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Release Notes for 2023
######################

mm-dd
*****

12-30
=====
There were some problem with changes to
:ref:`dock_dismod_at.sh-name` on 12-29 (that have been fixed):

#. When restarting a container the python virtual environment was not set.
#. 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 ,
:ref:`dock_dismod_at.sh@dismod_at_version` to 2023.12.29, and
:ref:`dock_dismod_at.sh@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
:ref:`install_settings.py@dismod_at_prefix` does not end with ``dismod_at`` .

12-05
=====
Add the Command Documentation wish list item.
This was completed by the :ref:`python_main@command`
table for the python main program.

12-01
=====
#. Advance dismod_at to use cppad_mixed-20231201.
#. Advance dock_dismod_at.sh
   :ref:`dock_dismod_at.sh@dismod_at_version` to 20231201, and
   :ref:`dock_dismod_at.sh@at_cascade_version` to 2023.11.30.
#. Add the :ref:`dock_dismod_at.sh@build_type` option to
   dock_dismod_at.sh (instead of building both debug and release
   versions in the same image).
#. Add the dock_dismod_at.sh wish list entry
   (which was completed on 12-29) .
#. Add the :ref:`wish_list@Bootstrapping` wish list entry.

11-30
=====
#. There was a bug in the hold_out command when
   :ref:`hold_out_command@cov_name` was present.
   This has been fixed.
#. The discussion about balancing
   :ref:`hold_out_command@Balancing@Covariates` was improved.

10-20
=====
#. Improve the documentation for :ref:`system_command_prc-name` .
   In addition, make the following change :
   If an error is detected, include the *command* in
   *file_stderr* , *result* .stderr , and the assert error message .
#. Advance dock_dismod_at.sh
   :ref:`dock_dismod_at.sh@dismod_at_version` to 202310.20 .


10-18
=====
**API Change:**

#. Add the average noise effect
   :ref:`E_i(theta)<
      data_like@Measurement Noise Covariates@Average Noise Effect, E_i(theta)
   >`
   before transforming the standard deviation.
   This changes the definition of the adjusted standard deviation
   :ref:`sigma_i(theta)<
      data_like@Adjusted Standard Deviation, sigma_i(theta)
   >`
   and the transformed standard deviation
   :ref:`delta_i(theta)<
      data_like@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 :ref:`db2csv_command@data.csv@meas_sigma` column.

#. Remove ``add_std_scale_log`` and ``add_var_scale_log`` from the
   possible values for :ref:`option_table@meas_noise_effect` in the
   option table (now the addition is done before the log scaling).

#. Advance dock_dismod_at.sh
   :ref:`dock_dismod_at.sh@dismod_at_version` to 20231018 and
   :ref:`dock_dismod_at.sh@at_cascade_version` to 2023.10.7.

08-09
=====
Advance dock_dismod_at.sh
:ref:`dock_dismod_at.sh@dismod_at_version` to 20230808 and
:ref:`dock_dismod_at.sh@at_cascade_version` to 2023.8.9.

08-08
=====
#. There was a bug in the :ref:`data_density_command-name` when the
   original data density was binomial
   (a binomial density it cannot be changed).
   This has been fixed.
#. The :ref:`binomial@Approximation` for the standard deviation
   corresponding to the binomial distribution was of by a factor of
   :math:`\sqrt{ 1 / n}` where *n* is the sample size.
   This has been fixed. In addition, the
   :ref:`user_binomial.py-name` example was modified to demonstrate
   that this works well.

07-06
=====
Advance dock_dismod_at.sh
:ref:`dock_dismod_at.sh@dismod_at_version` to 20230706 and
:ref:`dock_dismod_at.sh@at_cascade_version` to 2023.7.6.

07-05
=====
**API Change:** :

#. The :ref:`data_table@sample_size` column was added to the data table.
   The values in this column should be null except for rows that use the
   :ref:`density_table@density_name@binomial` density.
#. The :ref:`old2new_command-name` 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
=====
#. **API Change:** Change the average_integrand rate argument name to :ref:`average_integrand@rate_fun` .

#. 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
:ref:`dock_dismod_at.sh@dismod_at_version` to 20230628 and
:ref:`dock_dismod_at.sh@at_cascade_version` to 2023.6.28.

06-27
=====
If nan appeared for a real value in :ref:`create_table@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
=====
#. If :ref:`option_table@Other Database@other_database` is a relative path,
   it is now relative to the directory where the
   directory where :ref:`command@Primary Database` is located.
#. Advance dock_dismod_at.s
   :ref:`dock_dismod_at.sh@dismod_at_version` to 20230626 and
   :ref:`dock_dismod_at.sh@at_cascade_version` to 2023.6.26.

06-18
=====
#. If ``rate_eff_cov`` was in the
   :ref:`option_table@Other Database@other_input_table` option,
   dismod_at would use the other database for the ``rate`` table.
   This has been fixed.
#. The dock_dismod_at.sh
   :ref:`dock_dismod_at.sh@dismod_at_version`
   was advanced to 20230618,
   and the :ref:`dock_dismod_at.sh@at_cascade_version`
   was advanced to 2023.6.18 .
#. 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 under the heading
   :ref:`dock_dismod_at.sh@Working with Images`.
#. Testing of the debug version of at_cascade was removed because it is slow.

06-17
=====
The routines
:ref:`perturb_command-name` ,
:ref:`db2csv_command-name`  ,
:ref:`plot_rate_fit-name`  , and
:ref:`plot_data_fit-name`  ,
did not handle the
:ref:`option_table@Other Database@other_database` options correctly.
This has been fixed.

06-15
=====
#. Add documentation of the fact that the rate_eff_cov table is
   :ref:`rate_eff_cov_table@Optional` .
#. Fix :ref:`db2csv_command-name` when
   :ref:`option_table@Other Database@other_database` or
   :ref:`option_table@Other Database@other_input_table` is null.

06-14
=====
Add the :ref:`option_table@Other Database` options.

05-25
=====
Add the :ref:`user_binomial.py-name` example.

05-23
=====
The create_database :ref:`create_database@nslist_dict` argument was misspelled as nslict_dict.
This has been fixed.

05-12
=====
Add the :ref:`wish_list@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
=====
#. Add the
   :ref:`censor_density@Log Gaussian` and :ref:`censor_density@Log Laplace`
   to the discussion of censored densities.
   In addition, correct the evaluation of these densities
   when they are censored.
#. Advance the dock_dismod_at.sh
   :ref:`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:
:ref:`binomial-name` .

04-26
=====
The dock_dismod_at.sh
:ref:`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 :ref:`user_censor.py-name` 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 :ref:`user_shock_cov.py-title` example.

03-27
=====
Change the :ref:`user_jump_at_age.py-name` 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 :ref:`dock_dismod_at.sh-name` 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 :ref:`dock_dismod_at.sh@at_cascade_version`
to 2023.03.20.

03-09
=====
#. The :ref:`rate_eff_cov_table-name` only worked properly for covariates
   that had reference value zero. This has been fixed.
#. The dock_dismod_at.sh
   :ref:`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
=====
#. The program used to crash when the
   :ref:`rate_eff_cov_table-name` was empty and the
   :ref:`option_table@splitting_covariate` was not null.
   This has been fixed and the program now reports an error in this case.
#. The dock_dismod_at.sh
   :ref:`dock_dismod_at.sh@dismod_at_version` advanced to
   dismod_at-20230105 and the at_cascade version advanced to
   at_cascade-2023.1.5.

{xrst_end 2023}