outbreaks(mpox-2024): add number of countries

src/obr/outbreaks/__init__.py

@@ -4,6 +4,8 @@
 
 from ..plots import (
     get_counts,
+    get_countries_with_status,
+    get_countries_with_anyof_statuses,
     plot_epicurve,
     plot_timeseries_location_status,
     plot_age_gender,
@@ -50,14 +52,25 @@
 ]
 
 outbreak_mpox_2024 = [
-    ("data", get_counts, dict(date_col="Date_entry")),
+    ("data", get_counts, {"date_col": "Date_entry"}),
+    (
+        "data",
+        get_countries_with_status,
+        {"country_col": "Location_Admin0", "statuses": ["confirmed", "suspected"]},
+    ),
+    (
+        "data",
+        get_countries_with_anyof_statuses,
+        {"country_col": "Location_Admin0", "statuses": ["confirmed", "suspected"]},
+    ),
     (
         "figure/epicurve_source_report",
         plot_epicurve,
         {
             "title": "Date of report in primary source",
             "date_col": "Source_I_Date report",
             "groupby_col": "Case_status",
+            "values": ["confirmed", "suspected"],
         },
     ),
     (

src/obr/outbreaks/mpox-2024.html

@@ -43,6 +43,9 @@ <h2>Summary</h2>
             suspected cases as of {{ date }}
         </p>
 
+        <p>The Mpox 2024 outbreak has been detected in {{ n_countries_confirmed_or_suspected }} countries, with
+            either confirmed or suspected cases</p>.
+
         <figure>
 
             {{{ epicurve_source_report }}}
@@ -81,6 +84,8 @@ <h2>Summary</h2>
             used in this report are available from our data repository Should you identify any issues or have questions please
             raise an issue on <a href="https://github.com/globaldothealth/outbreak-data">GitHub</a> or write to
             us: <a href="mailto:[email protected]">[email protected]</a>.</p>
+            If you cite this report, please also cite the relevant sources, which are
+            mentioned in our <a href="https://github.com/globaldothealth/outbreak-data/wiki/GHL2024.D11.1E71">outbreak information page</a>.
 
     </main>
 </body>

tests/test_status_data.csv

@@ -0,0 +1,9 @@
+ID,Country,Case_status
+1,Antarctica,confirmed
+2,Antarctica,suspected
+3,Atlantis,confirmed
+4,Atlantis,confirmed
+5,Atlantis,confirmed
+6,Midgard,suspected
+7,Midgard,suspected
+8,Isengard,probable