`next_generation_matrix` --> `reproduction_number`

covid/ruffus_pipeline.py

@@ -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(),

covid/tasks/__init__.py

@@ -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",

covid/tasks/next_generation_matrix.py

@@ -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)