Remove case data from visualisation, reports and READMEs

.github/workflows/README.md

@@ -2,7 +2,7 @@
 
 | Action name                                    | Language   | Scheduled at (UTC time)                                       | Function                                           |
 |------------------------------------------------|------------|----------------------------------------------------------------|----------------------------------------------------|
-| [`ecdc_owid_data.yml`](ecdc_owid_data.yml)                         | R          | [12:07 every day](https://crontab.guru/#7_12_*_*_*)       | Get recorded cases and deaths from ECDC, and hospitalisations from OWID                       |
+| [`ecdc_owid_data.yml`](ecdc_owid_data.yml)                         | R          | [12:07 every day](https://crontab.guru/#7_12_*_*_*)       | Get recorded deaths from ECDC, and hospitalisations from OWID                       |
 | [`check-truth.yml`](check-truth.yml)           | Python & R | [13:00 every day](https://crontab.guru/#0_13_*_*_*)            | Check truth data                   |
 | [`ensemble.yml`](ensemble.yml)                 | R          | [11:15 every Tuesday and Wednesday](https://crontab.guru/#15_11_*_*_2,3)       | Create weekly ensemble                             |
 | [`release.yml`](release.yml) | R | [11:15 every Thursday](https://crontab.guru/#15_11_*_*_4) | Create GitHub release |

README.Rmd

@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
 
 # European COVID-19 Forecast Hub
 
-We are aggregating forecasts of new cases and deaths due to Covid-19 over the next four weeks in countries across Europe and the UK.
+We are aggregating forecasts of new hospitalisations and deaths due to Covid-19 over the next four weeks in countries across Europe and the UK.
 
 ##### Latest forecasts
 
@@ -45,7 +45,7 @@ We require some forecast parameters so that we can compare and ensemble forecast
 
 | Parameter | Description                           |
 |-----------|---------------------------------------|
-| Target    | Cases, hospitalisations and/or deaths |
+| Target    | Hospitalisations and/or deaths |
 | Count     | Incident                              |
 | Geography | EU/EFTA/UK nations (any/all)          |
 | Frequency | Weekly                                |

README.md

@@ -3,26 +3,26 @@
 
 # European COVID-19 Forecast Hub
 
-We are aggregating forecasts of new cases and deaths due to Covid-19
-over the next four weeks in countries across Europe and the UK.
+We are aggregating forecasts of new hospitalisations and deaths due to
+Covid-19 over the next four weeks in countries across Europe and the UK.
 
 ##### Latest forecasts
 
-  - View the [current
-    forecasts](https://covid19forecasthub.eu/visualisation)
-  - We publish a weekly
-    [evaluation](https://covid19forecasthub.eu/reports) of current
-    forecasts
-  - Raw forecast files are in the
-    [data-processed](https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/tree/main/data-processed)
-    folder
+- View the [current
+  forecasts](https://covid19forecasthub.eu/visualisation)
+- We publish a weekly
+  [evaluation](https://covid19forecasthub.eu/reports) of current
+  forecasts
+- Raw forecast files are in the
+  [data-processed](https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/tree/main/data-processed)
+  folder
 
 ##### README contents
 
-  - [Quick start](#quick-start)
-  - [About Covid-19 forecast hubs](#about-covid-19-forecasting-hubs)
-      - [European forecast hub team](#european-forecast-hub-team)
-      - [Data license and reuse](#data-license-and-reuse)
+- [Quick start](#quick-start)
+- [About Covid-19 forecast hubs](#about-covid-19-forecasting-hubs)
+  - [European forecast hub team](#european-forecast-hub-team)
+  - [Data license and reuse](#data-license-and-reuse)
 
 ## Quick start
 
@@ -42,13 +42,13 @@ directory](../../wiki/Creating-a-team-directory) - Add your
 We require some forecast parameters so that we can compare and ensemble
 forecasts. All forecasts should use the following structure:
 
-| Parameter | Description                           |
-| --------- | ------------------------------------- |
-| Target    | Cases, hospitalisations and/or deaths |
-| Count     | Incident                              |
-| Geography | EU/EFTA/UK nations (any/all)          |
-| Frequency | Weekly                                |
-| Horizon   | 1 to 4 weeks                          |
+| Parameter | Description                    |
+|-----------|--------------------------------|
+| Target    | Hospitalisations and/or deaths |
+| Count     | Incident                       |
+| Geography | EU/EFTA/UK nations (any/all)   |
+| Frequency | Weekly                         |
+| Horizon   | 1 to 4 weeks                   |
 
 There is no obligation to submit forecasts for all suggested targets or
 horizons, and it is up to you to decide which you are comfortable
@@ -97,17 +97,17 @@ This effort parallels forecasting hubs in the US and Germany. We follow
 a similar structure and data format, and re-use software provided by the
 ReichLab.
 
-  - The [US COVID-19 Forecast
-    Hub](https://github.com/reichlab/covid19-forecast-hub) is run by the
-    UMass-Amherst Influenza Forecasting Center of Excellence based at
-    the [Reich Lab](https://reichlab.io/).
+- The [US COVID-19 Forecast
+  Hub](https://github.com/reichlab/covid19-forecast-hub) is run by the
+  UMass-Amherst Influenza Forecasting Center of Excellence based at the
+  [Reich Lab](https://reichlab.io/).
 
-  - The [German and Polish COVID-19 Forecast
-    Hub](https://github.com/KITmetricslab/covid19-forecast-hub-de) is
-    run by members of the [Karlsruher Institut für Technologie
-    (KIT)](https://statistik.econ.kit.edu/index.ph) and the
-    [Computational Statistics Group at Heidelberg Institute for
-    Theoretical Studies](https://www.h-its.org/research/cst/).
+- The [German and Polish COVID-19 Forecast
+  Hub](https://github.com/KITmetricslab/covid19-forecast-hub-de) is run
+  by members of the [Karlsruher Institut für Technologie
+  (KIT)](https://statistik.econ.kit.edu/index.ph) and the [Computational
+  Statistics Group at Heidelberg Institute for Theoretical
+  Studies](https://www.h-its.org/research/cst/).
 
 ### European forecast hub team
 
@@ -119,38 +119,38 @@ is now maintained by the ECDC.
 
 Direct contributors to this repository include (in alphabetical order):
 
-  - Daniel Wolffram
-  - Hugo Gruson
-  - Jannik Deuschel
-  - [Johannes
-    Bracher](https://statistik.econ.kit.edu/mitarbeiter_2902.php)
-  - Katharine Sherratt
-  - Nikos Bosse
-  - [Sebastian
-    Funk](https://www.lshtm.ac.uk/aboutus/people/funk.sebastian)
+- Daniel Wolffram
+- Hugo Gruson
+- Jannik Deuschel
+- [Johannes
+  Bracher](https://statistik.econ.kit.edu/mitarbeiter_2902.php)
+- Katharine Sherratt
+- Nikos Bosse
+- [Sebastian
+  Funk](https://www.lshtm.ac.uk/aboutus/people/funk.sebastian)
 
 The [interactive visualization
 tool](https://covid19forecasthub.eu/visualisation/) (code available
 [here](https://github.com/SignaleRKI/forecast-europe)) has been
 developed by the [Signale Team at Robert Koch
-Institute](https://www.rki.de/EN/Content/infections/epidemiology/signals/signals_node.html):
-- Fabian Eckelmann - Knut Perseke - Alexander Ullrich
+Institute](https://www.rki.de/EN/Content/infections/epidemiology/signals/signals_node.html): -
+Fabian Eckelmann - Knut Perseke - Alexander Ullrich
 
 ### Data license and reuse
 
-  - The forecasts assembled in this repository have been created by
-    independent teams. Most provide a license in their respective
-    subfolder of `data-processed`.
-  - Parts of the processing, analysis and validation code have been
-    taken or adapted from the [US Covid-19 forecast
-    hub](https://github.com/reichlab/covid19-forecast-hub) and the
-    [Germany/Poland Covid-19 forecast
-    hub](https://github.com/KITmetricslab/covid19-forecast-hub-de) both
-    under an [MIT
-    license](https://github.com/reichlab/covid19-forecast-hub/blob/master/LICENSE).
-  - All code contained in this repository is under the [MIT
-    license](/LICENSE). **Please get in touch with us to re-use
-    materials from this repository.**
+- The forecasts assembled in this repository have been created by
+  independent teams. Most provide a license in their respective
+  subfolder of `data-processed`.
+- Parts of the processing, analysis and validation code have been taken
+  or adapted from the [US Covid-19 forecast
+  hub](https://github.com/reichlab/covid19-forecast-hub) and the
+  [Germany/Poland Covid-19 forecast
+  hub](https://github.com/KITmetricslab/covid19-forecast-hub-de) both
+  under an [MIT
+  license](https://github.com/reichlab/covid19-forecast-hub/blob/master/LICENSE).
+- All code contained in this repository is under the [MIT
+  license](/LICENSE). **Please get in touch with us to re-use materials
+  from this repository.**
 
 To cite the European Covid-19 Forecast Hub in project in publications,
 please use the following references:
@@ -167,8 +167,9 @@ Data:
 > NA
 
 <details>
-
-<summary>Bibtex</summary>
+<summary>
+Bibtex
+</summary>
 
 ``` bibtex
 NA

code/auto_download/check-revisions-owid-ecdc.r

@@ -9,7 +9,7 @@ library("vroom")
 latest_date <- lubridate::today()
 wday(latest_date) <- EuroForecastHub::get_hub_config("forecast_week_day")
 
-sources <- list(ECDC = c("Cases", "Deaths"), OWID = "Hospitalizations")
+sources <- list(ECDC = c("Deaths"), OWID = "Hospitalizations")
 
 cutoff_days <- 28
 

code/reports/rmdchunks/get-config-vars.Rmd

@@ -12,7 +12,6 @@ countries_hub <- get_hub_config("forecast_locations", config_file = params$confi
 # necessary to add a new target
 target_variables <- c(
   Hospitalisations = "inc hosp",
-  Cases = "inc case", 
   Deaths = "inc death"
 )
 ```

viz/prepare_forecast_data.py

@@ -105,8 +105,6 @@ def createForecastDataItem(row):
     target_type = ''
     if (target == 'inc death'):
         target_type = 'death'
-    elif (target == 'inc case'):
-        target_type = 'cases'
     elif (target == 'inc hosp'):
         target_type = 'hosp'
     else:

viz/prepare_truth_data.R

@@ -8,7 +8,6 @@ library(tidyr)
 # without hardcoding target types
 truth <- c(
   "inc_death" = "ECDC/truth_ECDC-Incident Deaths.csv",
-  "inc_case" = "ECDC/truth_ECDC-Incident Cases.csv",
   "inc_hosp" = "OWID/truncated_OWID-Incident Hospitalizations.csv"
 ) |>
   imap(~ read_csv(here("data-truth", .x)) %>% mutate(name = .y)) |>