Revised tb_DAH Impact analysis PR #1568

nchagoma503 · 2025-01-09T10:56:00Z

PR attempts to analyse the impact of TB diagnostic pathways, i.e, impact of unavailability of TB-related consumables and equipment.

nchagoma503 · 2025-01-09T11:06:59Z

@tamuri @tbhallett @tdm32 I am unable to generate picked files based on the model analysis setup and commands. My analysis files as follows:

I have been using the following command to run the scenario file locally: tlo scenario-run src/scripts/hiv/DAH/tb_DAH_scenarios2x.py

…e TB module when selecting persons for community chest xray. Also added outreach start data in the parameter file

…scenarios Double-checked parameters and addressed missing elements in outreach to ensure distinct scenario outputs.

…newton/Tb_DAH_analysis10x

…utum and xpert test changed tyoe_scaleup to target for community xray. Testing the effects of changes as the baseline CXR and CXR scaleup generating same output values Change the scaleup date to 2010

… not being printed, so added a logging for treatmentid in the culture class and will scale it up it works

…otprint

…e. Also change Tb community xray screening start date to simulation start date

nchagoma503 · 2025-02-28T18:19:27Z

@tdm32 . Here is PR: PR 1516-Revised DAH analysis as follows:

scenario and analysis script
tb code
sample outputs below
a. summary of consumables by scenario[summary of consumables.xlsx](https://github.com/user-
attachments/files/19030986/summary.of.consumables.xlsx)
b. summary of HR capacity by scenario.
staff_capacity_by_cadres.xlsx

c. summary of DALYs and mortality pattern[Draft outputs-280225.odt](https://github.com/user-
attachments/files/19030981/Drfat.outputs-280225.odt)

While culture testing has now been incorporated, it does not feature in the outputs marked under program scale-up. At this stage, I am willing to acknowledge this as a limitation. The primary objective of revisiting the analysis was to include consumables and calculate the associated costs, which has now been achieved.

tdm32 · 2025-03-07T10:41:21Z

@tdm32 . Here is PR: PR 1516-Revised DAH analysis as follows:

scenario and analysis script

tb code

sample outputs below
a. summary of consumables by scenario[summary of consumables.xlsx](https://github.com/user-
attachments/files/19030986/summary.of.consumables.xlsx)
b. summary of HR capacity by scenario.
staff_capacity_by_cadres.xlsx

c. summary of DALYs and mortality pattern[Draft outputs-280225.odt](https://github.com/user- attachments/files/19030981/Drfat.outputs-280225.odt)

While culture testing has now been incorporated, it does not feature in the outputs marked under program scale-up. At this stage, I am willing to acknowledge this as a limitation. The primary objective of revisiting the analysis was to include consumables and calculate the associated costs, which has now been achieved.

@nchagoma503 One of these links takes me to GitHub user-faghloumi

tdm32 · 2025-03-07T10:42:05Z

@tdm32 . Here is PR: PR 1516-Revised DAH analysis as follows:

scenario and analysis script

tb code

sample outputs below
a. summary of consumables by scenario[summary of consumables.xlsx](https://github.com/user-
attachments/files/19030986/summary.of.consumables.xlsx)
b. summary of HR capacity by scenario.
staff_capacity_by_cadres.xlsx

c. summary of DALYs and mortality pattern[Draft outputs-280225.odt](https://github.com/user- attachments/files/19030981/Drfat.outputs-280225.odt)

While culture testing has now been incorporated, it does not feature in the outputs marked under program scale-up. At this stage, I am willing to acknowledge this as a limitation. The primary objective of revisiting the analysis was to include consumables and calculate the associated costs, which has now been achieved.

@nchagoma503 please paste the figures here so we can see the outputs easily

tdm32 · 2025-03-07T10:46:04Z

@nchagoma503 We can't see the tracked changes in csv files but what values are you changing in HIV/MoH_numbers_tests, art_coverage, parameters, scaleup_parameters? The HIV module should be unchanged from master. Likewise, the only things changing in the TB module would be any scale-up parameters related to your scenarios.

tdm32 · 2025-03-07T11:02:24Z

@nchagoma503 Please link to exactly the analysis file and scripts which you are using. The link above points to a folder. You can delete all those which are not used in this PR.

tdm32 · 2025-03-07T11:44:00Z

@nchagoma503 Thanks for all your hard work on this. I can see you've commented out a few tests - likely because they were failing(?) - but this is not advisable.

tdm32

We can't see the tracked changes in csv files but what values ar you changing in HIV/MoH_numbers_tests, art_coverage, parameters, scaleup_parameters? The HIV module should be unchanged from master

tdm32 · 2025-03-07T10:52:24Z

src/scripts/hiv/DAH/10xscenarios.py

+                'tlo.methods.demography.detail': logging.WARNING,
+                'tlo.methods.healthburden': logging.INFO,
+                'tlo.methods.healthsystem.summary': logging.INFO,
+                'tlo.methods.tb10x': logging.INFO,


what is tb10x?

tdm32 · 2025-03-07T10:58:25Z

src/scripts/hiv/DAH/10xscenarios.py

+        }
+
+        if draw_number < self.number_of_draws:
+            return list(self._scenarios.values())[draw_number] | health_system_constraints


if health system constraints are initially identical for all scenario, this part is not needed

tdm32 · 2025-03-07T10:59:16Z

src/scripts/hiv/DAH/10xscenarios.py

+                },
+            },
+            # increase CXR by 90 percentage points
+            "CXR scaleup": {


where is CXR increased by 90%? In the resourcefile?

tdm32 · 2025-03-07T11:02:43Z

src/tlo/methods/hiv.py

@@ -335,6 +335,7 @@ def __init__(self, name=None, resourcefilepath=None, run_with_checks=False):
            "Probability that adolescent girls / young women will start PrEP",
        ),
        "prob_circ_after_hiv_test": Parameter(
+


just roll back this change

tdm32 · 2025-03-07T11:04:08Z

src/tlo/methods/tb.py

        # ------------------ scale-up parameters for scenario analysis ------------------ #
        "type_of_scaleup": Parameter(
            Types.STRING, "argument to determine type scale-up of program which will be implemented, "
                          "can be 'none', 'target' or 'max'",
        ),
+        "scenario_SI": Parameter(


if not used, then remove

tdm32 · 2025-03-07T11:39:31Z

src/tlo/methods/tb.py

@@ -2927,7 +3272,16 @@ def apply(self, population):
        # LATENT
        # proportion of population with latent TB - all pop
        num_latent = len(df[(df.tb_inf == "latent") & df.is_alive])
-        prev_latent = num_latent / len(df[df.is_alive])
+        # prev_latent = num_latent / len(df[df.is_alive])


why comment out this line and replace with the same thing?

tdm32 · 2025-03-07T11:40:19Z

src/tlo/methods/tb.py

-        prev_latent = num_latent / len(df[df.is_alive])
+        # prev_latent = num_latent / len(df[df.is_alive])
+        # Calculate the number of alive individuals
+        denominator = len(df[df.is_alive])


repeated from above

tdm32 · 2025-03-07T11:41:10Z

tests/test_analysis.py

@@ -392,25 +392,6 @@ def is_df_same_size_and_dtype(df1, df2):
                        else True
                    )

-                def is_list_same_size_and_dtype(l1, l2):


Please don't comment out large chunks of the tests. They are in place to ensure that the code is working correctly. If they are failing, this is a fault with the code.

tdm32 · 2025-03-07T11:42:13Z

tests/test_htm_scaleup.py

@@ -214,5 +214,4 @@ def test_htm_scale_up(seed):
    assert sim.modules["Tb"].parameters["prob_tx_success_5_14"] == new_tb_params.loc[
        new_tb_params.parameter == "tb_prob_tx_success_5_14", "target_value"].values[0]
    assert sim.modules["Tb"].parameters["first_line_test"] == new_tb_params.loc[
-        new_tb_params.parameter == "first_line_test", "target_value"].values[0]
-
+          new_tb_params.parameter == "first_line_test", "target_value"].values[0]


indentation is wrong here, revert back to master version

tdm32 · 2025-03-07T11:42:50Z

tests/test_tb.py

@@ -136,6 +136,27 @@ def test_basic_run(seed):
                         ]).all().all()


+# def test_tb_screening(seed):


Again, don't remove tests, particularly in they directly relate to the code you are working on.

this is an updated branch with all tests running successfully

82a4146

nchagoma503 added 28 commits January 9, 2025 11:23

removed unused imports in analysis scripts and removed f prefix in th…

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…e TB module when selecting persons for community chest xray. Also added outreach start data in the parameter file

re-sorted imports

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re-sorted imports

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re-sorted imports

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re-sorted imports

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re-sorted imports

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activated TB palliative care section of the code

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re-sorted imports

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re-sorted imports

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re-sorted imports

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re-sorted imports and added missing import argparse

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re-sorted imports and added missing import argparse

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re-sorted imports and added missing import argparse

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re-sorted imports and added missing import argparse

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re-sorted imports and added missing import argparse

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re-sorted imports and added missing import argparse

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re-sorted imports and added missing import argparse

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re-sorted imports and added missing import argparse

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adjusting time horizon to check the consistency of results

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fix: resolve identical values in baseline, outreach, and CXR scaleup …

c9a2fdf

…scenarios Double-checked parameters and addressed missing elements in outreach to ensure distinct scenario outputs.

Merge remote-tracking branch 'origin/newton/Tb_DAH_analysis10x' into …

e2a1daf

…newton/Tb_DAH_analysis10x

added test scaleup parameters in the scenario setup event targeted sp…

e8abf0c

…utum and xpert test changed tyoe_scaleup to target for community xray. Testing the effects of changes as the baseline CXR and CXR scaleup generating same output values Change the scaleup date to 2010

added test scaleup parameters in the scenario setup event targeted sp…

8e1a1c7

…utum and xpert test changed tyoe_scaleup to target for community xray. Testing the effects of changes as the baseline CXR and CXR scaleup generating same output values Change the scaleup date to 2010

added test scaleup parameters in the scenario setup event targeted sp…

ab849f1

…utum and xpert test changed tyoe_scaleup to target for community xray. Testing the effects of changes as the baseline CXR and CXR scaleup generating same output values Change the scaleup date to 2010

treatment_ID for TB culture, Tb_palliative_care and outreachscrenning…

b9575ad

… not being printed, so added a logging for treatmentid in the culture class and will scale it up it works

Added return statements to endoflife care and tb culture to return fo…

f09ca5c

…otprint

Added return statements to endoflife care and tb culture to return fo…

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…otprint

Added return statements to endoflife care and tb culture to return fo…

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…otprint

nchagoma503 added 22 commits February 26, 2025 15:14

resorted import statements

cb0ab3e

resorted import statements

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resorted import statements

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resorted import statements

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reworked screenining and refer procedure to check screening of cultur…

4695ccb

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

68fb47b

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

2dbc892

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

da4c8f1

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

d66ab20

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

f07441d

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

6a33140

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

e5a4b02

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

fc570e9

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

3360224

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

fc90385

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

3ae1378

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

e4a9556

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

146b3fc

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

a89a59b

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

73039d1

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

a5c879e

…e. Also change Tb community xray screening start date to simulation start date

reworked screenining and refer procedure to check screening of cultur…

7639ca8

…e. Also change Tb community xray screening start date to simulation start date

nchagoma503 marked this pull request as ready for review February 28, 2025 18:18

tdm32 requested changes Mar 7, 2025

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Revised tb_DAH Impact analysis PR #1568

Revised tb_DAH Impact analysis PR #1568

nchagoma503 commented Jan 9, 2025

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		@@ -136,6 +136,27 @@ def test_basic_run(seed):
		]).all().all()


		# def test_tb_screening(seed):

Revised tb_DAH Impact analysis PR #1568

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Revised tb_DAH Impact analysis PR #1568

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tdm32 commented Mar 7, 2025 •

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