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b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test.csv new file mode 100644 index 0000000000..02d1286257 --- /dev/null +++ b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/Test.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:79d1805d9389115bbd2a32296b6e81e4ae5f8465e4ef11b0708400e4e3f85407 +size 3501 diff --git a/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/VerticalProgrammes.csv b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/VerticalProgrammes.csv new file mode 100644 index 0000000000..1df2416902 --- /dev/null +++ b/resources/healthsystem/priority_policies/ResourceFile_PriorityRanking_ALLPOLICIES/VerticalProgrammes.csv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:419b8f59fe5bd8cbcc212c4b5425c42a7d1172416cd3488c81a3533c84092e2b +size 3499 diff --git a/src/tlo/methods/healthsystem.py b/src/tlo/methods/healthsystem.py index a8ad554a40..0ce5c3a6c1 100644 --- a/src/tlo/methods/healthsystem.py +++ b/src/tlo/methods/healthsystem.py @@ -36,6 +36,7 @@ HSIEventQueueItem, HSIEventWrapper, ) +from tlo.util import read_csv_files logger = logging.getLogger(__name__) logger.setLevel(logging.INFO) @@ -581,16 +582,16 @@ def read_parameters(self, data_folder): # Data on the priority of each Treatment_ID that should be adopted in the queueing system according to different # priority policies. Load all policies at this stage, and decide later which one to adopt. - self.parameters['priority_rank'] = pd.read_excel(path_to_resourcefiles_for_healthsystem / 'priority_policies' / - 'ResourceFile_PriorityRanking_ALLPOLICIES.xlsx', - sheet_name=None) + self.parameters['priority_rank'] = read_csv_files(path_to_resourcefiles_for_healthsystem / 'priority_policies' / + 'ResourceFile_PriorityRanking_ALLPOLICIES', + files=None) - self.parameters['HR_scaling_by_level_and_officer_type_table']: Dict = pd.read_excel( + self.parameters['HR_scaling_by_level_and_officer_type_table']: Dict = read_csv_files( path_to_resourcefiles_for_healthsystem / "human_resources" / "scaling_capabilities" / - "ResourceFile_HR_scaling_by_level_and_officer_type.xlsx", - sheet_name=None # all sheets read in + "ResourceFile_HR_scaling_by_level_and_officer_type", + files=None # all sheets read in ) # Ensure the mode of HR scaling to be considered in included in the tables loaded assert (self.parameters['HR_scaling_by_level_and_officer_type_mode'] in @@ -598,23 +599,23 @@ def read_parameters(self, data_folder): (f"Value of `HR_scaling_by_level_and_officer_type_mode` not recognised: " f"{self.parameters['HR_scaling_by_level_and_officer_type_mode']}") - self.parameters['HR_scaling_by_district_table']: Dict = pd.read_excel( + self.parameters['HR_scaling_by_district_table']: Dict = read_csv_files( path_to_resourcefiles_for_healthsystem / "human_resources" / "scaling_capabilities" / - "ResourceFile_HR_scaling_by_district.xlsx", - sheet_name=None # all sheets read in + "ResourceFile_HR_scaling_by_district", + files=None # all sheets read in ) # Ensure the mode of HR scaling by district to be considered in included in the tables loaded assert self.parameters['HR_scaling_by_district_mode'] in self.parameters['HR_scaling_by_district_table'], \ f"Value of `HR_scaling_by_district_mode` not recognised: {self.parameters['HR_scaling_by_district_mode']}" - self.parameters['yearly_HR_scaling']: Dict = pd.read_excel( + self.parameters['yearly_HR_scaling']: Dict = read_csv_files( path_to_resourcefiles_for_healthsystem / "human_resources" / "scaling_capabilities" / - "ResourceFile_dynamic_HR_scaling.xlsx", - sheet_name=None, # all sheets read in + "ResourceFile_dynamic_HR_scaling", + files=None, # all sheets read in dtype={ 'year': int, 'dynamic_HR_scaling_factor': float, @@ -961,7 +962,7 @@ def format_daily_capabilities(self, use_funded_or_actual_staffing: str) -> tuple self.parameters[f'Daily_Capabilities_{use_funded_or_actual_staffing}'] ) capabilities = capabilities.rename(columns={'Officer_Category': 'Officer_Type_Code'}) # neaten - + # Create new column where capabilities per staff are computed capabilities['Mins_Per_Day_Per_Staff'] = capabilities['Total_Mins_Per_Day']/capabilities['Staff_Count'] @@ -984,10 +985,10 @@ def format_daily_capabilities(self, use_funded_or_actual_staffing: str) -> tuple # Merge in information about facility from Master Facilities List mfl = self.parameters['Master_Facilities_List'] capabilities_ex = capabilities_ex.merge(mfl, on='Facility_ID', how='left') - + # Create a copy of this to store staff counts capabilities_per_staff_ex = capabilities_ex.copy() - + # Merge in information about officers # officer_types = self.parameters['Officer_Types_Table'][['Officer_Type_Code', 'Officer_Type']] # capabilities_ex = capabilities_ex.merge(officer_types, on='Officer_Type_Code', how='left') @@ -1000,7 +1001,7 @@ def format_daily_capabilities(self, use_funded_or_actual_staffing: str) -> tuple how='left', ) capabilities_ex = capabilities_ex.fillna(0) - + capabilities_per_staff_ex = capabilities_per_staff_ex.merge( capabilities[['Facility_ID', 'Officer_Type_Code', 'Mins_Per_Day_Per_Staff']], on=['Facility_ID', 'Officer_Type_Code'], @@ -1015,7 +1016,7 @@ def format_daily_capabilities(self, use_funded_or_actual_staffing: str) -> tuple + '_Officer_' + capabilities_ex['Officer_Type_Code'] ) - + # Give the standard index: capabilities_per_staff_ex = capabilities_per_staff_ex.set_index( 'FacilityID_' @@ -1055,7 +1056,7 @@ def _rescale_capabilities_to_capture_effective_capability(self): ) if rescaling_factor > 1 and rescaling_factor != float("inf"): self._daily_capabilities[officer] *= rescaling_factor - + # We assume that increased daily capabilities is a result of each staff performing more # daily patient facing time per day than contracted (or equivalently performing appts more # efficiently).