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Prev | Next | _reference |
| A | |
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age_avg_table | The Age Average Table |
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age_table | The Age Table |
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age_table.py | age_table: Example and Test |
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average_integrand | Compute The Average Integrand |
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avg_integrand | Model for the Average Integrand |
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avgint_table | The avgint Table: Defines Average Integrand Cases |
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avgint_table.py | avgint_table: Example and Test |
| B | |
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bilinear | dismod_at Bilinear Interpolation |
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bnd_mulcov_command | Bound The Covariate Multiplier Absolute Data Effect |
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bnd_mulcov_table | The Covariate and Multiplier Bound Table |
| C | |
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censor_density | The Censored Gaussian and Laplace Densities |
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command | The dismod_at Commands |
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connection_file | Get File Name For a Database Connection |
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covariate_table | The Covariate Table |
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covariate_table.py | covariate_table: Example and Test |
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create_connection | Create a Python sqlite3 Database Connection |
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create_database | Create a Dismod_at Database |
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create_database.py | create_database: Example and Test |
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create_table | Create a Database Table |
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create_table.py | create_table and Unicode: Example and Test |
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csv2db_command | Conversion of a Csv File to a Dismod_at Database |
| D | |
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data_density_command | Data Density Command: Change the Density for an Integrand |
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data_flow | The Dismod_at Data Flow |
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data_like | Data Likelihood and Weighted Residuals |
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data_sim_table | Simulated Measurements and Adjusted Standard Deviations |
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data_subset_table | The Data Subset Table |
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data_table | The Data Table |
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data_table.py | data_table: Example and Test |
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database | The Dismod_at Database Tables |
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db2csv_command | Create Csv Files that Summarize The Database |
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db2csv_command.py | db2csv Command: Example and Test |
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density_table | The Density Table |
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density_table.py | density_table: Example and Test |
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depend_command | The Depend Command |
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depend_command.py | depend Command: Example and Test |
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depend_var_table | Which Variables The Model Depends On |
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dismod_at | dismod_at-20221105: User Documentation and API |
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dismodat.py | Python Program Syntax |
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dock_dismod_at.sh | Install and Run dismod_at in a Docker Image |
| E | |
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example_install.sh | An Example Installation |
| F | |
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fit_command | The Fit Command |
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fit_command.py | fit Command: Example and Test |
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fit_data_subset_table | The Model and Weighted Residuals Corresponding to a Fit |
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fit_var_table | The Optimization Results for Variables |
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fixed_diff | Fixed Effects Differences Density Function |
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fixed_prior | Prior for Fixed Effect Values |
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fixed_value | The Fixed Effects Value Density Function |
| G | |
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get_name_type | Get Column Names and Types in a Table |
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get_name_type.py | get_name_type: Example and Test |
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get_row_list | Get Data From a Table |
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get_row_list.py | get_row_list: Example and Test |
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get_started | Dismod_at Getting Started Examples / Tests |
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get_started_db.py | Create get_started Input Tables: Example and Test |
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get_table_dict | Get All Data From a Table |
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get_table_dict.py | get_table_dict: Example and Test |
| H | |
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hes_fixed_table | Hessian of The Fixed Effect Objective Function |
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hes_random_table | Hessian of The Random Effect Objective Function |
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hold_out_command | Hold Out Command: Randomly Sub-sample The Data |
| I | |
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ihme_db.sh | Make a Local Copy an IHME Dismod_at Database |
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init_command | The Initialize Command |
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init_command.py | init Command: Example and Test |
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input | Tables That Are Only Used as Inputs |
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install | Installing dismod_at |
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install_unix | Installing dismod_at in Unix |
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integrand_table | The Integrand Table |
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integrand_table.py | integrand_table: Example and Test |
| L | |
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log_table | The Log Table |
| M | |
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math_abstract | An Introduction To The Mathematics of Dismod_at |
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math_ode | The Dismod_at Ordinary Differential Equation |
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metropolis | Metropolis MCMC Algorithm |
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mixed_info_table | The CppAD Mixed Information Table |
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model | The Age-Time Dismod Model |
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model_variables | The Model Variables |
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modify_command | Modify a Column of an Sqlite Database |
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modify_command.py | modify Command: Example and Test |
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mulcov_table | The mulcov Table: Covariate Multipliers |
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mulcov_table.py | mulcov_table: Example and Test |
| N | |
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node_table | The Node Table |
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node_table.py | node_table: Example and Test |
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nslist_pair_table | Lists of Node Smoothing Pairs |
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nslist_pair_table.py | nslist_pair_table: Example and Test |
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nslist_table | The Node Smoothing List Table |
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nslist_table.py | nslist_table: Example and Test |
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numeric_average | Numerical Approximation of Average Integrands |
| O | |
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old2new_command | Convert an Old Database to New Format |
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option_default | List of Option Default Values |
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option_table | The Option Table |
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option_table.py | option_table: Example and Test |
| P | |
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perturb_command | Perturb Command: Random Change to Start or Scale Tables |
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plot_curve | Plot Log-Scaled Values With Respect To Age and Time |
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plot_data_fit | Plot The Data Fit By Integrand |
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plot_rate_fit | Plot The Rates for a Fit |
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posterior | Simulating Posterior Distribution for Model Variables |
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predict_command | The Predict Command |
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predict_command.py | predict Command: Example and Test |
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predict_table | The Predict Table: Average Integrand Predictions |
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prev_dep | Prevalence Does Not Depend On Other Cause Mortality |
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prevalence_ode | The Prevalence Only ODE |
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prior_sim_table | Simulated Variation in Prior |
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prior_table | The Prior Table |
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prior_table.py | prior_table: Example and Test |
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python | Python Utilities |
| R | |
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random_diff | Random Effects Differences Density Function |
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random_prior | Prior for Random Effect Values |
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random_value | The Random Effects Value Density Function |
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rate_table | The Rate Table |
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rate_table.py | rate_table: Example and Test |
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release_notes | Changes and Additions to Dismod_at |
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replace_table | Replace A a Table |
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replace_table.py | replace_table: Example and Test |
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run_cmake.sh | bin/run_cmake.sh: User Configuration Options |
| S | |
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sample_command | The Sample Command |
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sample_command.py | sample Command: Example and Test |
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sample_table | The Sample Table: Samples of Variable Values |
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scale_var_table | Scaling Fixed Effects Objective and Constraints |
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set_command | Directly Setting Table Values |
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set_command.py | set Command: Example and Test |
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simulate_command | The Simulate Command |
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simulate_command.py | simulate Command: Example and Test |
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smooth_dage | Prior Density Function for Smoothing Age Difference |
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smooth_dtime | Prior Density Function for Smoothing Time Difference |
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smooth_grid_table | The Smooth Grid Table |
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smooth_grid_table.py | smooth_grid_table: Example and Test |
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smooth_table | The Smoothing Table |
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sql_command | Execute an SQL command |
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start_var_table | Starting Values Used During a Fit |
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statistic | Some Statistical Function Definitions |
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subgroup_table | The Subgroup Table |
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system_command_prc | Print Run and Check a System Command |
| T | |
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time_table | The Time Table |
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time_table.py | time_table: Example and Test |
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trace_fixed_table | The Fixed Effects Optimization Trace Table |
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truth_var_table | True Values Used During Simulations |
| U | |
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unicode_tuple | Convert an Iterable Object to a Unicode String |
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unicode_tuple.py | unicode_tuple: Example and Test |
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user_age_avg_split.py | Non-uniform Age Average Grid |
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user_average_integrand.py | Using the Python average_integrand Utility |
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user_bilevel_random.py | Example Fitting With Two Levels of Random Effects |
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user_bnd_mulcov.py | Bounding Covariate Multipliers Absolute Data Effect |
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user_cascade.py | Generating Priors For Next Level Down Node Tree |
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user_censor.py | Fitting Data That Has Negative Values Censored |
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user_change_grid.py | Remove an Age or Time From a Smoothing |
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user_compress.py | Using Data Interval Compression |
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user_connection_file.py | Example Using connection_file |
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user_const_random.py | Fitting With Non-Zero Constant Random Effects in Smoothing Grid |
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user_const_value.py | Constrain Omega Using const_value |
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user_continue_fit.py | Continuing a Fit From Where it Left Off |
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user_covid_19.py | Model The Covid-19 Epidemic |
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user_csv2db.py | csv2db_command: Example and Test |
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user_data_density.py | Fit With Outliers Using Data Density Command |
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user_data_sim.py | Explanation of Simulated Data Table, data_sim |
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user_diabetes.py | An Example / Speed Test Fitting Simulated Diabetes Data |
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user_diff_constraint.py | Fitting with Constraints on Differences in Age and Time |
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user_example | User Examples and Tests |
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user_fit_fixed_both.py | Fit Fixed First Then Both |
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user_fit_meas_noise.py | Group Measurement Noise Covariate Multipliers, Gamma |
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user_fit_random.py | Fitting Just Random Effects |
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user_fit_sim.py | Fitting Simulated Data Example |
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user_group_mulcov.py | Using Group Covariate Multipliers |
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user_hes_fixed_math.py | Check the Hessian of the Fixed Effects Objective |
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user_hes_random.py | Check the Hessian of the Random Effects Objective |
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user_hold_out_1.py | Using hold_out in Data, Subset Data, and Option Tables |
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user_hold_out_2.py | hold_out Command: Balancing Sex Covariate Values |
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user_ill_condition.py | An Ill Conditioned Example Where Re-Scaling is Helpful |
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user_jump_at_age.py | Zero Rate Until a Jump at a Known Age |
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user_lasso_covariate.py | Using Lasso on Covariate Multiplier |
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user_metropolis.py | Predict Average Integrand Using Results of a Fit |
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user_mulstd.py | Estimating Smoothing Standard Deviation Multiplies |
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user_no_children.py | Case with no Children; i.e., no Random Effects |
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user_one_function.py | Fitting One Function of Two Variables |
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user_plot_curve.py | Example Plotting Log-Scaled Values w.r.t Age and Time |
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user_plot_data_fit.py | Example Plotting The Data and Its Fit |
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user_plot_rate_fit.py | Example Plotting The Rates for a Fit |
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user_predict_fit.py | Predict Average Integrand Using Results of a Fit |
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user_predict_mulcov.py | Predict Covariate Multiplier Values |
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user_re_scale.py | Case Where Re-Scaling is Useful |
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user_residual.py | Weighted Residuals |
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user_sample_asy.py | Sample from Asymptotic Distribution for Model Variables |
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user_sample_asy_sim.py | Sampling From The Asymptotic Distribution for a Simulated Data Fit |
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user_sample_sim.py | Sample Posterior Using Simulated Data |
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user_sim_log.py | Simulating Data with Log Transformed Distribution |
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user_speed.py | A Simulate Data Speed Test |
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user_subgroup_mulcov.py | Example Fitting With Subgroup Covariate Multipliers |
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user_sum_residual.py | Sum of Residuals at Optimal Estimate |
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user_system_command_prc.py | Example Using system_command_prc |
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user_trace_init.py | Using Initialization Trace Option |
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user_trapezoidal.py | Using the Trapezoidal ODE Solver |
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user_warm_start.py | Continuing a Fit Using Ipopt Warm Start |
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user_zsum_child_rate.py | Constrain Sum of Child Rate Effect to Zero |
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user_zsum_mulcov_meas.py | Constrain Sum of Subgroup Measurement Covariate Multipliers to Zero |
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user_zsum_mulcov_rate.py | Constrain Sum of Subgroup Rate Covariate Multipliers to Zero |
| V | |
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var_table | Identifying Model Variables |
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variable_prior | Prior for the Model Variables |
| W | |
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weight_grid_table | The Weight Grid Table |
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weight_grid_table.py | weight_grid_table: Example and Test |
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weight_table | The Weight Table |
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whats_new_2015 | Changes and Additions to Dismod_at During 2015 |
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whats_new_2016 | Changes and Additions to Dismod_at During 2016 |
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whats_new_2017 | Changes and Additions to Dismod_at During 2017 |
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whats_new_2018 | Changes and Additions to Dismod_at During 2018 |
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whats_new_2019 | Changes and Additions to Dismod_at During 2019 |
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whats_new_2020 | Changes and Additions to Dismod_at During 2020 |
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whats_new_2021 | Changes and Additions to Dismod_at During 2021 |
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whats_new_2022 | Changes and Additions to Dismod_at During 2022 |
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wish_list | Dismod_at Wish List |