Small updates

diff --git a/covid_summary.md b/covid_summary.md
index edc961ec98261311089ffb852ac3b1d49b11e4e4..c7b1620e2de249b75fbc6d35aa8fedec0bc5a22b 100644 (file)
--- a/covid_summary.md
+++ b/covid_summary.md
@@ -1,20 +1,20 @@
 % Covid death data summary
 % Neil Smith
-% Created on 2021-02-21
+% Created on 2021-03-11
 
-> Last UK data from 20 Feb 2021.  Last international data from 14 Feb 2021.
+> Last UK data from 11 Mar 2021.  Last international data from 07 Mar 2021.
 
 ## Headlines (UK data)
 
 | []() | |
 |:---|---:|
-| Deaths reported so far | 120387 | 
-| Deaths in last 30 days | 25785 | 
-| Cases in last 30 days  | 480504 | 
+| Deaths reported so far | 125168 | 
+| Deaths in last 30 days | 11147 | 
+| Cases in last 30 days  | 237470 | 
 
 ## International comparison
 
-Based on weekly data. Last data from 14 Feb 2021
+Based on weekly data. Last data from 07 Mar 2021
 
 ### Total deaths
 
@@ -22,13 +22,13 @@ Based on weekly data. Last data from 14 Feb 2021
 
 | Country ID | Country name | Total deaths |
 |:-----------|:-------------|-------------:|
-| BEL | Belgium | 21720 |
-| DEU | Germany | 65076 |
-| ESP | Spain | 65449 |
-| FRA | France | 81814 |
-| GBR | United Kingdom | 117166 |
-| IRL | Ireland | 3948 |
-| ITA | Italy | 93577 |
+| BEL | Belgium | 22287 |
+| DEU | Germany | 71934 |
+| ESP | Spain | 71436 |
+| FRA | France | 88600 |
+| GBR | United Kingdom | 124501 |
+| IRL | Ireland | 4422 |
+| ITA | Italy | 99785 |
 
 ### Deaths per week
 
@@ -40,13 +40,13 @@ Based on weekly data. Last data from 14 Feb 2021
 
 ### Total deaths
 
-Deaths reported up to 20 Feb 2021: 120387
+Deaths reported up to 11 Mar 2021: 125168
 
 ![Total deaths](cases_and_deaths.png)
 
 ![Cases and deaths in last 60 days](cases_and_deaths_last_60_days.png)
 
-![Deaths compared to past five years](deaths-radar-2021.png)
+![Deaths compared to past five years](deaths_radar_2021.png)
 
 ### Hospital care
 Based on a 7-day moving average

diff --git a/data_import.py b/data_import.py
index 8ec03d13d550e6ce90f8bcaf69a54a939d5c36e3..833a6eb443a5c1bd41d6c009c339848350bf0f75 100644 (file)
--- a/data_import.py
+++ b/data_import.py
@@ -171,6 +171,7 @@ uk_query_string = (
 "metric=newCasesBySpecimenDate&"
 "metric=hospitalCases&"
 "metric=newDeaths28DaysByPublishDate&"
+"metric=cumDeaths28DaysByPublishDate&"
 "format=csv"
 )
 
@@ -210,6 +211,7 @@ uk_data.rename(
         'newCasesBySpecimenDate': 'new_cases',
         'hospitalCases': 'hospital_cases', 
         'newDeaths28DaysByPublishDate': 'new_deaths',
+        'cumDeaths28DaysByPublishDate': 'cum_deaths',
         'newAdmissions': 'new_admissions',
         'newPCRTestsByPublishDate': 'new_pcr_tests',
         'newTestsByPublishDate': 'new_tests',
@@ -221,6 +223,7 @@ uk_data.rename(
 uk_data[['date', 
          'hospital_cases', 'ventilator_beds',
          'new_cases', 'new_deaths', 
+         'cum_deaths',
          'hospital_cases', 'new_admissions',
          'new_pcr_tests', 'new_tests', 'new_pillar_1_2_tests'
         ]].to_sql(
@@ -236,6 +239,7 @@ uk_data[['date',
         "new_cases": Integer,
         "hospital_cases": Integer,
         "new_deaths": Integer,
+        "cum_deaths": Integer,
         "new_admissions": Integer,
         'new_pcr_tests': Integer, 
         'new_tests': Integer, 
@@ -305,3 +309,5 @@ insert into uk_data_7(date,
 with engine.connect() as connection:
     connection.execute(query_string)
 
+
+# %%

diff --git a/publish.py b/publish.py
index 8dd4b0d4da946baad0372de1495afa5ff3add313..d60a7ef7e4d7220327317d4faeec6d0a8a9f16bd 100644 (file)
--- a/publish.py
+++ b/publish.py
@@ -52,7 +52,9 @@ thirty_days_ago = last_uk_date - datetime.timedelta(days=30)
 
 
 # %%
-total_uk_deaths = singleton_sql_value(engine, 'select sum(new_deaths) from uk_data')
+# total_uk_deaths = singleton_sql_value(engine, 'select (cum_deaths) from uk_data')
+total_uk_deaths = singleton_sql_value(engine, 
+                                      'select cum_deaths from uk_data where cum_deaths > 0 order by date desc limit 1')
 deaths_in_past_month = singleton_sql_value(engine, f"select sum(new_deaths) from uk_data where date > '{thirty_days_ago.isoformat()}'")
 cases_in_past_month = singleton_sql_value(engine, f"select sum(new_cases) from uk_data where date > '{thirty_days_ago.isoformat()}'")
 total_uk_deaths, deaths_in_past_month, cases_in_past_month
@@ -132,7 +134,7 @@ with open('covid_summary.md', 'a') as f:
     f.write('\n')    
     f.write('![Cases and deaths in last 60 days](cases_and_deaths_last_60_days.png)\n')
     f.write('\n')
-    f.write('![Deaths compared to past five years](deaths-radar-2021.png)\n')
+    f.write('![Deaths compared to past five years](deaths_radar_2021.png)\n')
     f.write('\n')
 
 # %%

diff --git a/uk_deaths_import.md b/uk_deaths_import.md
index 612783c9d629b396cdf8d7372c009d0cd503b70f..baa5ae6647cd89cafbd6388149c1e8920e9cf400 100644 (file)
--- a/uk_deaths_import.md
+++ b/uk_deaths_import.md
@@ -52,16 +52,20 @@ connection_string = 'postgresql://covid:3NbjJTkT63@localhost/covid'
 engine = create_engine(connection_string)
 ```
 
+```python
+!ls uk-deaths-data/publishedweek*2021*xlsx
+```
+
 ```python Collapsed="false"
-england_wales_filename = 'uk-deaths-data/publishedweek052021.xlsx'
+england_wales_filename = 'uk-deaths-data/publishedweek082021.xlsx'
 ```
 
 ```python Collapsed="false"
-scotland_filename = 'uk-deaths-data/Scottish Government COVID-19 data (15 February 2021).xlsx'
+scotland_filename = 'uk-deaths-data/Scottish Government COVID-19 data (10 March 2021).xlsx'
 ```
 
 ```python
-n_ireland_filename = 'uk-deaths-data/Weekly_Deaths_0.xlsx'
+n_ireland_filename = 'uk-deaths-data/Weekly_Deaths.xlsx'
 ```
 
 ```python Collapsed="false"
@@ -136,7 +140,7 @@ rd.to_sql(
 ```
 
 ```python
-%sql select * from all_causes_deaths where year = 2021 limit 10
+%sql select * from all_causes_deaths where year = 2021 order by date_up_to desc limit 10
 ```
 
 ```python