, [1], [2], [3] advantage age, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36] age-time, [1] age_avg.csv age_avg_id age_avg_split, [1] age_avg_table, [1] age_id, [1], [2], [3], [4] age_list, [1], [2] age_lo, [1] age_lower, [1], [2] age_max, [1]

age_min, [1] age_table, [1] age_table.py age_table: age_up, [1] age_upper, [1], [2] algorithm all alpha, [1] alpha_du alpha_jk, [1] alpha_pr alpha_true also, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] an, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] and, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72] api, [1], [2], [3] approximation, [1], [2] are arg_list, [1] as, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] asymptotic, [1], [2], [3], [4] asymptotic_rcond_lower at, [1] at_cascade at_cascade_version average, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] average_integrand, [1] avg avg_integrand, [1], [2] avgint, [1], [2], [3], [4], [5], [6], [7], [8], [9] avgint_extra_columns, [1], [2] avgint_id, [1], [2] avgint_table, [1] avgint_table.py avgint_table:

B

b_i, [1] backward balancing, [1] bash batch be, [1] before begin_end below, [1] beta beta_bmi_true beta_income_true beta_j, [1] between, [1] bilinear, [1], [2]

binomial, [1], [2], [3], [4] black bnd_mulcov bnd_mulcov_command bnd_mulcov_id bnd_mulcov_table, [1], [2] bootstrapping both, [1], [2], [3] bound, [1], [2], [3] bound_frac_fixed bound_random bounding bounds, [1] build build_type, [1] by, [1]

C

c, [1] c(a c), [1] c++ c_i c_i(a c_theta call, [1] can, [1] canada capital, [1], [2], [3], [4] case, [1], [2], [3], [4] cases, [1] cause, [1] cen_gaussian cen_laplace cen_log_gaussian cen_log_laplace censor_density censored, [1], [2], [3], [4], [5], [6], [7], [8], [9] censoring change, [1], [2], [3], [4], [5] changes, [1] changing, [1] check, [1], [2], [3] chi chi(a chi_i(a child, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] child_nslist_id child_rate_value_prior child_smooth_id children, [1], [2], [3], [4] children; choice close cmake, [1] cmake_libdir code, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59] cohort cohorts, [1] col_name, [1], [2] col_type, [1] col_var_id, [1] column, [1], [2], [3] column_name columns, [1] command, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] command:, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] command_name commands, [1], [2] comment compare compatibility

compiler, [1] compress_interval compression, [1] compute computing conda, [1] condition conditioned configuration configure_csv connection, [1], [2], [3], [4], [5], [6], [7], [8], [9] connection_file, [1] const_value, [1], [2] constant, [1], [2], [3] constrain, [1], [2], [3] constraint constraints, [1], [2], [3], [4] container, [1], [2] contents, [1], [2], [3], [4], [5], [6], [7], [8] continuing, [1] convention convergence conversion convert, [1] copy corresponding cov_name cov_value_1 cov_value_2 covariance, [1] covariate, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36] covariate_id, [1], [2], [3] covariate_name, [1] covariate_table, [1] covariate_table.py covariate_table: covariates, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] coverage covid-19 cppad, [1] cppad_mixed create, [1], [2], [3], [4], [5], [6] create_connection create_database create_database.py create_database: create_table, [1] create_table.py creation, [1], [2] cross csv, [1] csv2db_command csv2db_command: cv, [1]

D

d, [1], [2] d_i, [1] d_ij, [1] d_j, [1] d_norm d_out dage_prior_id data, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77] data.csv data_density_command data_depend data_extra_columns, [1], [2] data_flow data_id, [1], [2], [3] data_like data_name data_sim data_sim_id data_sim_table, [1], [2], [3] data_sim_value data_subset_id, [1] data_subset_table, [1], [2], [3], [4] data_table, [1] data_table.py data_table: database, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29] db2csv db2csv_command db2csv_command.py debug default, [1] defines definition definitions deleted delta, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] delta), [1] delta^a delta_i delta_i(theta) delta_j, [1] densities density, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] density_id, [1], [2], [3], [4], [5] density_name, [1] density_table density_table.py

density_table: depend, [1], [2], [3] depend_command depend_command.py depend_var_id depend_var_table, [1] depends deprecated, [1] derivative derivative_test derivatives descendant deterministic, [1] deviation, [1], [2], [3], [4], [5], [6], [7] deviations, [1] diabetes diagrams diff_eq difference, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] difference_prior differences, [1], [2] differential, [1], [2] dir directly discussion, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32] dismod, [1] dismod-at dismod_at, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] dismod_at.at_cascade.build_type dismod_at.base dismod_at.dismod_at.build_type dismod_at.git dismod_at.mixed.build_type dismod_at_prefix dismod_at_version dismodat.py display distribution, [1], [2], [3], [4], [5], [6] dock_dismod_at.sh docker documentation does down download driver dtime_prior_id during, [1]

E

e, [1], [2] e_i(theta) effect, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] effected effects, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40] eigen empty, [1], [2] end environment epidemic epsilon_j equation, [1], [2] error, [1] estimate estimating

eta, [1], [2], [3], [4], [5], [6], [7], [8], [9] eta_factor eta_j, [1] example, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97], [98], [99], [100], [101], [102], [103], [104], [105], [106], [107], [108], [109], [110], [111], [112], [113], [114], [115], [116], [117], [118] example.db example_install.sh examples, [1], [2], [3], [4] excess, [1] exclude execute explanation, [1] expressions extended extra, [1], [2] extra_cxx_flags

F

file, [1], [2] file_name, [1], [2] file_stderr file_stdout files, [1] first fit, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22] fit_command fit_command.py fit_data_subset fit_data_subset_id fit_data_subset_table, [1] fit_value fit_var, [1], [2], [3] fit_var_id fit_var_table, [1], [2] fit_var_value

fitting, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] fix_like_fun.size_var fixed, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] fixed_diff fixed_effect_rel_error_bnd fixed_prior fixed_value float flow, [1] for, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29] foreign format, [1], [2] fortran from, [1], [2], [3], [4], [5], [6] fun function, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] functions, [1]

G

g(a g(y, [1] g_i gamma, [1], [2] gamma_j gaussian, [1], [2], [3], [4], [5], [6] generating get, [1], [2], [3] get_name_type get_name_type.py get_name_type: get_row_list get_row_list.py get_row_list: get_started, [1] get_started.db

get_started_db.py get_table_dict get_table_dict.py get_table_dict: getting git, [1] goal gradient, [1], [2] green grid, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] grids group, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] group_id, [1], [2], [3] group_name group_smooth_id gsl

H

has helpful hes_fixed.csv hes_fixed_id hes_fixed_table, [1] hes_fixed_value hes_random.csv hes_random_id

hes_random_table, [1], [2] hes_random_value hessian, [1], [2], [3], [4], [5], [6], [7], [8] hold, [1] hold_out, [1], [2], [3], [4], [5], [6], [7], [8], [9] hold_out_command hold_out_integrand hold_out_max_fit

I

i, [1], [2], [3] i.e. i_i i_i(a id identifying ill ill-conditioning image images, [1], [2] immunity implicit improvements in, [1], [2], [3], [4], [5], [6], [7] incidence indefinite inf_du inf_pr infinite infinity information init, [1] init_command init_command.py initial, [1], [2] initialization initialize input, [1], [2], [3] inputs install, [1], [2], [3], [4], [5] install_conda install_settings.py, [1] install_unix installation

installing, [1], [2] integer integral, [1] integrand, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23] integrand_id, [1], [2], [3], [4] integrand_list integrand_name, [1], [2], [3] integrand_table, [1] integrand_table.py integrand_table: integrands, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] integration, [1] interpolant interpolation interval, [1] introduction, [1], [2] iota, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] iota(a iota_after_20 iota_avg iota_eta iota_i(a iota_near_zero iota_parent_true iota_pos_rho_pos iota_pos_rho_zero iota_zero_rho_pos iota_zero_rho_zero ipopt, [1], [2] ipopt_info_table is, [1] it iter iterable, [1] its

J

j, [1] j_k

jump just

K

k, [1], [2], [3] k_i, [1]

key, [1], [2], [3], [4] known

L

l(y, [1] l_k^a l_k^v lag_dage lag_dtime lag_value lagrange, [1] lagrange_dage lagrange_dtime lagrange_value lambda, [1], [2], [3] lambda_j, [1] laplace, [1], [2], [3], [4], [5], [6], [7], [8] large lasso ld_library_path left legend lemma, [1], [2] level levels license

likelihood, [1], [2], [3], [4], [5] limited_memory_max_history_fixed limits, [1], [2] line linear, [1] list, [1], [2] lists log, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] log-density log-gaussian, [1], [2] log-laplace, [1] log-scaled, [1] log-student's-t log.csv log_f log_gaussian log_id log_laplace log_students log_table logging lower, [1], [2] ls_trials

M

m m_diff m_id main math_abstract mathematics max_abs_effect max_cov_diff, [1], [2] max_difference max_fit, [1] max_fit_parent max_mulcov, [1] max_num_iter max_plot, [1] maximum, [1], [2], [3] mcmc mean means, [1] meas_noise, [1] meas_noise_effect, [1], [2] meas_sigma meas_std, [1], [2], [3], [4] meas_stdcv meas_value, [1], [2], [3], [4], [5] measure_csv measure_cv measurement, [1], [2], [3], [4], [5], [6], [7], [8], [9] measurements message message_type messages method, [1] method_random metropolis, [1] mexico minimum, [1], [2] minimum_meas_cv, [1] minimum_prevalence_std mixed mixed_info mixed_info.csv mixed_info_id mixed_info_table mixed_name

mixed_value mm-dd, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] model, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32] model_meas_cv model_variables modify, [1] modify_command modify_command.py more mortality, [1], [2], [3] mtall, [1], [2], [3] mtexcess, [1] mtother, [1], [2] mtspecific, [1] mtstandard, [1] mtwith, [1] mu, [1], [2], [3], [4], [5] mu_ij, [1] mu_j, [1] mulcov, [1], [2], [3], [4], [5] mulcov_id, [1] mulcov_income_iota_true mulcov_meas_noise, [1] mulcov_meas_value, [1], [2] mulcov_prior mulcov_rate_value, [1], [2] mulcov_sex_rho_true mulcov_table, [1] mulcov_table.py mulcov_table: mulcov_type mulstd_dage mulstd_dage_prior_id mulstd_dage_prior_name mulstd_dtime mulstd_dtime_prior_id mulstd_dtime_prior_name mulstd_value mulstd_value_prior_id mulstd_value_prior_name multi-threading multiplier, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14] multipliers, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] multiplies

N

n1, [1] n11, [1], [2], [3] n111 n112 n12 n121 n_age, [1] n_children n_data, [1], [2] n_fit_dict n_fixed n_i n_random n_time, [1] name, [1], [2], [3], [4], [5], [6] names, [1], [2] nan negative new, [1] next no, [1], [2] no_effect_iota_true no_ode node, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] node_id, [1], [2], [3], [4], [5] node_name node_table, [1] node_table.py node_table: nodes, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] noise, [1], [2], [3], [4]

non-uniform non-zero non_zero_rates none nonsmooth, [1], [2] normalization north_america not, [1], [2], [3], [4] notation, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] note, [1] notes, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] nslist nslist_dict nslist_id, [1] nslist_name nslist_pair_id nslist_pair_table nslist_pair_table.py nslist_pair_table: nslist_table nslist_table.py nslist_table: nu, [1], [2], [3], [4], [5], [6], [7], [8] null, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] number number_metropolis number_nodes number_sample, [1] number_simulate numeric_average numerical

O

obj_value object objective, [1], [2], [3], [4], [5] ode, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] ode_step_size, [1], [2], [3], [4] of, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26] off old, [1] old2new old2new_command old2new_command.py omega, [1], [2] omega(a omega_i(a on, [1], [2], [3] one, [1], [2], [3] only, [1], [2], [3] optimal, [1], [2], [3], [4] optimization, [1] optimize, [1], [2] option, [1], [2], [3], [4], [5], [6]

option.csv option_default option_id option_name option_table, [1] option_table.py option_table: option_value optional options, [1] or, [1], [2], [3], [4], [5] order ordinary other, [1], [2], [3], [4], [5], [6], [7], [8] other_database other_input_table, [1] otherwise, [1] out, [1] outlier outliers output, [1], [2], [3], [4] outside

P

p p(a p(theta) p(u|theta) p_i0(t) pairs, [1] parallel parameters, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] parent, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] parent_node_id parent_node_name parent_rate_value_prior parent_smooth_id patching path, [1] paths pde, [1] pdf_file, [1], [2] perturb perturb_command pini, [1], [2], [3] pini(t) pkg-config pkg_config_path plot, [1], [2], [3] plot_curve plot_data plot_data_fit, [1] plot_limit plot_rate_fit, [1] plot_set plot_title, [1], [2] plotting, [1], [2], [3] plus point, [1], [2] positive posterior, [1], [2], [3], [4], [5], [6] predict, [1], [2], [3], [4], [5], [6], [7] predict.csv predict_command predict_command.py

predict_id predict_table, [1] prediction predictions, [1], [2], [3], [4], [5] prev_dep prevalence, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] prevalence_ode previous primary, [1], [2], [3], [4] print print_command print_level prior, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] prior_depend prior_id, [1], [2] prior_ij, [1] prior_info prior_mean prior_name prior_sim_dage prior_sim_dtime prior_sim_id prior_sim_table, [1], [2], [3] prior_sim_value prior_table, [1] prior_table.py prior_table: priors, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] problem, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] problems procedure, [1] program, [1], [2], [3], [4], [5] proof, [1], [2], [3] prototype, [1], [2] purpose, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51] python, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] python3, [1] python3_executable, [1] python_log_command python_main pythonpath

Q

q_k	quasi_fixed, [1], [2] quote_string

R

r r_ik ran_like_fun.size_var random, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35] random_diff random_prior random_seed, [1], [2], [3], [4], [5], [6], [7] random_value randomly rate, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27] rate_case, [1], [2] rate_eff_cov_id rate_eff_cov_table, [1] rate_eff_cov_table.py rate_eff_cov_table: rate_fun rate_id, [1], [2] rate_name rate_set rate_table, [1] rate_table.py rate_table: rate_true rate_value rates, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] re-scaling, [1] readonly real, [1] rectangle rectangular, [1], [2], [3] red reference, [1], [2], [3], [4] reference_bmi reference_income references refinement regularization_size release, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12]

release_notes relrisk, [1] remark, [1] remission, [1], [2] remove, [1], [2] removing replace replace_table replace_table.py replace_table: repository representation, [1] required, [1] requirements, [1], [2] res_dage res_dtime res_value residual, [1], [2], [3], [4] residual_dage residual_dtime residual_value residuals, [1], [2], [3], [4], [5], [6], [7] respect restoration result, [1] results, [1], [2] resume return_stderr return_stdout rho, [1] rho(a rho_i(a rho_parent_true row_expression row_id row_list, [1] row_var_id, [1] run, [1], [2], [3]

S

s, [1], [2], [3], [4] s(a s_i, [1] s_i(a s_id s_index s_j s_out sam_avg sam_std sample, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] sample_command sample_command.py sample_id sample_index, [1] sample_size, [1], [2] sample_table, [1] samples, [1], [2] sampling scale, [1], [2], [3] scale_var, [1] scale_var_id scale_var_table, [1] scale_var_value scaled scaling, [1], [2], [3], [4], [5], [6], [7], [8], [9] see, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] seed, [1] set set_command set_command.py setting setup sex shock side sigma, [1], [2], [3] sigma_i(theta) sigma_ij, [1] sigma_j sim_a sim_mulcov sim_no_effect_rate sim_std_random_effect sim_t sim_v sim_value simulate, [1], [2], [3], [4] simulate_command simulate_command.py simulate_index, [1], [2], [3], [4] simulated, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] simulating, [1], [2] simulation, [1], [2], [3], [4], [5], [6], [7] simulations, [1] sincidence, [1], [2] sir size smooth

smooth_dage smooth_dtime smooth_grid_id smooth_grid_table smooth_grid_table.py smooth_grid_table: smooth_id, [1], [2], [3] smooth_name smooth_table, [1] smoothing, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] solution, [1], [2], [3] solver some source, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61] spaces special specific_compiler speed, [1] split_value splitting_covariate sql sql_command sqlite sqlite3, [1] ss standard, [1], [2], [3], [4], [5], [6], [7], [8], [9] start, [1], [2], [3], [4] start_var, [1] start_var_id start_var_table, [1] start_var_value started starting, [1], [2] statements statistic statistical statistics, [1] std, [1] step, [1], [2], [3], [4], [5], [6], [7] stochastic string student's-t students sub-sample subgroup, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] subgroup_id, [1], [2], [3] subgroup_name subgroup_smooth_id subgroup_table, [1] subset, [1], [2], [3], [4], [5], [6], [7] subsmooth suitesparse sum, [1], [2], [3], [4] summarize susceptible, [1], [2] symbol, [1] syntax, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33] system, [1] system_command_prc, [1] system_specific_library_list

T

t t), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16] t^s t^theta t^u t_i t_l t_u table, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85], [86], [87], [88], [89], [90], [91], [92], [93], [94], [95], [96], [97] table:, [1], [2], [3] table_dict, [1] table_name, [1], [2], [3], [4] table_out tables, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] tables: tbl_name, [1], [2] tbl_name_id term test, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38] testing tests, [1] text that, [1], [2] the, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48], [49], [50], [51], [52], [53], [54], [55], [56], [57], [58], [59], [60], [61], [62], [63], [64], [65], [66], [67], [68], [69], [70], [71], [72] then theorem theta, [1], [2], [3], [4] theta) theta_j theta_k this, [1] thread time, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30]

time_id, [1], [2], [3], [4] time_list, [1], [2] time_lo, [1] time_lower, [1], [2] time_max time_min time_table, [1] time_table.py time_table: time_up, [1] time_upper, [1], [2] tincidence, [1] to, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] tolerance tools/install_settings.py: trace, [1], [2] trace_fixed trace_fixed.csv trace_fixed_id trace_fixed_table trace_init_fit_model, [1] transformed, [1] trapezoidal, [1] tree true, [1], [2], [3], [4], [5], [6], [7], [8] truth, [1], [2], [3], [4] truth_var, [1], [2] truth_var_id truth_var_table, [1] truth_var_value two, [1] type types

U

u, [1], [2] u_ik u_j u_k^a u_k^v u_tuple unicode unicode: unicode_tuple unicode_tuple.py unicode_tuple: uniform, [1], [2] unique united_states unix unix_time until upper, [1] usage used, [1], [2] useful user, [1], [2], [3] user's user_age_avg_split.py user_average_integrand.py user_bilevel_random.py user_binomial.py user_bnd_mulcov.py user_cascade.py user_censor.py user_change_grid.py user_compress.py user_connection_file.py user_const_random.py user_const_value.py user_continue_fit.py user_covid_19.py user_csv2db.py user_data_density.py user_data_sim.py user_diabetes.py user_diff_constraint.py user_example user_fit_fixed_both.py

user_fit_meas_noise.py user_fit_random.py user_fit_sim.py user_group_mulcov.py user_hes_fixed_math.py user_hes_random.py user_hold_out_1.py user_hold_out_2.py user_ill_condition.py user_jump_at_age.py user_lasso_covariate.py user_metropolis.py user_mulstd.py user_no_children.py user_one_function.py user_other_database.py user_plot_curve.py user_plot_data_fit.py user_plot_rate_fit.py user_predict_fit.py user_predict_mulcov.py user_predict_sample.py user_rate_eff_cov_table.py user_re_scale.py user_residual.py user_sample_asy.py user_sample_asy_sim.py user_sample_sim.py user_shock_cov.py user_sim_log.py user_speed.py, [1] user_subgroup_mulcov.py user_sum_residual.py user_system_command_prc.py user_trace_init.py user_trapezoidal.py user_warm_start.py user_zero_meas_value.py user_zsum_child_rate.py user_zsum_mulcov_meas.py user_zsum_mulcov_rate.py using, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18] utilities utility

V

v^theta v^u v_ij, [1] v_j^theta v_j^u value, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] value_expression value_prior_id values, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] var_id, [1], [2], [3] var_table, [1]

var_type, [1] var_value variable, [1] variable.csv variable_prior variables, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31], [32] variance, [1], [2] variation, [1] vector verbose_makefile version versions, [1]

W

w(a w.r.t w.r.t., [1], [2], [3], [4], [5] w_i, [1] warm warm_start warn_on_stderr warning, [1] wbar_i weight, [1], [2], [3], [4], [5], [6] weight_grid_id weight_grid_table weight_grid_table.py weight_grid_table:

weight_id, [1], [2], [3], [4] weight_name weight_table, [1] weighted, [1], [2], [3], [4], [5], [6], [7] weighted_residual where, [1], [2] which windows wish wish_list with, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] withc, [1] working world write_command

X

x	x0 x_ij, [1]

Y

y, [1], [2], [3] y_i

year years

Z

z, [1], [2] z_name zero, [1], [2], [3], [4]

zero_meas_value zero_sum_child_rate, [1] zero_sum_mulcov_group, [1]