From 45fd35a855ca2cb95fc77c5185359397592818ce Mon Sep 17 00:00:00 2001 From: Sebastian Funk Date: Fri, 8 Dec 2023 15:50:15 +0000 Subject: [PATCH] Remove case data from visualisation, reports and READMEs --- .github/workflows/README.md | 2 +- README.Rmd | 4 +- README.md | 115 +++++++++--------- .../auto_download/check-revisions-owid-ecdc.r | 2 +- code/reports/rmdchunks/get-config-vars.Rmd | 1 - viz/prepare_forecast_data.py | 2 - viz/prepare_truth_data.R | 1 - 7 files changed, 62 insertions(+), 65 deletions(-) diff --git a/.github/workflows/README.md b/.github/workflows/README.md index c99c631156..cbbbf07832 100644 --- a/.github/workflows/README.md +++ b/.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 | diff --git a/README.Rmd b/README.Rmd index 06eaf36598..e79e6c8ba5 100644 --- a/README.Rmd +++ b/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 | diff --git a/README.md b/README.md index def47e06e8..58c8ac8ca8 100644 --- a/README.md +++ b/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
- -Bibtex + +Bibtex + ``` bibtex NA diff --git a/code/auto_download/check-revisions-owid-ecdc.r b/code/auto_download/check-revisions-owid-ecdc.r index 4a747cd9e2..125384f768 100644 --- a/code/auto_download/check-revisions-owid-ecdc.r +++ b/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 diff --git a/code/reports/rmdchunks/get-config-vars.Rmd b/code/reports/rmdchunks/get-config-vars.Rmd index 6bb81226bd..c5864117ee 100644 --- a/code/reports/rmdchunks/get-config-vars.Rmd +++ b/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" ) ``` diff --git a/viz/prepare_forecast_data.py b/viz/prepare_forecast_data.py index 9fb83f92ee..d5077c6bc7 100644 --- a/viz/prepare_forecast_data.py +++ b/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: diff --git a/viz/prepare_truth_data.R b/viz/prepare_truth_data.R index 2fcc91479f..54907c54da 100644 --- a/viz/prepare_truth_data.R +++ b/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)) |>