2023#

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Release Notes for 2023#

mm-dd#

12-30#

There were some problem with changes to dock_dismod_at.sh on 12-29 (that have been fixed):

  1. When restarting a container the python virtual environment was not set.

  2. The second checkout of dismod_at.git could fail because bin/run_cmake.sh had changed.

12-29#

Advance dock_dismod_at.sh version of Ubuntu from 20.04 to 23.04 , dismod_at_version to 2023.12.29, and at_cascade_version to 2023.12.22. Advancing to Ubuntu 23.04 Also note the dock_dismod_at.sh wish list item, so it was removed. Also note that dismod_at-2023.12.29 has a minor fix for the case where dismod_at_prefix does not end with dismod_at .

12-05#

Add the Command Documentation wish list item.

12-01#

  1. Advance dismod_at to use cppad_mixed-20231201.

  2. Advance dock_dismod_at.sh dismod_at_version to 20231201, and at_cascade_version to 2023.11.30.

  3. Add the build_type option to dock_dismod_at.sh (instead of building both debug and release versions in the same image).

  4. Add the dock_dismod_at.sh wish list entry (which was completed on 12-29) .

  5. Add the Bootstrapping wish list entry.

11-30#

  1. There was a bug in the hold_out command when cov_name was present. This has been fixed.

  2. The discussion about balancing Covariates was improved.

10-20#

  1. Improve the documentation for system_command_prc . In addition, make the following change : If an error is detected, include the command in file_stderr , result .stderr , and the assert error message .

  2. Advance dock_dismod_at.sh dismod_at_version to 202310.20 .

10-18#

API Change:

  1. Add the average noise effect E_i(theta) before transforming the standard deviation. This changes the definition of the adjusted standard deviation sigma_i(theta) and the transformed standard deviation delta_i(theta) . This switched the roles of sigma and delta in many places in the examples and documentation. One notable case is that the db2csv meas_delta column was changed to the meas_sigma column.

  2. Remove add_std_scale_log and add_var_scale_log from the possible values for meas_noise_effect in the option table (now the addition is done before the log scaling).

  3. Advance dock_dismod_at.sh dismod_at_version to 20231018 and at_cascade_version to 2023.10.7.

08-09#

Advance dock_dismod_at.sh dismod_at_version to 20230808 and at_cascade_version to 2023.8.9.

08-08#

  1. There was a bug in the data_density_command when the original data density was binomial (a binomial density it cannot be changed). This has been fixed.

  2. The Approximation for the standard deviation corresponding to the binomial distribution was of by a factor of \(\sqrt{ 1 / n}\) where n is the sample size. This has been fixed. In addition, the user_binomial.py example was modified to demonstrate that this works well.

07-06#

Advance dock_dismod_at.sh dismod_at_version to 20230706 and at_cascade_version to 2023.7.6.

07-05#

API Change: :

  1. The sample_size column was added to the data table. The values in this column should be null except for rows that use the binomial density.

  2. The old2new_command was changed so that it adds the sample_size column to the data table with the value null for every row. (The previous functionality of the old2new command was removed.)

07-01#

  1. API Change: Change the average_integrand rate argument name to rate_fun .

  2. Improve the documentation for average_integrand. In addition, fix a call to the rate pini rate function that passed an int for age (it should only use float ).

06-28#

Advance dock_dismod_at.sh dismod_at_version to 20230628 and at_cascade_version to 2023.6.28.

06-27#

If nan appeared for a real value in row_list , one would get the following error message:

sqlite3.OperationalError: no such column: nan

The error message for this case was improved.

06-26#

  1. If other_database is a relative path, it is now relative to the directory where the directory where Primary Database is located.

  2. Advance dock_dismod_at.s dismod_at_version to 20230626 and at_cascade_version to 2023.6.26.

06-18#

  1. If rate_eff_cov was in the other_input_table option, dismod_at would use the other database for the rate table. This has been fixed.

  2. The dock_dismod_at.sh dismod_at_version was advanced to 20230618, and the at_cascade_version was advanced to 2023.6.18 .

  3. The dock_dismod_at.sh script was changed so that it just builds (does not run) the dismod_at image. Suggestions for how to run the image were added to the Syntax.

  4. Testing of the debug version of at_cascade was removed because it is slow.

06-17#

The routines perturb_command , db2csv_command , plot_rate_fit , and plot_data_fit , did not handle the other_database options correctly. This has been fixed.

06-15#

  1. Add documentation of the fact that the rate_eff_cov table is Optional .

  2. Fix db2csv_command when other_database or other_input_table is null.

06-14#

Add the Other Database options.

05-25#

Add the user_binomial.py example.

05-23#

The create_database nslist_dict argument was misspelled as nslict_dict. This has been fixed.

05-12#

Add the Batch Command wish list item, and remove the Information Matrix and Speed Up Simple Commands items. Combining commands is a better and more general solution to the problem of having to reinitialize the dismod_at model for each command.

05-04#

  1. Add the Log Gaussian and Log Laplace to the discussion of censored densities. In addition, correct the evaluation of these densities when they are censored.

  2. Advance the dock_dismod_at.sh dismod_at_version to dismod_at-20230504 and the at_cascade version to at_cascade-2023.5.3.

05-03#

Replace the Binomial Distribution wish list item by the follow page: binomial .

04-26#

The dock_dismod_at.sh dismod_at_version advanced to dismod_at-20230425 and the at_cascade version advanced to at_cascade-2023.4.26.

04-25#

In the examples, move the assignment to new from just before a call to dismod_at.create_connection to inside the call. In addition, add the readonly argument. For example, in user_censor.py the text

new          = False
connection   = dismod_at.create_connection(root_node_database, new)

was changed to

connection   = dismod_at.create_connection(
   root_node_database, new = False, readonly = False
)

Where possible, readonly was set to True .

04-06#

Add the Speed Up Simple Commands wish list item.

03-31#

Add the Information Matrix wish list item.

03-28#

Add the Example Fitting a Covariate with a Shock example.

03-27#

Change the user_jump_at_age.py example to estimate iota from prevalence (instead of Sincidence which directly measures iota). This is a better example because it requires an age point just before and just after the jump.

03-22#

Modify the PATH and PYTHONPATH environment variables, in the dock_dismod_at.sh dismod_at and at_cascade images, so that the dismod_at executable and the dismod_at, at_cascade python libraries are in the system path.

03-20#

Advance at_cascade_version to 2023.03.20.

03-09#

  1. The rate_eff_cov_table only worked properly for covariates that had reference value zero. This has been fixed.

  2. The dock_dismod_at.sh dismod_at_version advanced to dismod_at-20230309 and the at_cascade version advanced to at_cascade-2023.3.8.

01-05#

  1. The program used to crash when the rate_eff_cov_table was empty and the splitting_covariate was not null. This has been fixed and the program now reports an error in this case.

  2. The dock_dismod_at.sh dismod_at_version advanced to dismod_at-20230105 and the at_cascade version advanced to at_cascade-2023.1.5.