Exclude serodata before first reported death

monash-emu · Jul 27, 2023 · 7f8a9d2 · 7f8a9d2
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Showing 3 changed files with 9 additions and 6 deletions.
diff --git a/autumn/projects/sm_covid2/common_school/included_countries.yml b/autumn/projects/sm_covid2/common_school/included_countries.yml
@@ -228,8 +228,6 @@ national_sero:
   ECU: Ecuador
   EGY: Egypt
   ESP: Spain
-  EST: Estonia
-  ETH: Ethiopia
   FRA: France
   GBR: United Kingdom
   HND: Honduras
@@ -247,7 +245,6 @@ national_sero:
   LBN: Lebanon
   LTU: Lithuania
   MEX: Mexico
-  MNG: Mongolia
   MWI: Malawi
   NGA: Nigeria
   NOR: Norway

diff --git a/data/inputs/school-closure/serodata_national.csv b/data/inputs/school-closure/serodata_national.csv
diff --git a/notebooks/user/rragonnet/project_specific/School_Closure/country_inclusion.ipynb b/notebooks/user/rragonnet/project_specific/School_Closure/country_inclusion.ipynb
@@ -318,6 +318,7 @@
    "outputs": [],
    "source": [
     "# Remove estimates where vaccine coverage is too high at the time\n",
+    "# and when survey date is before first reported death\n",
     "max_vacc_seroprev_ratio = .10\n",
     "\n",
     "from datetime import datetime\n",
@@ -331,14 +332,19 @@
     "\n",
     "filtered_sero_data_national[\"low_vaccination\"] = [None] * len(filtered_sero_data_national)\n",
     "\n",
-    "vcc = []\n",
     "for idx in filtered_sero_data_national.index:\n",
+    "    iso3 = filtered_sero_data_national.loc[idx, 'alpha_3_code']\n",
     "    seroprev = filtered_sero_data_national.loc[idx, 'serum_pos_prevalence']\n",
     "    \n",
     "    start_date = datetime.fromisoformat(filtered_sero_data_national.loc[idx, 'sampling_start_date'])\n",
     "    end_date = datetime.fromisoformat(filtered_sero_data_national.loc[idx, 'sampling_end_date'])\n",
     "    midpoint = start_date + (end_date - start_date) / 2  \n",
     "\n",
+    "    first_date_with_death = pd.to_datetime(owid_data[(owid_data[\"iso_code\"] == iso3) & (owid_data[\"new_deaths\"] > 0.)]['date']).min()\n",
+    "    if midpoint <= first_date_with_death:\n",
+    "        print()\n",
+    "        filtered_sero_data_national.loc[idx, \"low_vaccination\"] = False\n",
+    "\n",
     "    if len(vacc_data[(vacc_data[\"iso_code\"] == iso3) & (vacc_data[\"date\"] >= midpoint)]) == 0:\n",
     "        filtered_sero_data_national.loc[idx, \"low_vaccination\"] = False\n",
     "    else:\n",