From 1ede071c34536aed68f2655202d71ac833226803 Mon Sep 17 00:00:00 2001 From: GitHub Action - check truth Date: Tue, 18 Jun 2024 13:22:28 +0000 Subject: [PATCH] Check truth data --- code/validation/check_truth.txt | 32 + data-truth/README.md | 19 +- data-truth/plots/Cases.svg | 2008 ++++++++--------- data-truth/plots/Deaths.svg | 1623 +++++++------ data-truth/plots/revisions-Cases.svg | 714 +++--- data-truth/plots/revisions-Deaths.svg | 460 ++-- .../plots/revisions-Hospitalizations.svg | 50 +- 7 files changed, 2412 insertions(+), 2494 deletions(-) diff --git a/code/validation/check_truth.txt b/code/validation/check_truth.txt index 23de09d9e..df43c2de5 100644 --- a/code/validation/check_truth.txt +++ b/code/validation/check_truth.txt @@ -11802,3 +11802,35 @@ Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub- - The following locations are missing: ['Netherlands']. +Latest check of truth data: 2024-06-18 + +WARNING +Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub-europe/data-truth/ECDC/truncated_ECDC-Incident Cases.csv' at 2024-06-08: + +- 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/ECDC/truncated_ECDC-Incident Deaths.csv' at 2024-06-08: + +- The following locations are missing: ['Austria', 'Belgium', 'Croatia', 'Cyprus', '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 2024-06-08: + +- The following locations are missing: ['Croatia', 'Cyprus', '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 2024-06-08: + +- The following locations are missing: ['Austria', 'Belgium', 'Croatia', 'Cyprus', '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/OWID/truncated_OWID-Incident Hospitalizations.csv' at 2024-06-08: + +- The following locations are missing: ['Netherlands']. + +WARNING +Error(s) in '/home/runner/work/covid19-forecast-hub-europe/covid19-forecast-hub-europe/data-truth/OWID/truth_OWID-Incident Hospitalizations.csv' at 2024-06-15: + +- The following locations are missing: ['Netherlands']. + diff --git a/data-truth/README.md b/data-truth/README.md index c76e81ba3..ed7cfef5e 100644 --- a/data-truth/README.md +++ b/data-truth/README.md @@ -69,19 +69,19 @@ indicating data expecting to be substanially revised. ### Cases and deaths - Cases: Austria, Belgium, Bulgaria, Croatia, Cyprus, Czechia, Denmark, - Estonia, Greece, Hungary, Iceland, Ireland, Italy, Latvia, - Liechtenstein, Lithuania, Luxembourg, Malta, Netherlands, Norway, - Poland, Portugal, Romania, Slovakia, Slovenia, Sweden + Estonia, Greece, Hungary, Iceland, Ireland, Italy, Liechtenstein, + Lithuania, Luxembourg, Malta, Netherlands, Norway, Poland, Portugal, + Romania, Slovakia, Slovenia, Sweden - Deaths: Bulgaria, Croatia, Cyprus, Czechia, Denmark, Estonia, Greece, - Ireland, Italy, Latvia, Liechtenstein, Lithuania, Malta, Poland, - Portugal, Romania, Slovakia, Slovenia, Sweden + Ireland, Italy, Liechtenstein, Lithuania, Malta, Poland, Portugal, + Romania, Slovakia, Slovenia, Sweden - **Data warning!** Recent missing data for cases in: Croatia, Cyprus, - Denmark, Italy, and Latvia + Denmark, Estonia, and Italy - **Data warning!** Recent missing data for deaths in: Croatia, Cyprus, - Denmark, Italy, and Latvia + Denmark, Estonia, and Italy We further evaluate forecasts of cases and deaths against data provided [ECDC](https://www.ecdc.europa.eu/), which we recommend using as the @@ -137,11 +137,6 @@ 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? - ## `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 dbff5e91a..2db89ac87 100644 --- a/data-truth/plots/Cases.svg +++ b/data-truth/plots/Cases.svg @@ -24,1378 +24,1238 @@ - - + + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + - - + + - - - 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- - - - + + + + + - - - - - - + + + + + + + @@ -372,22 +386,25 @@ - - - - - + + + + + - - - - - - - - + + + + + + + + + + + @@ -401,22 +418,23 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -453,6 +471,7 @@ + @@ -466,21 +485,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -494,22 +514,23 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -524,22 +545,23 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -576,6 +598,7 @@ + @@ -588,21 +611,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -616,21 +640,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -643,20 +668,21 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -678,21 +704,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -705,19 +732,20 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -731,21 +759,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -758,21 +787,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -1080,46 +1110,46 @@ 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 @@ -1130,26 +1160,26 @@ 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 @@ -1160,41 +1190,41 @@ 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 @@ -1205,11 +1235,11 @@ 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 @@ -1310,19 +1340,21 @@ 40000 60000 80000 -0 -1000 -2000 -3000 -4000 +0 +1000 +2000 +3000 +4000 0 1000 2000 3000 End of MMWR week Cases -Commit date - -2024-06-10 +Commit date + + +2024-06-04 +2024-06-18 diff --git a/data-truth/plots/revisions-Deaths.svg b/data-truth/plots/revisions-Deaths.svg index 1abe1fa73..0a4ad3dbc 100644 --- a/data-truth/plots/revisions-Deaths.svg +++ b/data-truth/plots/revisions-Deaths.svg @@ -45,6 +45,7 @@ + @@ -73,6 +74,7 @@ + @@ -102,6 +104,7 @@ + @@ -130,23 +133,24 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -168,6 +172,7 @@ + @@ -195,7 +200,9 @@ - + + + @@ -223,6 +230,7 @@ + @@ -251,23 +259,24 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -282,23 +291,24 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -313,23 +323,24 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -343,24 +354,27 @@ - - - - - + + + + + - - - - - - - - + + + + + + + + + + + @@ -374,22 +388,23 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -426,6 +441,8 @@ + + @@ -459,6 +476,10 @@ + + + + @@ -472,21 +493,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -500,21 +522,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -551,6 +574,7 @@ + @@ -586,6 +610,7 @@ + @@ -598,21 +623,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -635,21 +661,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -663,21 +690,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -690,21 +718,22 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -719,23 +748,24 @@ - - - - - + + + + + - - - - - - + + + + + + + @@ -1043,42 +1073,42 @@ 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 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 @@ -1089,24 +1119,24 @@ 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 @@ -1117,11 +1147,11 @@ 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 @@ -1130,22 +1160,22 @@ 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 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 @@ -1156,11 +1186,11 @@ 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 @@ -1268,8 +1298,10 @@ 50 End of MMWR week Deaths -Commit date - -2024-06-10 +Commit date + + +2024-06-04 +2024-06-18 diff --git a/data-truth/plots/revisions-Hospitalizations.svg b/data-truth/plots/revisions-Hospitalizations.svg index ef2ef9164..7a15938ee 100644 --- a/data-truth/plots/revisions-Hospitalizations.svg +++ b/data-truth/plots/revisions-Hospitalizations.svg @@ -50,8 +50,9 @@ - - + + + @@ -121,6 +122,7 @@ + @@ -179,26 +181,28 @@ 1500 End of MMWR week Hospitalizations -Commit date - - - - - - - - - - -2024-04-08 -2024-04-15 -2024-04-22 -2024-04-29 -2024-05-06 -2024-05-13 -2024-05-20 -2024-05-27 -2024-06-10 -2024-06-17 +Commit date + + + + + + + + + + + +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 +2024-06-11 +2024-06-18