From d099964f923b1662ef5d30009ac9a8d15a7f5f8f Mon Sep 17 00:00:00 2001 From: GitHub Action - check truth Date: Tue, 4 Jun 2024 13:21:42 +0000 Subject: [PATCH] Check truth data --- code/validation/check_truth.txt | 27 + data-truth/README.md | 11 +- data-truth/plots/Cases.svg | 1007 ++++----- data-truth/plots/Deaths.svg | 1499 +++++++------- data-truth/plots/Hospitalisations.svg | 116 +- data-truth/plots/revisions-Cases.svg | 1515 ++++++-------- data-truth/plots/revisions-Deaths.svg | 1826 ++++++++--------- .../plots/revisions-Hospitalizations.svg | 86 +- 8 files changed, 2880 insertions(+), 3207 deletions(-) diff --git a/code/validation/check_truth.txt b/code/validation/check_truth.txt index 24fcd3865..58190f279 100644 --- a/code/validation/check_truth.txt +++ b/code/validation/check_truth.txt @@ -11414,3 +11414,30 @@ Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub- - The following locations are missing: ['Czechia']. +Latest check of truth data: 2024-06-04 + +WARNING +Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub-europe/data-truth/ECDC/truncated_ECDC-Incident Deaths.csv' at 2024-05-25: + +- The following locations are missing: ['Austria', 'Belgium', 'Croatia', 'Czechia', 'Denmark', 'Estonia', 'Greece', 'Hungary', 'Iceland', 'Ireland', 'Italy', 'Latvia', 'Luxembourg', 'Malta', 'Netherlands', 'Norway', 'Poland', 'Slovakia', 'Slovenia', 'Sweden']. + +WARNING +Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub-europe/data-truth/ECDC/truth_ECDC-Incident Cases.csv' at 2024-05-25: + +- The following locations are missing: ['Croatia', 'Denmark', 'Estonia', 'Italy', 'Latvia']. + +WARNING +Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub-europe/data-truth/ECDC/truth_ECDC-Incident Deaths.csv' at 2024-05-25: + +- The following locations are missing: ['Austria', 'Belgium', 'Croatia', 'Denmark', 'Estonia', 'Hungary', 'Iceland', 'Italy', 'Latvia', 'Luxembourg', 'Netherlands', 'Norway']. + +WARNING +Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub-europe/data-truth/ECDC/truncated_ECDC-Incident Cases.csv' at 2024-05-25: + +- The following locations are missing: ['Belgium', 'Croatia', 'Cyprus', 'Denmark', 'Estonia', 'Italy', 'Latvia', 'Netherlands', 'Norway', 'Slovakia']. + +WARNING +Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub-europe/data-truth/OWID/truncated_OWID-Incident Hospitalizations.csv' at 2024-06-01: + +- The following locations are missing: ['Czechia']. + diff --git a/data-truth/README.md b/data-truth/README.md index 34e305592..4f11de941 100644 --- a/data-truth/README.md +++ b/data-truth/README.md @@ -77,11 +77,11 @@ indicating data expecting to be substanially revised. Hungary, Ireland, Italy, Latvia, Liechtenstein, Lithuania, Malta, Poland, Portugal, Romania, Slovakia, Slovenia, Sweden -- **Data warning!** Recent missing data for cases in: Belgium, Denmark, - Iceland, Latvia, and Luxembourg +- **Data warning!** Recent missing data for cases in: Croatia, Denmark, + Estonia, Italy, and Latvia -- **Data warning!** Recent missing data for deaths in: Denmark, Hungary, - Latvia, and Poland +- **Data warning!** Recent missing data for deaths in: Croatia, Denmark, + Estonia, Hungary, Italy, and Latvia We further evaluate forecasts of cases and deaths against data provided [ECDC](https://www.ecdc.europa.eu/), which we recommend using as the @@ -137,6 +137,9 @@ account the truncation of the data. The latest case/death data is plotted below, with the dashed line indicating data expecting to be substanially revised. + ## `geom_line()`: Each group consists of only one observation. + ## ℹ Do you need to adjust the group aesthetic? + ![Plot of cases](plots/Cases.svg) ![Plot of deaths](plots/Deaths.svg) ## Additional data sources diff --git a/data-truth/plots/Cases.svg b/data-truth/plots/Cases.svg index 9ae7e1514..16d87bc54 100644 --- a/data-truth/plots/Cases.svg +++ b/data-truth/plots/Cases.svg @@ -34,19 +34,19 @@ - - - + + + + - - - - - + + + + @@ -58,20 +58,25 @@ - - - - - - + + + + + + + + + - - - - - - - + + + + + + + + + @@ -87,19 +92,19 @@ - - - + + + + - - - - - - + + + + + @@ -111,24 +116,23 @@ - - - - - - - + + + + + + + + - - - - - - - - - - + + + + + + + + @@ -140,20 +144,23 @@ - - - - - - + + + + + + + + - + + - - - - - + + + + + @@ -165,23 +172,24 @@ - - - - - - - + + + + + + + + - - - - - - - - - + + + + + + + + + @@ -193,22 +201,22 @@ - - - - - - - + + + + + + + + - - - 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- + + - -Bulgaria + +Bulgaria @@ -1252,91 +1080,76 @@ Czechia -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 Apr 2023 Jul 2023 Oct 2023 Jan 2024 Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 Apr 2023 Jul 2023 Oct 2023 @@ -1347,130 +1160,121 @@ Oct 2023 Jan 2024 Apr 2024 -Apr -Jul -Oct -Apr -Jul -Oct -Apr -Jul -Oct -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 Apr 2023 Jul 2023 Oct 2023 Jan 2024 Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 0 5000 10000 15000 -0 -5000 -10000 -15000 -20000 +500 +1000 0 -5 -10 -0 -5000 -10000 -15000 -20000 -0 -2000 -4000 +50 +100 +150 +0 +500 +1000 +1500 +0 +2000 +4000 6000 -0 -10000 -20000 -30000 -40000 -0 -100 -200 -0 -500 -1000 -1500 -2000 -0 -1000 -2000 -3000 -0 -2000 -4000 -6000 -10000 -20000 -30000 -40000 -50000 -0 -20000 -40000 -60000 -80000 -0 -1000 -2000 -3000 -4000 -0 -1000 -2000 -3000 -0 -500 -1000 -1500 -2000 -500 -1000 -1500 -2000 -500 -1000 -0 -50 -100 -150 -0 -500 -1000 -1500 +0 +20 +40 +60 +0 +500 +1000 +1500 +0 +5000 +10000 +0 +2000 +4000 +6000 +0 +1000 +2000 +3000 +0 +1000 +2000 +3000 +4000 +0 +1000 +2000 +3000 +4000 +0 +500 +1000 +1500 +2000 +0 +5000 +10000 +15000 +20000 +0 +5 +10 +0 +5000 +10000 +15000 +20000 0 2500 5000 @@ -1482,17 +1286,18 @@ 400 600 800 -0 -20 -40 -60 -0 -500 -1000 -1500 -0 -5000 -10000 +0 +100 +200 +0 +500 +1000 +1500 +2000 +0 +1000 +2000 +3000 0 10000 20000 @@ -1500,32 +1305,24 @@ 0 1000 2000 -0 -1000 -2000 -3000 -0 -1000 -2000 -3000 -4000 -0 -1000 -2000 -3000 -4000 +0 +20000 +40000 +60000 +80000 +0 +1000 +2000 +3000 +4000 +0 +1000 +2000 +3000 End of MMWR week Cases -Commit date - 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- + + - -Norway + +Romania @@ -976,57 +860,57 @@ -Poland +Slovakia - - + + - -Hungary + +Italy - - + + - -Iceland + +Latvia - - + + - -Ireland + +Liechtenstein - - + + - -Italy + +Lithuania - - + + - -Latvia + +Luxembourg @@ -1036,57 +920,57 @@ -Liechtenstein +Malta - - + + - -Denmark + +Denmark - - + + - -Estonia + +Estonia - - + + - -Finland + +Greece - - + + - -France + +Hungary - - + + - -Germany + +Iceland @@ -1096,57 +980,57 @@ -Greece +Ireland - - + + - -Austria + +Austria - - + + - -Belgium + +Belgium - - + + - -Bulgaria + +Bulgaria - - + + - -Croatia + +Croatia - - + + - -Cyprus + +Cyprus @@ -1159,261 +1043,233 @@ Czechia -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr -Jul -Oct -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr -Jul -Oct -Apr -Jul -Oct -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr -Jul -Oct -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr -Jul -Oct -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr -Jul -Oct -Apr -Jul -Oct -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr +Jul +Oct +Apr +Jul +Oct +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr +Jul +Oct +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr +Jul +Oct +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr +Jul +Oct +Apr +Jul +Oct +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 0 20 40 60 -0 -25 -50 -75 -100 -125 -0.0 -0.5 -1.0 -1.5 -2.0 -0 -50 -100 -150 -200 -0 -1 -2 -3 -0 -100 -200 -300 -400 -0 -5 -10 -15 -0 -50 -100 -150 -200 -250 -0 -20 -40 -0 -100 -200 -0 -100 -200 -300 -400 -0 -10 -20 -30 -40 -50 -0 -5 -10 -15 -20 -25 -0 -50 -100 -150 -200 -0 -5 -10 -15 -0 -2 -4 -6 -0.0 -2.5 -5.0 -7.5 -10.0 -12.5 -0 -20 -40 -0 -5 -10 -15 -2 -4 -6 -0 -10 -20 -30 -10 -20 -30 -40 -50 -0 -30 -60 -90 -0 -5 -10 -15 -20 -25 -0.0 -2.5 -5.0 -7.5 -0 -20 -40 -60 -End of MMWR week +0 +5 +10 +15 +0 +2 +4 +6 +0.0 +2.5 +5.0 +7.5 +10.0 +12.5 +0 +1 +2 +3 +2 +4 +6 +0 +10 +20 +30 +0 +20 +40 +0 +5 +10 +15 +20 +25 +0.0 +2.5 +5.0 +7.5 +0 +20 +40 +60 +0 +5 +10 +15 +20 +25 +0 +25 +50 +75 +100 +125 +0.0 +0.5 +1.0 +1.5 +2.0 +0 +50 +100 +150 +200 +0 +20 +40 +0 +5 +10 +15 +0 +5 +10 +15 +0 +50 +100 +150 +200 +250 +10 +20 +30 +40 +50 +0 +30 +60 +90 +0 +100 +200 +300 +400 +0 +10 +20 +30 +40 +50 +End of MMWR week Deaths -Commit date - - - -2024-04-07 -2024-05-05 -2024-05-26 +Commit date + +2024-06-04 diff --git a/data-truth/plots/revisions-Hospitalizations.svg b/data-truth/plots/revisions-Hospitalizations.svg index 5bb21ead6..7e2d9661d 100644 --- a/data-truth/plots/revisions-Hospitalizations.svg +++ b/data-truth/plots/revisions-Hospitalizations.svg @@ -32,32 +32,32 @@ - - - - - - + + + + + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + @@ -120,16 +120,16 @@ - + - - + + - + - + @@ -162,11 +162,11 @@ Netherlands -Apr 2023 -Jul 2023 -Oct 2023 -Jan 2024 -Apr 2024 +Apr 2023 +Jul 2023 +Oct 2023 +Jan 2024 +Apr 2024 Apr 2023 Jul 2023 Oct 2023 @@ -202,16 +202,16 @@ -2024-03-22 -2024-03-29 -2024-04-05 -2024-04-12 -2024-04-19 -2024-04-26 -2024-05-03 -2024-05-10 -2024-05-17 -2024-05-24 -2024-05-31 +2024-03-26 +2024-04-02 +2024-04-09 +2024-04-16 +2024-04-23 +2024-04-30 +2024-05-07 +2024-05-14 +2024-05-21 +2024-05-28 +2024-06-04