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commit 04009e7
Merge: d1630f5 68200f9
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 14:27:05 2021 +0000

    Merge pull request epiforecasts#443 from epiforecasts/feature-boostrap-5-in-docs

    Switch to bootstrap 5 for pkgdown

commit 68200f9
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 13:52:07 2021 +0000

    switch to bootstrap 5 for pkgdown

commit d1630f5
Merge: 71d7b1f ddbdb8e
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 13:48:12 2021 +0000

    Merge pull request epiforecasts#442 from epiforecasts/fix-logo

    Fix giant logo by specifying width instead of height

commit ddbdb8e
Merge: a19643f 71d7b1f
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 13:47:52 2021 +0000

    Merge branch 'master' into fix-logo

commit a19643f
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Wed Dec 1 14:30:11 2021 +0100

    Fix giant logo by specifying width instead of height
    fix epiforecasts#440

commit 71d7b1f
Merge: 2e5cabc fb10488
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 10:21:14 2021 +0000

    Merge pull request epiforecasts#438 from epiforecasts/rm-joss-action

    Remove action re-building JOSS paper

commit fb10488
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Tue Nov 30 19:09:00 2021 +0100

    Remove action re-building JOSS paper

commit 2e5cabc
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Mon Nov 29 13:43:29 2021 +0000

    Update NEWS.md

commit d1350d9
Merge: 8c77b82 782256c
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Mon Nov 29 13:41:00 2021 +0000

    Merge pull request epiforecasts#436 from epiforecasts/fix-germany

    fix Germany case/death data

commit 782256c
Author: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date:   Mon Nov 29 07:40:01 2021 +0000

    add missing sum

commit 4c7cb8c
Author: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date:   Mon Nov 29 07:19:09 2021 +0000

    fix Germany case/death data

commit 8c77b82
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Tue Oct 12 10:20:55 2021 +0100

    Check package once a week vs daily

commit b5b9cbf
Merge: c782b57 91d0f0c
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Sep 30 13:01:56 2021 +0100

    Merge pull request epiforecasts#428 from RichardMN/update-Vietnam-url-and-docs

    Update vietnam url and docs

commit 91d0f0c
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Thu Sep 30 09:12:37 2021 +0300

    Rebuilt all country data table and Vietnam documentation

commit 1d6c024
Author: Tri Luu <ilumitr@users.noreply.github.com>
Date:   Thu Sep 30 09:38:37 2021 +0700

    Update stable API URL of Vietnam
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@RichardMN
RichardMN committed Dec 2, 2021
1 parent c42b9eb commit 88035e2
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2 changes: 1 addition & 1 deletion .github/workflows/check-full.yaml
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Expand Up @@ -7,7 +7,7 @@ name: R-CMD-check
branches:
- master
schedule:
- cron: '0 0 * * *'
- cron: '0 0 * * 1'
pull_request:
branches:
- '*'
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23 changes: 0 additions & 23 deletions .github/workflows/draft-pdf.yml
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4 changes: 4 additions & 0 deletions NEWS.md
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Expand Up @@ -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.
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8 changes: 4 additions & 4 deletions R/Germany.R
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Expand Up @@ -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$deaths_new))
) %>%
ungroup()
},
Expand All @@ -116,8 +116,8 @@ Germany <- R6::R6Class("Germany",
.data$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()
}
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12 changes: 6 additions & 6 deletions R/Vietnam.R
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Expand Up @@ -4,7 +4,7 @@
#' @description Information for downloading, cleaning
#' and processing covid-19 region data for Vietnam.
#'
#' @source \url{https://covid.ncsc.gov.vn}
#' @source \url{https://covid19.ncsc.gov.vn}
#' @export
#' @concept dataset
#' @family subnational
Expand All @@ -29,10 +29,10 @@ Vietnam <- R6::R6Class("Vietnam",
#' @field common_data_urls List of named links to raw data.
common_data_urls = list(
# nolint start
"case_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=case_by_time",
"death_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=death_by_time",
"recovered_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=recovered_by_time",
"provinces" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces"
"case_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=case_by_time",
"death_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=death_by_time",
"recovered_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=recovered_by_time",
"provinces" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces"
# nolint end
),
#' @field source_data_cols existing columns within the raw data
Expand All @@ -44,7 +44,7 @@ Vietnam <- R6::R6Class("Vietnam",
"Public COVID-19 for Vietnam, curated by NCSC's COVID-19 team",
#' @field source_url Website address for explanation/introduction of the
#' data
source_url = "https://covid.ncsc.gov.vn",
source_url = "https://covid19.ncsc.gov.vn",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -11,7 +11,7 @@ knitr::opts_chunk$set(
)
```

# Subnational data for the COVID-19 outbreak <img src="man/figures/logo.png" align="right" alt="" height="150" />
# Subnational data for the COVID-19 outbreak <img src="man/figures/logo.png" align="right" alt="" width="120" />

[![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)

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24 changes: 12 additions & 12 deletions README.md
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@@ -1,5 +1,5 @@

# Subnational data for the COVID-19 outbreak <img src="man/figures/logo.png" align="right" alt="" height="150" />
# Subnational data for the COVID-19 outbreak <img src="man/figures/logo.png" align="right" alt="" width="120" />

[![R-CMD-check](https://github.com/epiforecasts/covidregionaldata/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/covidregionaldata/actions)
[![Codecov test
Expand Down Expand Up @@ -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
#> <date> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 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
#> <date> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 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 <dbl>,
#> # deaths_total <dbl>, recovered_new <dbl>, recovered_total <dbl>,
#> # hosp_new <dbl>, hosp_total <dbl>, tested_new <dbl>, tested_total <dbl>
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1 change: 1 addition & 0 deletions _pkgdown.yml
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@@ -1,5 +1,6 @@
url: epiforecasts.io/covidregionaldata/
template:
bootstrap: 5
params:
bootswatch: lumen
docsearch:
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2 changes: 1 addition & 1 deletion man/Vietnam.Rd
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