Fixup: Phylogenetic: Add Frequencies

Switch from wide_bandwidth to proportion_wide
Document frequencies parameter choices in the config file

Author: j23414

phylogenetic/defaults/config.yaml

@@ -79,10 +79,12 @@ traits:
   ]
 
 tip_frequencies:
-  min_date: "1980-01-01"
+  # 2000 since there is an increase in WNV at that time
+  min_date: "2000-01-01"
   max_date: "6M"
-  narrow_bandwidth: 0.2
-  wide_bandwidth: 0.6
+  # Quarterly narrow_bandwidth or every 3 months (3 /12.0 = 0.25)
+  narrow_bandwidth: 0.25
+  proportion_wide: 0.0
 
 export:
   description: "defaults/description.md"

phylogenetic/rules/export.smk

@@ -69,7 +69,7 @@ rule tip_frequencies:
         min_date = config["tip_frequencies"]["min_date"],
         max_date = config["tip_frequencies"]["max_date"],
         narrow_bandwidth = config["tip_frequencies"]["narrow_bandwidth"],
-        wide_bandwidth = config["tip_frequencies"]["wide_bandwidth"]
+        proportion_wide = config["tip_frequencies"]["proportion_wide"]
     shell:
         r"""
         augur frequencies \
@@ -80,6 +80,6 @@ rule tip_frequencies:
             --min-date {params.min_date} \
             --max-date {params.max_date} \
             --narrow-bandwidth {params.narrow_bandwidth} \
-            --wide-bandwidth {params.wide_bandwidth} \
+            --proportion-wide {params.proportion_wide} \
             --output {output.tip_freq}
         """