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user_example

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User Examples and Tests

See Also

get_started

Run One Example

If you have built dismod_at and are in the directory dismod_at.git , you can run one of these examples with the command

python3_executable example/user/ name

where python3_executable is the python3 program and name is the name of the example. The name of the example includes the .py extension at the end, but does not include user_ at the front.

user_speed.py

The user_speed.py example is an exception; see its Syntax .

example.db

Each of these examples will create a corresponding database called

build/example/user/example.db

which can be inspected using any sqlite viewer; e.g., http://sqlitebrowser.org/.

Examples With Explanation

user_age_avg_split.py	Non-uniform Age Average Grid
user_average_integrand.py	Using the Python average_integrand Utility
user_bilevel_random.py	Example Fitting With Two Levels of Random Effects
user_binomial.py	Fitting Binomial Data Example
user_bnd_mulcov.py	Bounding Covariate Multipliers Absolute Data Effect
user_cascade.py	Generating Priors For Next Level Down Node Tree
user_censor.py	Fitting Data That Has Negative Values Censored
user_change_grid.py	Remove an Age or Time From a Smoothing
user_compress.py	Using Data Interval Compression
user_connection_file.py	Example Using connection_file
user_const_value.py	Constrain Omega Using const_value
user_continue_fit.py	Continuing a Fit From Where it Left Off
user_covid_19.py	Model The Covid-19 Epidemic
user_csv2db.py	csv2db_command: Example and Test
user_data_density.py	Fit With Outliers Using Data Density Command
user_data_sim.py	Explanation of Simulated Data Table, data_sim
user_diabetes.py	An Example Fitting Simulated Diabetes Data
user_fit_fixed_both.py	Fit Fixed First Then Both
user_fit_meas_noise.py	Group Measurement Noise Covariate Multipliers, Gamma
user_fit_random.py	Fitting Just Random Effects
user_fit_sim.py	Fitting Simulated Data Example
user_group_mulcov.py	Using Group Covariate Multipliers
user_hes_fixed_math.py	Check the Hessian of the Fixed Effects Objective
user_hes_random.py	Check the Hessian of the Random Effects Objective
user_hold_out_1.py	Using hold_out in Data, Subset Data, and Option Tables
user_hold_out_2.py	hold_out Command: Balancing Sex Covariate Values
user_ill_condition.py	An Ill Conditioned Example Where Re-Scaling is Helpful
user_jump_at_age.py	Zero Rate Until a Jump at a Known Age
user_lasso_covariate.py	Using Lasso on Covariate Multiplier
user_mulstd.py	Estimating Smoothing Standard Deviation Multiplies
user_no_children.py	Case with no Children; i.e., no Random Effects
user_rate_eff_cov_table.py	Example Using The Node Covariate Table
user_one_function.py	Fitting One Function of Two Variables
user_other_database.py	Using Data Interval Compression
user_plot_curve.py	Example Plotting Log-Scaled Values w.r.t Age and Time
user_plot_data_fit.py	Example Plotting The Data and Its Fit
user_plot_rate_fit.py	Example Plotting The Rates for a Fit
user_predict_fit.py	Predict Average Integrand Using Results of a Fit
user_predict_mulcov.py	Predict Covariate Multiplier Values
user_residual.py	Weighted Residuals
user_sample_asy.py	Sample from Asymptotic Distribution for Model Variables
user_sample_asy_sim.py	Sampling From The Asymptotic Distribution for a Simulated Data Fit
user_sample_sim.py	Sample Posterior Using Simulated Data
user_shock_cov.py	Example Fitting a Covariate with a Shock
user_sim_log.py	Simulating Data with Log Transformed Distribution
user_speed.py	A Simulate Data Speed Test
user_subgroup_mulcov.py	Example Fitting With Subgroup Covariate Multipliers
user_sum_residual.py	Sum of Residuals at Optimal Estimate
user_system_command_prc.py	Example Using system_command_prc
user_trace_init.py	Using Initialization Trace Option
user_trapezoidal.py	Using the Trapezoidal ODE Solver
user_warm_start.py	Continuing a Fit Using Ipopt Warm Start
user_zsum_child_rate.py	Constrain Sum of Child Rate Effect to Zero
user_zsum_mulcov_meas.py	Constrain Sum of Subgroup Measurement Covariate Multipliers to Zero
user_zsum_mulcov_rate.py	Constrain Sum of Subgroup Rate Covariate Multipliers to Zero

More Examples

user_metropolis.py	Predict Average Integrand Using Results of a Fit
user_const_random.py	Fitting With Non-Zero Constant Random Effects in Smoothing Grid
user_diff_constraint.py	Fitting with Constraints on Differences in Age and Time
user_re_scale.py	Case Where Re-Scaling is Useful