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joseph-palmer committed Jul 14, 2021
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -15,7 +15,7 @@ knitr::opts_chunk$set(

[![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) [![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/) [![DOI](https://zenodo.org/badge/271601189.svg)](https://zenodo.org/badge/latestdoi/271601189)
[![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/) [![DOI](https://zenodo.org/badge/271601189.svg)](https://zenodo.org/badge/latestdoi/271601189)

[![DOI](https://joss.theoj.org/papers/10.21105/joss.03290/status.svg)](https://doi.org/10.21105/joss.03290)

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47 changes: 24 additions & 23 deletions README.md
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Expand Up @@ -13,6 +13,7 @@ downloads](http://cranlogs.r-pkg.org/badges/grand-total/covidregionaldata?color=
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
Expand Down Expand Up @@ -79,7 +80,7 @@ the temporary directory by default),

``` r
start_using_memoise()
#> Using a cache at: /tmp/RtmpvmRzcu
#> Using a cache at: /tmp/RtmpRJrpfd
```

To stop using `memoise` use,
Expand All @@ -104,19 +105,19 @@ the Google COVID-19 open data project), use:
``` r
nots <- get_national_data()
#> Downloading data from https://covid19.who.int/WHO-COVID-19-global-data.csv
#> Rows: 130227 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Rows: 132,360
#> Columns: 8
#> Delimiter: ","
#> chr (3): Country_code, Country, WHO_region
#> dbl (4): New_cases, Cumulative_cases, New_deaths, Cumulative_deaths
#> date (1): Date_reported
#> chr [3]: Country_code, Country, WHO_region
#> dbl [4]: New_cases, Cumulative_cases, New_deaths, Cumulative_deaths
#> date [1]: Date_reported
#>
#> Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
#> Use `spec()` to retrieve the guessed column specification
#> Pass a specification to the `col_types` argument to quiet this message
#> Cleaning data
#> Processing data
nots
#> # A tibble: 130,349 x 15
#> # A tibble: 132,482 x 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
Expand All @@ -129,7 +130,7 @@ nots
#> 8 2020-01-03 Americas AMRO Antigua & Bar… AG 0 0
#> 9 2020-01-03 Americas AMRO Argentina AR 0 0
#> 10 2020-01-03 Asia EURO Armenia AM 0 0
#> # … with 130,339 more rows, and 8 more variables: deaths_new <dbl>,
#> # … with 132,472 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>
```
Expand Down Expand Up @@ -170,7 +171,7 @@ for example by level 1 region in the UK, use:
``` r
uk_nots <- get_regional_data(country = "UK", verbose = FALSE)
uk_nots
#> # A tibble: 6,786 x 26
#> # A tibble: 6,903 x 26
#> date region region_code cases_new cases_total deaths_new deaths_total
#> <date> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 2020-01-30 East Mi… E12000004 NA NA NA NA
Expand All @@ -183,7 +184,7 @@ uk_nots
#> 8 2020-01-30 Scotland S92000003 NA NA NA NA
#> 9 2020-01-30 South E… E12000008 NA NA NA NA
#> 10 2020-01-30 South W… E12000009 NA NA NA NA
#> # … with 6,776 more rows, and 19 more variables: recovered_new <dbl>,
#> # … with 6,893 more rows, and 19 more variables: recovered_new <dbl>,
#> # recovered_total <dbl>, hosp_new <dbl>, hosp_total <dbl>, tested_new <dbl>,
#> # tested_total <dbl>, areaType <chr>, cumCasesByPublishDate <dbl>,
#> # cumCasesBySpecimenDate <dbl>, newCasesByPublishDate <dbl>,
Expand Down Expand Up @@ -235,21 +236,21 @@ using the following,
#>
#> To cite covidregionaldata in publications use:
#>
#> Joseph Palmer, Katharine Sherratt, Richard Martin-Nielsen, Jonnie
#> Bevan, Hamish Gibbs, Sebastian Funk and Sam Abbott (2021).
#> covidregionaldata: Subnational data for COVID-19 epidemiology, DOI:
#> Sam Abbott, Katharine Sherratt, Joe Palmer, Richard Martin-Nielsen,
#> Jonnie Bevan, Hamish Gibbs, and Sebastian Funk (2020).
#> covidregionaldata: Subnational Data for the COVID-19 Outbreak, DOI:
#> 10.5281/zenodo.3957539
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {covidregionaldata: Subnational data for COVID-19 epidemiology},
#> author = {Joseph Palmer and Katharine Sherratt and Richard Martin-Nielsen and Jonnie Bevan and Hamish Gibbs and Sebastian Funk and Sam Abbott},
#> journal = {Journal of Open Source Software},
#> year = {2021},
#> volume = {6},
#> number = {62},
#> pages = {3290},
#> title = {covidregionaldata: Subnational Data for the COVID-19 Outbreak},
#> author = {Sam Abbott and Katharine Sherratt and Joe Palmer and Richard Martin-Nielsen and Jonnie Bevan and Hamish Gibbs and Sebastian Funk},
#> journal = {-},
#> year = {2020},
#> volume = {-},
#> number = {-},
#> pages = {-},
#> doi = {10.5281/zenodo.3957539},
#> }

Expand All @@ -264,7 +265,7 @@ would like to thank the [CMMID COVID-19 working
group](https://cmmid.github.io/groups/ncov-group.html) for insightful
comments and feedback.

We welcome contributions and new contributors! We particularly
We welcome contributions and new contributors\! We particularly
appreciate help adding new data sources for countries at sub-national
level, or work on priority problems in the
[issues](https://github.com/epiforecasts/covidregionaldata/issues).
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