add tests for HTM scale-up

Author: tdm32

resources/ResourceFile_HIV.xlsx

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:4374824d53560c242209c1bc9de234ef5f1558b7274652efe1781167e44ad0ba
-size 161921
+oid sha256:e2e350ab8e94335c48220455cd573386b67064675ec4ebe126a345234aeb70d5
+size 161944

resources/malaria/ResourceFile_malaria.xlsx

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:924528f79e315c390b940881944e4756bbbba60ad05f6bbc925b0c1a10977d9b
-size 67588
+oid sha256:d9cb6ef00e472cf0951585fdbc2d6b3398ef7ef7f16b126cc435d67df42189f2
+size 68529

src/tlo/methods/hiv.py

@@ -1226,26 +1226,35 @@ def update_parameters(self):
                 scaled_params.loc[
                     scaled_params.parameter == "rdt_testing_rates", "scaleup_value"].values[0]
 
-
             # treatment reaches XX
             # no default between testing and treatment, governed by tx availability
 
             # coverage IPTp reaches XX
+            # given during ANC visits and MalariaIPTp Event which selects ALL eligible women
 
-            # treatment success reaches 1
+            # treatment success reaches 1 - default is currently 1 also
             self.sim.modules["Malaria"].parameters["prob_of_treatment_success"] = scaled_params.loc[
                 scaled_params.parameter == "prob_of_treatment_success", "scaleup_value"].values[0]
 
             # bednet and ITN coverage
-            # set IRS for all districts
+            # set IRS for 4 high-risk districts
             # lookup table created in malaria read_parameters
             # produces self.itn_irs called by malaria poll to draw incidence
             # need to overwrite this
-            self.sim.modules["Malaria"].itn_irs['irs_rate'] = scaled_params.loc[
+            highrisk_distr_num = self.sim.modules["Malaria"].parameters["highrisk_districts"]["district_num"]
+
+            # Find indices where District_Num is in highrisk_distr_num
+            mask = self.sim.modules["Malaria"].itn_irs['irs_rate'].index.get_level_values('District_Num').isin(
+                highrisk_distr_num)
+
+            # IRS values can be 0 or 0.8 - no other value in lookup table
+            self.sim.modules["Malaria"].itn_irs['irs_rate'].loc[mask] = scaled_params.loc[
                 scaled_params.parameter == "irs_district", "scaleup_value"].values[0]
 
-            # set ITN or all districts
-            # itn_district
+            # set ITN for all districts
+            # Set these values to 0.7 - this is the max value possible in lookup table
+            # equivalent to 0.7 of all pop sleeping under bednet
+            # household coverage could be 100%, but not everyone in household sleeping under bednet
             self.sim.modules["Malaria"].itn_irs['itn_rate'] = scaled_params.loc[
                 scaled_params.parameter == "itn_district", "scaleup_value"].values[0]
 

src/tlo/methods/malaria.py

@@ -180,6 +180,8 @@ def __init__(self, name=None, resourcefilepath=None):
         "prob_of_treatment_success": Parameter(
             Types.REAL, "probability malaria treatment cures and clears parasitaemia"
         ),
+        "highrisk_districts": Parameter(Types.LIST, "list of four malaria high-risk districts"
+        ),
     }
 
     PROPERTIES = {
@@ -234,6 +236,7 @@ def read_parameters(self, data_folder):
 
         p["sev_symp_prob"] = workbook["severe_symptoms"]
         p["rdt_testing_rates"] = workbook["WHO_TestData2023"]
+        p["highrisk_districts"] = workbook["highrisk_districts"]
 
         p["inf_inc"] = pd.read_csv(self.resourcefilepath / "malaria" / "ResourceFile_malaria_InfInc_expanded.csv")
         p["clin_inc"] = pd.read_csv(self.resourcefilepath / "malaria" / "ResourceFile_malaria_ClinInc_expanded.csv")

tests/test_HTMscaleup.py

@@ -4,7 +4,6 @@
 from pathlib import Path
 
 import pandas as pd
-import pytest
 
 from tlo import Date, Simulation
 from tlo.methods import (
@@ -67,6 +66,27 @@ def get_sim(seed, scaleup_hiv=False, scaleup_tb=False, scaleup_malaria=False, sc
     return sim
 
 
+def check_initial_params(sim):
+
+    original_params = pd.read_excel(
+        os.path.join(resourcefilepath, "ResourceFile_HIV.xlsx"),
+        sheet_name="parameters",
+    )
+
+    # todo do we need to be exhaustive and check every parameter here?
+    # check initial parameters
+    assert sim.modules["Hiv"].parameters["beta"] == \
+           original_params.loc[original_params.parameter_name == "beta", "value"].values[0]
+    assert sim.modules["Hiv"].parameters["prob_prep_for_fsw_after_hiv_test"] == original_params.loc[
+        original_params.parameter_name == "prob_prep_for_fsw_after_hiv_test", "value"].values[0]
+    assert sim.modules["Hiv"].parameters["prob_prep_for_agyw"] == original_params.loc[
+        original_params.parameter_name == "prob_prep_for_agyw", "value"].values[0]
+    assert sim.modules["Hiv"].parameters["probability_of_being_retained_on_prep_every_3_months"] == original_params.loc[
+        original_params.parameter_name == "probability_of_being_retained_on_prep_every_3_months", "value"].values[0]
+    assert sim.modules["Hiv"].parameters["prob_circ_after_hiv_test"] == original_params.loc[
+        original_params.parameter_name == "prob_circ_after_hiv_test", "value"].values[0]
+
+
 def test_hiv_scale_up(seed):
     """ test hiv program scale-up changes parameters correctly
     and on correct date """
@@ -86,17 +106,7 @@ def test_hiv_scale_up(seed):
     sim = get_sim(seed=seed, scaleup_hiv=True, scaleup_start_date=scaleup_start_date)
 
     # check initial parameters
-    # todo do we need to be exhaustive and check every parameter here?
-    assert sim.modules["Hiv"].parameters["beta"] == \
-           original_params.loc[original_params.parameter_name == "beta", "value"].values[0]
-    assert sim.modules["Hiv"].parameters["prob_prep_for_fsw_after_hiv_test"] == original_params.loc[
-        original_params.parameter_name == "prob_prep_for_fsw_after_hiv_test", "value"].values[0]
-    assert sim.modules["Hiv"].parameters["prob_prep_for_agyw"] == original_params.loc[
-        original_params.parameter_name == "prob_prep_for_agyw", "value"].values[0]
-    assert sim.modules["Hiv"].parameters["probability_of_being_retained_on_prep_every_3_months"] == original_params.loc[
-        original_params.parameter_name == "probability_of_being_retained_on_prep_every_3_months", "value"].values[0]
-    assert sim.modules["Hiv"].parameters["prob_circ_after_hiv_test"] == original_params.loc[
-        original_params.parameter_name == "prob_circ_after_hiv_test", "value"].values[0]
+    check_initial_params(sim)
 
     # Make the population
     sim.make_initial_population(n=popsize)
@@ -113,7 +123,7 @@ def test_hiv_scale_up(seed):
     assert sim.modules["Hiv"].parameters["prob_circ_after_hiv_test"] == new_params.loc[
         new_params.parameter == "prob_circ_after_hiv_test", "scaleup_value"].values[0]
 
-    # check TB and malaria parameters unchanged
+    # check malaria parameters unchanged
     mal_workbook = pd.read_excel(
         os.path.join(resourcefilepath, "malaria/ResourceFile_Malaria.xlsx"),
         sheet_name=None,
@@ -126,5 +136,94 @@ def test_hiv_scale_up(seed):
     pd.testing.assert_series_equal(sim.modules["Malaria"].parameters["rdt_testing_rates"]["Rate_rdt_testing"],
                                    mal_rdt_testing["Rate_rdt_testing"])
 
+    # all irs coverage levels should be < 1.0
+    assert sim.modules["Malaria"].itn_irs['irs_rate'].all() < 1.0
+    # itn rates for 2019 onwards
+    assert sim.modules["Malaria"].parameters["itn"] == mal_original_params.loc[
+        mal_original_params.parameter_name == "itn", "value"].values[0]
+
+    # check tb parameters unchanged
+    tb_workbook = pd.read_excel(
+        os.path.join(resourcefilepath, "ResourceFile_TB.xlsx"),
+        sheet_name=None,
+    )
+    tb_original_params = tb_workbook["parameters"]
+    tb_testing = tb_workbook["NTP2019"]
+
+    pd.testing.assert_series_equal(sim.modules["Tb"].parameters["rate_testing_active_tb"]["treatment_coverage"],
+                                   tb_testing["treatment_coverage"])
+    assert sim.modules["Tb"].parameters["prob_tx_success_ds"] == tb_original_params.loc[
+        tb_original_params.parameter_name == "prob_tx_success_ds", "value"].values[0]
+    assert sim.modules["Tb"].parameters["prob_tx_success_mdr"] == tb_original_params.loc[
+        tb_original_params.parameter_name == "prob_tx_success_mdr", "value"].values[0]
+    assert sim.modules["Tb"].parameters["prob_tx_success_0_4"] == tb_original_params.loc[
+        tb_original_params.parameter_name == "prob_tx_success_0_4", "value"].values[0]
+    assert sim.modules["Tb"].parameters["prob_tx_success_5_14"] == tb_original_params.loc[
+        tb_original_params.parameter_name == "prob_tx_success_5_14", "value"].values[0]
+    assert sim.modules["Tb"].parameters["first_line_test"] == tb_original_params.loc[
+        tb_original_params.parameter_name == "first_line_test", "value"].values[0]
+
+
+def test_htm_scale_up(seed):
+    """ test hiv/tb/malaria program scale-up changes parameters correctly
+    and on correct date """
+
+    workbook = pd.read_excel(
+        os.path.join(resourcefilepath, "ResourceFile_HIV.xlsx"),
+        sheet_name=None,
+    )
+
+    # Load data on HIV prevalence
+    original_params = workbook["parameters"]
+    new_params = workbook["scaleup_parameters"]
+    scaleup_start_date = Date(2011, 1, 1)
+
+    popsize = 100
+
+    sim = get_sim(seed=seed, scaleup_hiv=True, scaleup_tb=True, scaleup_malaria=True,
+                  scaleup_start_date=scaleup_start_date)
+
+    # check initial parameters
+    check_initial_params(sim)
+
+    # Make the population
+    sim.make_initial_population(n=popsize)
+    sim.simulate(end_date=scaleup_start_date + pd.DateOffset(days=1))
+
+    # check HIV parameters changed
+    assert sim.modules["Hiv"].parameters["beta"] < original_params.loc[original_params.parameter_name == "beta", "value"].values[0]
+    assert sim.modules["Hiv"].parameters["prob_prep_for_fsw_after_hiv_test"] == new_params.loc[
+        new_params.parameter == "prob_prep_for_fsw_after_hiv_test", "scaleup_value"].values[0]
+    assert sim.modules["Hiv"].parameters["prob_prep_for_agyw"] == new_params.loc[
+        new_params.parameter == "prob_prep_for_agyw", "scaleup_value"].values[0]
+    assert sim.modules["Hiv"].parameters["probability_of_being_retained_on_prep_every_3_months"] == new_params.loc[
+        new_params.parameter == "probability_of_being_retained_on_prep_every_3_months", "scaleup_value"].values[0]
+    assert sim.modules["Hiv"].parameters["prob_circ_after_hiv_test"] == new_params.loc[
+        new_params.parameter == "prob_circ_after_hiv_test", "scaleup_value"].values[0]
 
+    # check malaria parameters changed
+    assert sim.modules["Malaria"].parameters["prob_malaria_case_tests"] == new_params.loc[
+        new_params.parameter == "prob_malaria_case_tests", "scaleup_value"].values[0]
+    assert sim.modules["Malaria"].parameters["rdt_testing_rates"]["Rate_rdt_testing"].eq(new_params.loc[
+        new_params.parameter == "rdt_testing_rates", "scaleup_value"].values[0]).all()
+
+    # some irs coverage levels should now = 1.0
+    assert sim.modules["Malaria"].itn_irs['irs_rate'].any() == 1.0
+    # itn rates for 2019 onwards
+    assert sim.modules["Malaria"].parameters["itn"] == new_params.loc[
+        new_params.parameter == "itn", "scaleup_value"].values[0]
+
+    # check tb parameters changed
+    assert sim.modules["Tb"].parameters["rate_testing_active_tb"]["treatment_coverage"].eq(new_params.loc[
+        new_params.parameter == "tb_treatment_coverage", "scaleup_value"].values[0]).all()
+    assert sim.modules["Tb"].parameters["prob_tx_success_ds"] == new_params.loc[
+        new_params.parameter == "tb_prob_tx_success_ds", "scaleup_value"].values[0]
+    assert sim.modules["Tb"].parameters["prob_tx_success_mdr"] == new_params.loc[
+        new_params.parameter == "tb_prob_tx_success_mdr", "scaleup_value"].values[0]
+    assert sim.modules["Tb"].parameters["prob_tx_success_0_4"] == new_params.loc[
+        new_params.parameter == "tb_prob_tx_success_0_4", "scaleup_value"].values[0]
+    assert sim.modules["Tb"].parameters["prob_tx_success_5_14"] == new_params.loc[
+        new_params.parameter == "tb_prob_tx_success_5_14", "scaleup_value"].values[0]
+    assert sim.modules["Tb"].parameters["first_line_test"] == new_params.loc[
+        new_params.parameter == "first_line_test", "scaleup_value"].values[0]