diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml deleted file mode 100644 index 5b7b614c..00000000 --- a/.github/workflows/draft-pdf.yml +++ /dev/null @@ -1,23 +0,0 @@ -on: [push] - -jobs: - paper: - runs-on: ubuntu-latest - name: Paper Draft - steps: - - name: Checkout - uses: actions/checkout@v2 - - name: Build draft PDF - uses: openjournals/openjournals-draft-action@master - with: - journal: joss - # This should be the path to the paper within your repo. - paper-path: inst/paper/paper.md - - name: Upload - uses: actions/upload-artifact@v1 - with: - name: paper - # This is the output path where Pandoc will write the compiled - # PDF. Note, this should be the same directory as the input - # paper.md - path: inst/paper/paper.pdf diff --git a/NEWS.md b/NEWS.md index d1882d93..61e9897b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -11,6 +11,10 @@ This release is currently under development * Updated the package logo to include the newly supported data sets. +## Bug fixes + +- Fixed a bug in the data sourced from Germany so that instead of treating it as a line list of individuals it is treated as a relatively finely resolved count data which needs to be summed up (by @sbfnk). + # covidregionaldata 0.9.2 This release adds support for the Covid19 Data Hub which includes Google and Apple mobility data amongst a large range of other data sets, data from the European Commission's Joint Research Centre which is at both the regional and national level, and individual sources for regional data from several countries. Package updates have been made in line with a software review at the [Journal of Open Source Software](https://github.com/openjournals/joss-reviews/issues/3290). Finally, this release exposes more of the testing infrastructure to users and adds a package hexsticker. diff --git a/R/Germany.R b/R/Germany.R index a4108765..3108357a 100644 --- a/R/Germany.R +++ b/R/Germany.R @@ -94,8 +94,8 @@ Germany <- R6::R6Class("Germany", .data$date ) %>% summarise( - cases_new = as.numeric(sum(.data$cases_new > 0)), - deaths_new = as.numeric(sum(.data$deaths_new > 0)) + cases_new = as.numeric(sum(.data$cases_new)), + deaths_new = as.numeric(sum(.data$deaths_new)) ) %>% ungroup() }, @@ -116,8 +116,8 @@ Germany <- R6::R6Class("Germany", .data$level_2_region, .data$date ) %>% summarise( - cases_new = as.numeric(sum(.data$cases_new > 0)), - deaths_new = as.numeric(sum(.data$deaths_new > 0)) + cases_new = as.numeric(sum(.data$cases_new)), + deaths_new = as.numeric(sum(.data$deaths_new)) ) %>% ungroup() } diff --git a/README.Rmd b/README.Rmd index 6dac1dd8..feac3205 100644 --- a/README.Rmd +++ b/README.Rmd @@ -11,11 +11,11 @@ knitr::opts_chunk$set( ) ``` -# Subnational data for the COVID-19 outbreak +# Subnational data for the COVID-19 outbreak [![R-CMD-check](https://github.com/epiforecasts/covidregionaldata/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/covidregionaldata/actions) [![Codecov test coverage](https://codecov.io/gh/epiforecasts/covidregionaldata/branch/master/graph/badge.svg)](https://codecov.io/gh/epiforecasts/covidregionaldata?branch=master) [![Data status](https://img.shields.io/badge/Data-status-lightblue.svg?style=flat)](https://epiforecasts.io/covidregionaldata/articles/supported-countries.html) [![metacran downloads](http://cranlogs.r-pkg.org/badges/grand-total/covidregionaldata?color=ff69b4)](https://cran.r-project.org/package=covidregionaldata) -[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epiforecasts/covidregionaldata/blob/master/LICENSE.md/) [![GitHub contributors](https://img.shields.io/github/contributors/epiforecasts/covidregionaldata)](https://github.com/epiforecasts/covidregionaldata/graphs/contributors) [![Discord](https://img.shields.io/discord/864828485981306890?logo=Discord)](https://discord.gg/9YPDDADVt3) [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-yellow.svg)](https://makeapullrequest.com/) [![GitHub commits](https://img.shields.io/github/commits-since/epiforecasts/covidregionaldata/0.9.2.svg?color=orange)](https://GitHub.com/epiforecasts/covidregionaldata/commit/master/) +[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epiforecasts/covidregionaldata/blob/master/LICENSE.md/) [![GitHub contributors](https://img.shields.io/github/contributors/epiforecasts/covidregionaldata)](https://github.com/epiforecasts/covidregionaldata/graphs/contributors) [![Discord](https://img.shields.io/discord/864828485981306890?logo=Discord)](https://discord.gg/9YPDDADVt3) [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-yellow.svg)](https://makeapullrequest.com/) [![GitHub commits](https://img.shields.io/github/commits-since/epiforecasts/covidregionaldata/0.9.2.svg?color=orange)](https://GitHub.com/epiforecasts/covidregionaldata/commit/master/) [![JOSS](https://joss.theoj.org/papers/10.21105/joss.03290/status.svg)](https://doi.org/10.21105/joss.03290) [![Zenodo](https://zenodo.org/badge/271601189.svg)](https://zenodo.org/badge/latestdoi/271601189) diff --git a/README.md b/README.md index b452cac6..537bfece 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ -# Subnational data for the COVID-19 outbreak +# Subnational data for the COVID-19 outbreak [![R-CMD-check](https://github.com/epiforecasts/covidregionaldata/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/covidregionaldata/actions) [![Codecov test @@ -118,18 +118,18 @@ nots <- get_national_data() #> Processing data nots #> # A tibble: 142,911 × 15 -#> date un_region who_region country iso_code cases_new cases_total -#> -#> 1 2020-01-03 Asia EMRO Afghanistan AF 0 0 -#> 2 2020-01-03 Europe EURO Albania AL 0 0 -#> 3 2020-01-03 Africa AFRO Algeria DZ 0 0 -#> 4 2020-01-03 Oceania WPRO American Samoa AS 0 0 -#> 5 2020-01-03 Europe EURO Andorra AD 0 0 -#> 6 2020-01-03 Africa AFRO Angola AO 0 0 -#> 7 2020-01-03 Americas AMRO Anguilla AI 0 0 +#> date un_region who_region country iso_code cases_new cases_total +#> +#> 1 2020-01-03 Asia EMRO Afghanistan AF 0 0 +#> 2 2020-01-03 Europe EURO Albania AL 0 0 +#> 3 2020-01-03 Africa AFRO Algeria DZ 0 0 +#> 4 2020-01-03 Oceania WPRO American Samoa AS 0 0 +#> 5 2020-01-03 Europe EURO Andorra AD 0 0 +#> 6 2020-01-03 Africa AFRO Angola AO 0 0 +#> 7 2020-01-03 Americas AMRO Anguilla AI 0 0 #> 8 2020-01-03 Americas AMRO Antigua & Barbuda AG 0 0 -#> 9 2020-01-03 Americas AMRO Argentina AR 0 0 -#> 10 2020-01-03 Asia EURO Armenia AM 0 0 +#> 9 2020-01-03 Americas AMRO Argentina AR 0 0 +#> 10 2020-01-03 Asia EURO Armenia AM 0 0 #> # … with 142,901 more rows, and 8 more variables: deaths_new , #> # deaths_total , recovered_new , recovered_total , #> # hosp_new , hosp_total , tested_new , tested_total diff --git a/_pkgdown.yml b/_pkgdown.yml index 881c72f3..27a7fa1e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,5 +1,6 @@ url: epiforecasts.io/covidregionaldata/ template: + bootstrap: 5 params: bootswatch: lumen docsearch: