Commit 4afc60f0 authored by Chris Jewell's avatar Chris Jewell
Browse files

`next_generation_matrix` --> `reproduction_number`

parent 215a0ee0
......@@ -14,7 +14,7 @@ from covid.tasks import (
assemble_data,
mcmc,
thin_posterior,
next_generation_matrix,
reproduction_number,
overall_rt,
predict,
summarize,
......@@ -91,11 +91,11 @@ def run_pipeline(global_config, results_directory, cli_options):
rf.transform(
input=[[process_data, thin_samples]],
filter=rf.formatter(),
output=wd("ngm.nc"),
)(next_generation_matrix)
output=wd("reproduction_number.nc"),
)(reproduction_number)
rf.transform(
input=next_generation_matrix,
input=reproduction_number,
filter=rf.formatter(),
output=wd("national_rt.xlsx"),
)(overall_rt)
......@@ -146,7 +146,7 @@ def run_pipeline(global_config, results_directory, cli_options):
# Summarisation
rf.transform(
input=next_generation_matrix,
input=reproduction_number,
filter=rf.formatter(),
output=wd("rt_summary.csv"),
)(summarize.rt)
......@@ -221,7 +221,7 @@ def run_pipeline(global_config, results_directory, cli_options):
insample7,
insample14,
medium_term,
next_generation_matrix,
reproduction_number,
]
],
rf.formatter(),
......
......@@ -3,7 +3,7 @@
from covid.tasks.assemble_data import assemble_data
from covid.tasks.inference import mcmc
from covid.tasks.thin_posterior import thin_posterior
from covid.tasks.next_generation_matrix import next_generation_matrix
from covid.tasks.next_generation_matrix import reproduction_number
from covid.tasks.overall_rt import overall_rt
from covid.tasks.predict import predict
import covid.tasks.summarize as summarize
......@@ -18,7 +18,7 @@ __all__ = [
"assemble_data",
"mcmc",
"thin_posterior",
"next_generation_matrix",
"reproduction_number",
"overall_rt",
"predict",
"summarize",
......
......@@ -47,7 +47,7 @@ def calc_posterior_rit(samples, initial_state, times, covar_data):
)
def next_generation_matrix(input_files, output_file):
def reproduction_number(input_files, output_file):
covar_data = xarray.open_dataset(input_files[0], group="constant_data")
......@@ -101,4 +101,4 @@ if __name__ == "__main__":
)
args = parser.parse_args()
next_generation_matrix([args.data, args.samples], args.output)
reproduction_number([args.data, args.samples], args.output)
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