To run the STH simulation model, import the STH_Simulation() function from the helsim_RUN module in the sth_simulation package.
The STH_Simulation() function requires the following inputs:
paramFileName: str
This is the name of the input text file with the
model parameters.
demogName: str
This is the subset of demography parameters to be
extracted from the Demographies.txt file.
MDAFilePath: str
This is the path to the input CSV file with the
MDA times and with the respective coverage
fractions for each age group.
PrevKKSACFilePath: str
This is the path where the output CSV file with
the simulated PrevKKSAC will be saved.
PrevMHISACFilePath: str
This is the path where the output CSV file with
the simulated PrevMHISAC will be saved.
RkFilePath: str
This is the path to the input CSV file with the
random seed, R0, and k to be used for each simulation.
If not provided, the code will use the parameters
in the input text file.
nYears: int
This is the number of years for which the
simulations will be performed.
outputFrequency: int
This is the number of time points saved down
in the CSV file for each year.
numReps: int
This is the number of simulations. If not provided,
the number of simulations will be inferred from the
input text file or CSV file.
SaveOutput: bool
If True, the last state of the simulations will
be saved in a pickle file. If False, the last
state of the simulations will not be saved.
OutSimFilePath: str
This is the path where the output pickle file with
the last state of the simulations will be saved. It
is only required when SaveOutput = True.
InSimFilePath: str
This is the path where the input pickle file with
the last state of the simulations has been saved.
If this is provided, the code will resume the
previous simulations from this state. If this is
not provided, the code will start new simulations
from scratch.
useCloudStorage: bool
Indicates whether the model should treat incoming
paths as GCS gs:// urls (True) or filesystem paths
(False). If True, use the supplied 'cloudModule' module
to access 'pickled' data in InSimFilePath. Otherwise
load from the filesystem path in InSimFilePath as normal
using pickle.load().
cloudModule: module
Cloud storage access module which provides a function
get_blob( FileUrl ) to access 'pickled' data.
logger: module
Logging module possibly provided by app including this module.
Some examples are included in the Jupyter notebook sth_tests.ipynb in the tests folder.
Install pipenv according to the instructions for your OS, then cd to the project directory and run:
$ pipenv install . # sets up per-project python environment ('env')
$ pipenv shell # starts a per-project shell using that env
(ntd-model-sth) $ python sth_run.py # runs the model