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Convert Excel files to CSV - Cardiometabolic disorders (#1570)
* convert to .csv file format * use read_csv_files method to read the newly converted csv files * deleting info.csv files as we are not using them in the model
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‎src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py

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@@ -23,6 +23,7 @@
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simplified_births,
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symptommanager,
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)
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from tlo.util import read_csv_files
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# %%
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resourcefilepath = Path("./resources")
@@ -189,7 +190,7 @@ def convert_output(output_path):
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)
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# get prevalence + lower and upper values
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prev_range = pd.read_excel(resourcefilepath / "cmd" / "ResourceFile_cmd_condition_prevalence.xlsx", sheet_name=None)
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prev_range = read_csv_files(resourcefilepath / "cmd" / "ResourceFile_cmd_condition_prevalence", files=None)
193194
baseline_error = [(prev_range[f'{condition}']['value'].values - prev_range[f'{condition}']['lower'].values),
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(prev_range[f'{condition}']['upper'].values - prev_range[f'{condition}']['value'].values)]
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if 'gbd_value' in prev_range[f'{condition}']:
@@ -494,10 +495,10 @@ def make_incidence_plot(condition, type):
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condition_title = condition_title.title()
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if type == 'incidence':
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inc_range = pd.read_excel(resourcefilepath / "cmd" / f"ResourceFile_cmd_condition_and_events_{type}.xlsx",
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sheet_name=None)
498+
inc_range = read_csv_files(resourcefilepath / "cmd" / f"ResourceFile_cmd_condition_and_events_{type}",
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files=None)
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else:
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inc_range = pd.read_excel(resourcefilepath / "cmd" / f"ResourceFile_cmd_event_{type}.xlsx", sheet_name=None)
501+
inc_range = read_csv_files(resourcefilepath / "cmd" / f"ResourceFile_cmd_event_{type}", files=None)
501502
asymptomatic_error = [(inc_range[f'{condition}']['value'].values - inc_range[f'{condition}']['lower'].values),
502503
(inc_range[f'{condition}']['upper'].values - inc_range[f'{condition}']['value'].values)]
503504

‎src/scripts/schistosomiasis/schisto_calibration_check.py

+3-2
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@
2323
simplified_births,
2424
symptommanager,
2525
)
26+
from tlo.util import read_csv_files
2627

2728
resourcefilepath = Path("./resources")
2829
outputpath = Path("./outputs")
@@ -105,8 +106,8 @@ def get_model_prevalence_by_district(spec: str):
105106

106107
def get_expected_prevalence_by_district(species: str):
107108
"""Get the prevalence of a particular species from the data (which is for year 2010/2011)."""
108-
expected_district_prevalence = pd.read_excel(resourcefilepath / 'ResourceFile_Schisto.xlsx',
109-
sheet_name='District_Params_' + species.lower())
109+
expected_district_prevalence = read_csv_files(resourcefilepath / 'ResourceFile_Schisto',
110+
files='District_Params_' + species.lower())
110111
expected_district_prevalence.set_index("District", inplace=True)
111112
expected_district_prevalence = expected_district_prevalence.loc[:, 'Prevalence'].to_dict()
112113
return expected_district_prevalence

‎src/tlo/methods/cardio_metabolic_disorders.py

+25-24
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@
3030
from tlo.methods.hsi_event import HSI_Event
3131
from tlo.methods.hsi_generic_first_appts import GenericFirstAppointmentsMixin
3232
from tlo.methods.symptommanager import Symptom
33-
from tlo.util import random_date
33+
from tlo.util import random_date, read_csv_files
3434

3535
if TYPE_CHECKING:
3636
from tlo.methods.hsi_generic_first_appts import HSIEventScheduler
@@ -259,32 +259,33 @@ def __init__(self, name=None, resourcefilepath=None, do_log_df: bool = False, do
259259
def read_parameters(self, data_folder):
260260
"""Read parameter values from files for condition onset, removal, deaths, and initial prevalence.
261261

262-
ResourceFile_cmd_condition_onset.xlsx = parameters for onset of conditions
263-
ResourceFile_cmd_condition_removal.xlsx = parameters for removal of conditions
264-
ResourceFile_cmd_condition_death.xlsx = parameters for death rate from conditions
265-
ResourceFile_cmd_condition_prevalence.xlsx = initial and target prevalence for conditions
266-
ResourceFile_cmd_condition_symptoms.xlsx = symptoms for conditions
267-
ResourceFile_cmd_condition_hsi.xlsx = HSI parameters for conditions
268-
ResourceFile_cmd_condition_testing.xlsx = community testing parameters for conditions (currently only
269-
hypertension)
270-
ResourceFile_cmd_events.xlsx = parameters for occurrence of events
271-
ResourceFile_cmd_events_death.xlsx = parameters for death rate from events
272-
ResourceFile_cmd_events_symptoms.xlsx = symptoms for events
273-
ResourceFile_cmd_events_hsi.xlsx = HSI parameters for events
262+
Folders
263+
ResourceFile_cmd_condition_onset = parameters for onset of conditions
264+
ResourceFile_cmd_condition_removal = parameters for removal of conditions
265+
ResourceFile_cmd_condition_death = parameters for death rate from conditions
266+
ResourceFile_cmd_condition_prevalence = initial and target prevalence for conditions
267+
ResourceFile_cmd_condition_symptoms = symptoms for conditions
268+
ResourceFile_cmd_condition_hsi = HSI parameters for conditions
269+
ResourceFile_cmd_condition_testing = community testing parameters for conditions (currently only
270+
hypertension)
271+
ResourceFile_cmd_events = parameters for occurrence of events
272+
ResourceFile_cmd_events_death = parameters for death rate from events
273+
ResourceFile_cmd_events_symptoms = symptoms for events
274+
ResourceFile_cmd_events_hsi = HSI parameters for events
274275

275276
"""
276277
cmd_path = Path(self.resourcefilepath) / "cmd"
277-
cond_onset = pd.read_excel(cmd_path / "ResourceFile_cmd_condition_onset.xlsx", sheet_name=None)
278-
cond_removal = pd.read_excel(cmd_path / "ResourceFile_cmd_condition_removal.xlsx", sheet_name=None)
279-
cond_death = pd.read_excel(cmd_path / "ResourceFile_cmd_condition_death.xlsx", sheet_name=None)
280-
cond_prevalence = pd.read_excel(cmd_path / "ResourceFile_cmd_condition_prevalence.xlsx", sheet_name=None)
281-
cond_symptoms = pd.read_excel(cmd_path / "ResourceFile_cmd_condition_symptoms.xlsx", sheet_name=None)
282-
cond_hsi = pd.read_excel(cmd_path / "ResourceFile_cmd_condition_hsi.xlsx", sheet_name=None)
283-
cond_testing = pd.read_excel(cmd_path / "ResourceFile_cmd_condition_testing.xlsx", sheet_name=None)
284-
events_onset = pd.read_excel(cmd_path / "ResourceFile_cmd_events.xlsx", sheet_name=None)
285-
events_death = pd.read_excel(cmd_path / "ResourceFile_cmd_events_death.xlsx", sheet_name=None)
286-
events_symptoms = pd.read_excel(cmd_path / "ResourceFile_cmd_events_symptoms.xlsx", sheet_name=None)
287-
events_hsi = pd.read_excel(cmd_path / "ResourceFile_cmd_events_hsi.xlsx", sheet_name=None)
278+
cond_onset = read_csv_files(cmd_path / "ResourceFile_cmd_condition_onset", files=None)
279+
cond_removal = read_csv_files(cmd_path / "ResourceFile_cmd_condition_removal", files=None)
280+
cond_death = read_csv_files(cmd_path / "ResourceFile_cmd_condition_death", files=None)
281+
cond_prevalence = read_csv_files(cmd_path / "ResourceFile_cmd_condition_prevalence", files=None)
282+
cond_symptoms = read_csv_files(cmd_path / "ResourceFile_cmd_condition_symptoms", files=None)
283+
cond_hsi = read_csv_files(cmd_path / "ResourceFile_cmd_condition_hsi", files=None)
284+
cond_testing = read_csv_files(cmd_path / "ResourceFile_cmd_condition_testing", files=None)
285+
events_onset = read_csv_files(cmd_path / "ResourceFile_cmd_events", files=None)
286+
events_death = read_csv_files(cmd_path / "ResourceFile_cmd_events_death", files=None)
287+
events_symptoms = read_csv_files(cmd_path / "ResourceFile_cmd_events_symptoms", files=None)
288+
events_hsi = read_csv_files(cmd_path / "ResourceFile_cmd_events_hsi", files=None)
288289

289290
self.load_parameters_from_dataframe(pd.read_csv(cmd_path / "ResourceFile_cmd_parameters.csv"))
290291

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