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b/resources/ResourceFile_TB/scaleup_parameters.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e7f5f29cc8816eaafbb60add9d69b4d0e86f93082e76c42fc6b29b85e454bbd3 +size 340 diff --git a/resources/ResourceFile_TB/testing_rates.csv b/resources/ResourceFile_TB/testing_rates.csv new file mode 100644 index 0000000000..ae3f43586c --- /dev/null +++ b/resources/ResourceFile_TB/testing_rates.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ee52c1e343b0e634c05c2eb281f925174fe951b356856acaede2435e8f543d94 +size 1016 diff --git a/resources/malaria/ResourceFile_malaria.xlsx b/resources/malaria/ResourceFile_malaria.xlsx deleted file mode 100644 index 7537f3ace9..0000000000 --- a/resources/malaria/ResourceFile_malaria.xlsx +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:7f256d5007b36e2428ae844747bd766bb6086540c5135408d606dd821e185d9f -size 69578 diff --git a/resources/malaria/ResourceFile_malaria/MAP_CommoditiesData2023.csv b/resources/malaria/ResourceFile_malaria/MAP_CommoditiesData2023.csv new file mode 100644 index 0000000000..5a2903781b --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/MAP_CommoditiesData2023.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0cb717d1639a4b212f1b974c9aecfa26f7982c4e40eb8c8d68a9a2808ae6944b +size 9783 diff --git a/resources/malaria/ResourceFile_malaria/MAP_IRSrates.csv b/resources/malaria/ResourceFile_malaria/MAP_IRSrates.csv new file mode 100644 index 0000000000..ba363aa865 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/MAP_IRSrates.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:79c9362873e293e421f3c939f29a375140b7fd1e9ac0cc77db4448230421cfce +size 10120 diff --git a/resources/malaria/ResourceFile_malaria/MAP_ITNrates.csv b/resources/malaria/ResourceFile_malaria/MAP_ITNrates.csv new file mode 100644 index 0000000000..fca1c2b759 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/MAP_ITNrates.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a7295ed12e41236c5e7ce30931cc48e46dea8ab235352a5025e1f96f6cbdcb6c +size 7608 diff --git a/resources/malaria/ResourceFile_malaria/MAP_InfectionData2023.csv b/resources/malaria/ResourceFile_malaria/MAP_InfectionData2023.csv new file mode 100644 index 0000000000..f62ad813f4 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/MAP_InfectionData2023.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4fc91a5288e169397932495e126e231ec0ade0bea0767c48bb2d11eb93ece1c8 +size 1108 diff --git a/resources/malaria/ResourceFile_malaria/NMCP.csv b/resources/malaria/ResourceFile_malaria/NMCP.csv new file mode 100644 index 0000000000..1e50d26083 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/NMCP.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:93611c646e97f540f521fc58808d1180ff7347fed50228cd5b18ce5bedbeba12 +size 1651 diff --git a/resources/malaria/ResourceFile_malaria/PfPR_MAPdata.csv b/resources/malaria/ResourceFile_malaria/PfPR_MAPdata.csv new file mode 100644 index 0000000000..fc420097a6 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/PfPR_MAPdata.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a3404a4d076b57c59c92e0c9377bd84cee33c8b0ab3fd3c9533a5b7715218dd1 +size 1641 diff --git a/resources/malaria/ResourceFile_malaria/WHO_CaseData2023.csv b/resources/malaria/ResourceFile_malaria/WHO_CaseData2023.csv new file mode 100644 index 0000000000..edb4212014 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/WHO_CaseData2023.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:35d8f62efe3cabd8046f1f3bb31acaabdc5f697ba67cc458bb73ef9bd2a3a3d3 +size 1358 diff --git a/resources/malaria/ResourceFile_malaria/WHO_MalReport.csv b/resources/malaria/ResourceFile_malaria/WHO_MalReport.csv new file mode 100644 index 0000000000..8b70346d9a --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/WHO_MalReport.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4d210f3135ea22d4f5eea0b1d6c361df1d75af4dd2ba915f8b8c0d2f3c82a722 +size 1667 diff --git a/resources/malaria/ResourceFile_malaria/WHO_TestData2023.csv b/resources/malaria/ResourceFile_malaria/WHO_TestData2023.csv new file mode 100644 index 0000000000..067d8bc6ab --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/WHO_TestData2023.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:166944bd1976b1cf6c15dabe2d89b7d3291977761d7991de44a3fe7e869c8f1c +size 1322 diff --git a/resources/malaria/ResourceFile_malaria/WHOcommodities.csv b/resources/malaria/ResourceFile_malaria/WHOcommodities.csv new file mode 100644 index 0000000000..d3307b52b5 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/WHOcommodities.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4a9e39a2b8f081e24eb180386275d90262b15ceaa1114e77eb1616d970b105f5 +size 398 diff --git a/resources/malaria/ResourceFile_malaria/highrisk_districts.csv b/resources/malaria/ResourceFile_malaria/highrisk_districts.csv new file mode 100644 index 0000000000..8501c5f516 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/highrisk_districts.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:525c87516dd3cf56fdf72f29ef0ac2d2dcafd14edf6169ea841187f217cb2282 +size 75 diff --git a/resources/malaria/ResourceFile_malaria/inc1000py_MAPdata.csv b/resources/malaria/ResourceFile_malaria/inc1000py_MAPdata.csv new file mode 100644 index 0000000000..563941dce4 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/inc1000py_MAPdata.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8a68cf7c4270ab37e53ff78a1457db6a9a0dde3794072437bddc6a715611f438 +size 486 diff --git a/resources/malaria/ResourceFile_malaria/interventions.csv b/resources/malaria/ResourceFile_malaria/interventions.csv new file mode 100644 index 0000000000..413d513965 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/interventions.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:51822b5693c75e056362a7a52d22a685084e2b46d7184df144728e254a5339b4 +size 1144 diff --git a/resources/malaria/ResourceFile_malaria/mortalityRate_MAPdata.csv b/resources/malaria/ResourceFile_malaria/mortalityRate_MAPdata.csv new file mode 100644 index 0000000000..56cbca1243 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/mortalityRate_MAPdata.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:181ebe0b5371f2a607353e6e9a42371880eb7a1ec60f24bb5927be420fc07413 +size 1881 diff --git a/resources/malaria/ResourceFile_malaria/parameters.csv b/resources/malaria/ResourceFile_malaria/parameters.csv new file mode 100644 index 0000000000..8c29a8d524 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/parameters.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3616d41e17fe9f394268835709f502da39cfed8c1df253c88a7811641c05afb1 +size 784 diff --git a/resources/malaria/ResourceFile_malaria/scaleup_parameters.csv b/resources/malaria/ResourceFile_malaria/scaleup_parameters.csv new file mode 100644 index 0000000000..92788c7637 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/scaleup_parameters.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7710c479094fd4ba5cc3d49487ea85730e8d632dd8e82d9648d7948833aa439f +size 208 diff --git a/resources/malaria/ResourceFile_malaria/severe_symptoms.csv b/resources/malaria/ResourceFile_malaria/severe_symptoms.csv new file mode 100644 index 0000000000..9ac7fbd6b9 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/severe_symptoms.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e7003d947ee06b6a28e3a4eafd783ea96488383a1bcf0d9e1ad4e9d4bbec3152 +size 352 diff --git a/resources/malaria/ResourceFile_malaria/txCov_MAPdata.csv b/resources/malaria/ResourceFile_malaria/txCov_MAPdata.csv new file mode 100644 index 0000000000..68d662a5c4 --- /dev/null +++ b/resources/malaria/ResourceFile_malaria/txCov_MAPdata.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:60c450a83c86f2e08df790cb645fc530667d8b6e960269143778b1112b86deed +size 710 diff --git a/src/tlo/methods/epi.py b/src/tlo/methods/epi.py index 0ad0c75c1f..4aae66dc5e 100644 --- a/src/tlo/methods/epi.py +++ b/src/tlo/methods/epi.py @@ -7,6 +7,7 @@ from tlo.events import IndividualScopeEventMixin, PopulationScopeEventMixin, RegularEvent from tlo.methods import Metadata from tlo.methods.hsi_event import HSI_Event +from tlo.util import read_csv_files logger = logging.getLogger(__name__) logger.setLevel(logging.INFO) @@ -71,9 +72,7 @@ def __init__(self, name=None, resourcefilepath=None): def read_parameters(self, data_folder): p = self.parameters - workbook = pd.read_excel( - Path(self.resourcefilepath) / 'ResourceFile_EPI_WHO_estimates.xlsx', sheet_name=None - ) + workbook = read_csv_files(Path(self.resourcefilepath) / 'ResourceFile_EPI_WHO_estimates', files=None) self.load_parameters_from_dataframe(workbook["parameters"]) diff --git a/src/tlo/methods/hiv.py b/src/tlo/methods/hiv.py index e14a6c39fe..8400486458 100644 --- a/src/tlo/methods/hiv.py +++ b/src/tlo/methods/hiv.py @@ -25,7 +25,6 @@ """ from __future__ import annotations -import os from typing import TYPE_CHECKING, List import numpy as np @@ -40,7 +39,7 @@ from tlo.methods.hsi_event import HSI_Event from tlo.methods.hsi_generic_first_appts import GenericFirstAppointmentsMixin from tlo.methods.symptommanager import Symptom -from tlo.util import create_age_range_lookup +from tlo.util import create_age_range_lookup, read_csv_files if TYPE_CHECKING: from tlo.methods.hsi_generic_first_appts import HSIEventScheduler @@ -423,10 +422,7 @@ def read_parameters(self, data_folder): # Shortcut to parameters dict p = self.parameters - workbook = pd.read_excel( - os.path.join(self.resourcefilepath, "ResourceFile_HIV.xlsx"), - sheet_name=None, - ) + workbook = read_csv_files(self.resourcefilepath/'ResourceFile_HIV', files=None) self.load_parameters_from_dataframe(workbook["parameters"]) # Load data on HIV prevalence diff --git a/src/tlo/methods/malaria.py b/src/tlo/methods/malaria.py index ea1f35ad02..aa6cc0e33d 100644 --- a/src/tlo/methods/malaria.py +++ b/src/tlo/methods/malaria.py @@ -20,7 +20,7 @@ from tlo.methods.hsi_event import HSI_Event from tlo.methods.hsi_generic_first_appts import GenericFirstAppointmentsMixin from tlo.methods.symptommanager import Symptom -from tlo.util import random_date +from tlo.util import random_date, read_csv_files if TYPE_CHECKING: from tlo.methods.hsi_generic_first_appts import DiagnosisFunction, HSIEventScheduler @@ -228,7 +228,8 @@ def __init__(self, name=None, resourcefilepath=None): } def read_parameters(self, data_folder): - workbook = pd.read_excel(self.resourcefilepath / 'malaria' / 'ResourceFile_malaria.xlsx', sheet_name=None) + # workbook = pd.read_excel(self.resourcefilepath / 'malaria' / 'ResourceFile_malaria.xlsx', sheet_name=None) + workbook = read_csv_files(self.resourcefilepath / 'malaria' / 'ResourceFile_malaria', files=None) self.load_parameters_from_dataframe(workbook['parameters']) p = self.parameters diff --git a/src/tlo/methods/measles.py b/src/tlo/methods/measles.py index 39f9828860..585aadf511 100644 --- a/src/tlo/methods/measles.py +++ b/src/tlo/methods/measles.py @@ -1,7 +1,6 @@ from __future__ import annotations import math -import os from typing import TYPE_CHECKING, List import pandas as pd @@ -13,7 +12,7 @@ from tlo.methods.hsi_event import HSI_Event from tlo.methods.hsi_generic_first_appts import GenericFirstAppointmentsMixin from tlo.methods.symptommanager import Symptom -from tlo.util import random_date +from tlo.util import random_date, read_csv_files if TYPE_CHECKING: from tlo.methods.hsi_generic_first_appts import HSIEventScheduler @@ -102,11 +101,7 @@ def __init__(self, name=None, resourcefilepath=None): def read_parameters(self, data_folder): """Read parameter values from file """ - - workbook = pd.read_excel( - os.path.join(self.resourcefilepath, "ResourceFile_Measles.xlsx"), - sheet_name=None, - ) + workbook = read_csv_files(self.resourcefilepath/'ResourceFile_Measles', files=None) self.load_parameters_from_dataframe(workbook["parameters"]) self.parameters["symptom_prob"] = workbook["symptoms"] diff --git a/src/tlo/methods/schisto.py b/src/tlo/methods/schisto.py index 0e9735286a..385b8cd77d 100644 --- a/src/tlo/methods/schisto.py +++ b/src/tlo/methods/schisto.py @@ -14,7 +14,7 @@ from tlo.methods.hsi_event import HSI_Event from tlo.methods.hsi_generic_first_appts import GenericFirstAppointmentsMixin from tlo.methods.symptommanager import Symptom -from tlo.util import random_date +from tlo.util import random_date, read_csv_files if TYPE_CHECKING: from tlo.methods.hsi_generic_first_appts import HSIEventScheduler @@ -123,7 +123,7 @@ def read_parameters(self, data_folder): """Read parameters and register symptoms.""" # Load parameters - workbook = pd.read_excel(Path(self.resourcefilepath) / 'ResourceFile_Schisto.xlsx', sheet_name=None) + workbook = read_csv_files(Path(self.resourcefilepath) / 'ResourceFile_Schisto', files=None) self.parameters = self._load_parameters_from_workbook(workbook) for _spec in self.species.values(): self.parameters.update(_spec.load_parameters_from_workbook(workbook)) diff --git a/src/tlo/methods/tb.py b/src/tlo/methods/tb.py index b0f0cd22f6..ee84ebb0bb 100644 --- a/src/tlo/methods/tb.py +++ b/src/tlo/methods/tb.py @@ -3,8 +3,6 @@ It schedules TB treatment and follow-up appointments along with preventive therapy for eligible people (HIV+ and paediatric contacts of active TB cases """ - -import os from functools import reduce import pandas as pd @@ -17,7 +15,7 @@ from tlo.methods.dxmanager import DxTest from tlo.methods.hsi_event import HSI_Event from tlo.methods.symptommanager import Symptom -from tlo.util import random_date +from tlo.util import parse_csv_values_for_columns_with_mixed_datatypes, random_date, read_csv_files logger = logging.getLogger(__name__) logger.setLevel(logging.INFO) @@ -399,9 +397,7 @@ def read_parameters(self, data_folder): """ # 1) Read the ResourceFiles - workbook = pd.read_excel( - os.path.join(self.resourcefilepath, "ResourceFile_TB.xlsx"), sheet_name=None - ) + workbook = read_csv_files(self.resourcefilepath/"ResourceFile_TB", files=None) self.load_parameters_from_dataframe(workbook["parameters"]) p = self.parameters @@ -912,6 +908,10 @@ def update_parameters_for_program_scaleup(self): """ options for program scale-up are 'target' or 'max' """ p = self.parameters scaled_params_workbook = p["scaleup_parameters"] + for col in scaled_params_workbook.columns: + scaled_params_workbook[col] = scaled_params_workbook[col].apply( + parse_csv_values_for_columns_with_mixed_datatypes + ) if p['type_of_scaleup'] == 'target': scaled_params = scaled_params_workbook.set_index('parameter')['target_value'].to_dict() diff --git a/tests/test_hiv.py b/tests/test_hiv.py index 5a27cf2c33..b3d61a25b8 100644 --- a/tests/test_hiv.py +++ b/tests/test_hiv.py @@ -35,6 +35,7 @@ HSI_Hiv_StartOrContinueTreatment, HSI_Hiv_TestAndRefer, ) +from tlo.util import read_csv_files try: resourcefilepath = Path(os.path.dirname(__file__)) / '../resources' @@ -1210,8 +1211,7 @@ def test_baseline_hiv_prevalence(seed): # get data on 2010 prevalence # HIV resourcefile - xls = pd.ExcelFile(resourcefilepath / "ResourceFile_HIV.xlsx") - prev_data = pd.read_excel(xls, sheet_name="DHS_prevalence") + prev_data = read_csv_files(resourcefilepath / 'ResourceFile_HIV', files="DHS_prevalence") adult_prev_1549_data = prev_data.loc[ (prev_data.Year == 2010, "HIV prevalence among general population 15-49")].values[0] / 100 diff --git a/tests/test_htm_scaleup.py b/tests/test_htm_scaleup.py index fcb538f19c..95ee6e9509 100644 --- a/tests/test_htm_scaleup.py +++ b/tests/test_htm_scaleup.py @@ -19,6 +19,7 @@ symptommanager, tb, ) +from tlo.util import parse_csv_values_for_columns_with_mixed_datatypes, read_csv_files resourcefilepath = Path(os.path.dirname(__file__)) / "../resources" @@ -54,7 +55,8 @@ def get_sim(seed): def check_initial_params(sim): - original_params = pd.read_excel(resourcefilepath / 'ResourceFile_HIV.xlsx', sheet_name='parameters') + original_params = read_csv_files(resourcefilepath / 'ResourceFile_HIV', files='parameters') + original_params.value = original_params.value.apply(parse_csv_values_for_columns_with_mixed_datatypes) # check initial parameters assert sim.modules["Hiv"].parameters["beta"] == \ @@ -73,8 +75,9 @@ def test_hiv_scale_up(seed): """ test hiv program scale-up changes parameters correctly and on correct date """ - original_params = pd.read_excel(resourcefilepath / 'ResourceFile_HIV.xlsx', sheet_name="parameters") - new_params = pd.read_excel(resourcefilepath / 'ResourceFile_HIV.xlsx', sheet_name="scaleup_parameters") + original_params = read_csv_files(resourcefilepath / 'ResourceFile_HIV', files="parameters") + original_params.value = original_params.value.apply(parse_csv_values_for_columns_with_mixed_datatypes) + new_params = read_csv_files(resourcefilepath / 'ResourceFile_HIV', files="scaleup_parameters") popsize = 100 @@ -104,10 +107,12 @@ def test_hiv_scale_up(seed): new_params.parameter == "prob_circ_after_hiv_test", "target_value"].values[0] # check malaria parameters unchanged - mal_original_params = pd.read_excel(resourcefilepath / 'malaria' / 'ResourceFile_malaria.xlsx', - sheet_name="parameters") - mal_rdt_testing = pd.read_excel(resourcefilepath / 'malaria' / 'ResourceFile_malaria.xlsx', - sheet_name="WHO_TestData2023") + mal_original_params = read_csv_files(resourcefilepath / 'malaria' / 'ResourceFile_malaria', + files="parameters") + mal_original_params.value = mal_original_params.value.apply(parse_csv_values_for_columns_with_mixed_datatypes) + + mal_rdt_testing = read_csv_files(resourcefilepath / 'malaria' / 'ResourceFile_malaria', + files="WHO_TestData2023") assert sim.modules["Malaria"].parameters["prob_malaria_case_tests"] == mal_original_params.loc[ mal_original_params.parameter_name == "prob_malaria_case_tests", "value"].values[0] @@ -121,8 +126,9 @@ def test_hiv_scale_up(seed): mal_original_params.parameter_name == "itn", "value"].values[0] # check tb parameters unchanged - tb_original_params = pd.read_excel(resourcefilepath / 'ResourceFile_TB.xlsx', sheet_name="parameters") - tb_testing = pd.read_excel(resourcefilepath / 'ResourceFile_TB.xlsx', sheet_name="NTP2019") + tb_original_params = read_csv_files(resourcefilepath / 'ResourceFile_TB', files="parameters") + tb_original_params.value = tb_original_params.value.apply(parse_csv_values_for_columns_with_mixed_datatypes) + tb_testing = read_csv_files(resourcefilepath / 'ResourceFile_TB', files="NTP2019") pd.testing.assert_series_equal(sim.modules["Tb"].parameters["rate_testing_active_tb"]["treatment_coverage"], tb_testing["treatment_coverage"]) @@ -143,8 +149,9 @@ def test_htm_scale_up(seed): and on correct date """ # Load data on HIV prevalence - original_hiv_params = pd.read_excel(resourcefilepath / 'ResourceFile_HIV.xlsx', sheet_name="parameters") - new_hiv_params = pd.read_excel(resourcefilepath / 'ResourceFile_HIV.xlsx', sheet_name="scaleup_parameters") + original_hiv_params = read_csv_files(resourcefilepath / 'ResourceFile_HIV', files="parameters") + original_hiv_params.value = original_hiv_params.value.apply(parse_csv_values_for_columns_with_mixed_datatypes) + new_hiv_params = read_csv_files(resourcefilepath / 'ResourceFile_HIV', files="scaleup_parameters") popsize = 100 @@ -178,8 +185,8 @@ def test_htm_scale_up(seed): new_hiv_params.parameter == "prob_circ_after_hiv_test", "target_value"].values[0] # check malaria parameters changed - new_mal_params = pd.read_excel(resourcefilepath / 'malaria' / 'ResourceFile_malaria.xlsx', - sheet_name="scaleup_parameters") + new_mal_params = read_csv_files(resourcefilepath / 'malaria' / 'ResourceFile_malaria', + files="scaleup_parameters") assert sim.modules["Malaria"].parameters["prob_malaria_case_tests"] == new_mal_params.loc[ new_mal_params.parameter == "prob_malaria_case_tests", "target_value"].values[0] @@ -193,7 +200,8 @@ def test_htm_scale_up(seed): new_mal_params.parameter == "itn", "target_value"].values[0] # check tb parameters changed - new_tb_params = pd.read_excel(resourcefilepath / 'ResourceFile_TB.xlsx', sheet_name="scaleup_parameters") + new_tb_params = read_csv_files(resourcefilepath / 'ResourceFile_TB', files="scaleup_parameters") + new_tb_params.target_value = new_tb_params.target_value.apply(parse_csv_values_for_columns_with_mixed_datatypes) assert sim.modules["Tb"].parameters["rate_testing_active_tb"]["treatment_coverage"].eq(new_tb_params.loc[ new_tb_params.parameter == "tb_treatment_coverage", "target_value"].values[0]).all()