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Table of Contents

dismod_at-20221105: User Documentation and API
dismod_at-20221105: User Documentation and API
    Table of Contents
     An Introduction To The Mathematics of Dismod_at
    An Introduction To The Mathematics of Dismod_at
        The Dismod_at Ordinary Differential Equation
        The Censored Gaussian and Laplace Densities
        The Prevalence Only ODE
     Installing dismod_at
    Installing dismod_at
        Install and Run dismod_at in a Docker Image
         Installing dismod_at in Unix
        Installing dismod_at in Unix
            bin/run_cmake.sh: User Configuration Options
            An Example Installation
     Dismod_at Getting Started Examples / Tests
    Dismod_at Getting Started Examples / Tests
        Create get_started Input Tables: Example and Test
     User Examples and Tests
    User Examples and Tests
        Non-uniform Age Average Grid
        Example Fitting With Two Levels of Random Effects
        Bounding Covariate Multipliers Absolute Data Effect
        Generating Priors For Next Level Down Node Tree
        Fitting Data That Has Negative Values Censored
        Remove an Age or Time From a Smoothing
        Using Data Interval Compression
        Fitting With Non-Zero Constant Random Effects in Smoothing Grid
        Constrain Omega Using const_value
        Continuing a Fit From Where it Left Off
        Model The Covid-19 Epidemic
        csv2db_command: Example and Test
        Fit With Outliers Using Data Density Command
        Explanation of Simulated Data Table, data_sim
        An Example / Speed Test Fitting Simulated Diabetes Data
        Fitting with Constraints on Differences in Age and Time
        Fit Fixed First Then Both
        Group Measurement Noise Covariate Multipliers, Gamma
        Fitting Just Random Effects
        Fitting Simulated Data Example
        Using Group Covariate Multipliers
        Check the Hessian of the Fixed Effects Objective
        Check the Hessian of the Random Effects Objective
        Using hold_out in Data, Subset Data, and Option Tables
        hold_out Command: Balancing Sex Covariate Values
        An Ill Conditioned Example Where Re-Scaling is Helpful
        Zero Rate Until a Jump at a Known Age
        Using Lasso on Covariate Multiplier
        Estimating Smoothing Standard Deviation Multiplies
        Case with no Children; i.e., no Random Effects
        Fitting One Function of Two Variables
        Example Plotting Log-Scaled Values w.r.t Age and Time
        Example Plotting The Data and Its Fit
        Example Plotting The Rates for a Fit
        Predict Average Integrand Using Results of a Fit
        Predict Covariate Multiplier Values
        Case Where Re-Scaling is Useful
        Weighted Residuals
        Sample from Asymptotic Distribution for Model Variables
        Sampling From The Asymptotic Distribution for a Simulated Data Fit
        Sample Posterior Using Simulated Data
        Simulating Data with Log Transformed Distribution
        A Simulate Data Speed Test
        Example Fitting With Subgroup Covariate Multipliers
        Sum of Residuals at Optimal Estimate
        Example Using system_command_prc
        Using Initialization Trace Option
        Using the Trapezoidal ODE Solver
        Continuing a Fit Using Ipopt Warm Start
        Constrain Sum of Child Rate Effect to Zero
        Constrain Sum of Subgroup Measurement Covariate Multipliers to Zero
        Constrain Sum of Subgroup Rate Covariate Multipliers to Zero
     The Dismod_at Database Tables
    The Dismod_at Database Tables
         Tables That Are Only Used as Inputs
        Tables That Are Only Used as Inputs
             The Age Table
            The Age Table
                age_table: Example and Test
             The avgint Table: Defines Average Integrand Cases
            The avgint Table: Defines Average Integrand Cases
                avgint_table: Example and Test
             The Covariate Table
            The Covariate Table
                covariate_table: Example and Test
             The Data Table
            The Data Table
                data_table: Example and Test
             The Density Table
            The Density Table
                density_table: Example and Test
             The Integrand Table
            The Integrand Table
                integrand_table: Example and Test
             The mulcov Table: Covariate Multipliers
            The mulcov Table: Covariate Multipliers
                mulcov_table: Example and Test
             The Node Table
            The Node Table
                node_table: Example and Test
             Lists of Node Smoothing Pairs
            Lists of Node Smoothing Pairs
                nslist_pair_table: Example and Test
             The Node Smoothing List Table
            The Node Smoothing List Table
                nslist_table: Example and Test
             The Option Table
            The Option Table
                List of Option Default Values
                option_table: Example and Test
             The Prior Table
            The Prior Table
                prior_table: Example and Test
             The Rate Table
            The Rate Table
                rate_table: Example and Test
             The Smooth Grid Table
            The Smooth Grid Table
                smooth_grid_table: Example and Test
            The Smoothing Table
            The Subgroup Table
             The Time Table
            The Time Table
                time_table: Example and Test
             The Weight Grid Table
            The Weight Grid Table
                weight_grid_table: Example and Test
            The Weight Table
         The Dismod_at Data Flow
        The Dismod_at Data Flow
            The Age Average Table
            The Covariate and Multiplier Bound Table
            Simulated Measurements and Adjusted Standard Deviations
            The Data Subset Table
            Which Variables The Model Depends On
            The Model and Weighted Residuals Corresponding to a Fit
            The Optimization Results for Variables
            Hessian of The Fixed Effect Objective Function
            Hessian of The Random Effect Objective Function
            The Log Table
            The CppAD Mixed Information Table
            The Predict Table: Average Integrand Predictions
            Simulated Variation in Prior
            The Sample Table: Samples of Variable Values
            Scaling Fixed Effects Objective and Constraints
            Starting Values Used During a Fit
            The Fixed Effects Optimization Trace Table
            True Values Used During Simulations
            Identifying Model Variables
     The Age-Time Dismod Model
    The Age-Time Dismod Model
        The Model Variables
        Model for the Average Integrand
        Data Likelihood and Weighted Residuals
         Prior for the Model Variables
        Prior for the Model Variables
            The Fixed Effects Value Density Function
            The Random Effects Value Density Function
            Prior Density Function for Smoothing Age Difference
            Prior Density Function for Smoothing Time Difference
            Fixed Effects Differences Density Function
            Random Effects Differences Density Function
            Prior for Fixed Effect Values
            Prior for Random Effect Values
        Some Statistical Function Definitions
        dismod_at Bilinear Interpolation
        Simulating Posterior Distribution for Model Variables
        Prevalence Does Not Depend On Other Cause Mortality
        Numerical Approximation of Average Integrands
     The dismod_at Commands
    The dismod_at Commands
        Python Program Syntax
        Bound The Covariate Multiplier Absolute Data Effect
        Data Density Command: Change the Density for an Integrand
         The Depend Command
        The Depend Command
            depend Command: Example and Test
         The Fit Command
        The Fit Command
            fit Command: Example and Test
        Hold Out Command: Randomly Sub-sample The Data
         The Initialize Command
        The Initialize Command
            init Command: Example and Test
        Convert an Old Database to New Format
         The Predict Command
        The Predict Command
            predict Command: Example and Test
         The Sample Command
        The Sample Command
            sample Command: Example and Test
         Directly Setting Table Values
        Directly Setting Table Values
            set Command: Example and Test
         The Simulate Command
        The Simulate Command
            simulate Command: Example and Test
     Python Utilities
    Python Utilities
         Compute The Average Integrand
        Compute The Average Integrand
            Using the Python average_integrand Utility
         Get File Name For a Database Connection
        Get File Name For a Database Connection
            Example Using connection_file
        Create a Python sqlite3 Database Connection
         Create a Dismod_at Database
        Create a Dismod_at Database
            create_database: Example and Test
         Create a Database Table
        Create a Database Table
            create_table and Unicode: Example and Test
        Conversion of a Csv File to a Dismod_at Database
         Create Csv Files that Summarize The Database
        Create Csv Files that Summarize The Database
            db2csv Command: Example and Test
            Make a Local Copy an IHME Dismod_at Database
         Get Column Names and Types in a Table
        Get Column Names and Types in a Table
            get_name_type: Example and Test
         Get Data From a Table
        Get Data From a Table
            get_row_list: Example and Test
         Get All Data From a Table
        Get All Data From a Table
            get_table_dict: Example and Test
         Metropolis MCMC Algorithm
        Metropolis MCMC Algorithm
            Predict Average Integrand Using Results of a Fit
         Modify a Column of an Sqlite Database
        Modify a Column of an Sqlite Database
            modify Command: Example and Test
        Perturb Command: Random Change to Start or Scale Tables
        Plot Log-Scaled Values With Respect To Age and Time
        Plot The Data Fit By Integrand
        Plot The Rates for a Fit
         Replace A a Table
        Replace A a Table
            replace_table: Example and Test
        Execute an SQL command
        Print Run and Check a System Command
         Convert an Iterable Object to a Unicode String
        Convert an Iterable Object to a Unicode String
            unicode_tuple: Example and Test
     Changes and Additions to Dismod_at
    Changes and Additions to Dismod_at
        Changes and Additions to Dismod_at During 2022
        Changes and Additions to Dismod_at During 2021
        Changes and Additions to Dismod_at During 2020
        Changes and Additions to Dismod_at During 2019
        Changes and Additions to Dismod_at During 2018
        Changes and Additions to Dismod_at During 2017
        Changes and Additions to Dismod_at During 2016
        Changes and Additions to Dismod_at During 2015
    Dismod_at Wish List
    Alphabetic Listing of Cross Reference Tags
    Keyword Index
    Search This Web Site
    External Internet References