diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 843a42e2..0f84236d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -43,7 +43,7 @@ repos: rev: v3.4.0 hooks: - id: check-added-large-files - args: ['--maxkb=600'] + args: ['--maxkb=200'] - id: end-of-file-fixer exclude: '\.Rd' - repo: local diff --git a/README.Rmd b/README.Rmd index 983758db..348726d5 100644 --- a/README.Rmd +++ b/README.Rmd @@ -11,7 +11,7 @@ knitr::opts_chunk$set( ) ``` -# Subnational data for the COVID-19 outbreak +# Subnational data for the COVID-19 outbreak [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![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) diff --git a/README.md b/README.md index 0d70c2e9..b856afa3 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 [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html) @@ -27,11 +27,11 @@ both official sources, such as Public Health England in the UK, and from other Covid-19 data collections, including the World Health Organisation (WHO), European Centre for Disease Prevention and Control (ECDC), John Hopkins University (JHU), Google Open Data and others. This package is -designed to streamline Covid-19 data extraction, cleaning, and -processing from a range of data sources in an open and transparent way. -This allows users to inspect and scrutinise the data, and tools used to -process it, at every step. For all countries supported, data includes a -daily time-series of cases and, wherever available, data on deaths, +designed to streamline Covid-19 data extraction, cleaning, and processing +from a range of data sources in an open and transparent way. This allows +users to inspect and scrutinise the data, and tools used to process it, +at every step. For all countries supported, data includes a daily +time-series of cases and, wherever available, data on deaths, hospitalisations, and tests. National level data is also supported using a range of data sources as well as line list data and links to intervention data sets. @@ -78,7 +78,7 @@ the temporary directory by default), ``` r start_using_memoise() -#> Using a cache at: /tmp/RtmprQRl5f +#> Using a cache at: /tmp/RtmpJAeC7J ``` To stop using `memoise` use, @@ -103,7 +103,7 @@ 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: 125,724 +#> Rows: 124,425 #> Columns: 8 #> Delimiter: "," #> chr [3]: Country_code, Country, WHO_region @@ -115,7 +115,7 @@ nots <- get_national_data() #> Cleaning data #> Processing data nots -#> # A tibble: 125,846 x 15 +#> # A tibble: 124,425 x 15 #> date un_region who_region country iso_code cases_new cases_total #> #> 1 2020-01-03 Asia EMRO Afghanistan AF 0 0 @@ -128,7 +128,7 @@ 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 125,836 more rows, and 8 more variables: deaths_new , +#> # … with 124,415 more rows, and 8 more variables: deaths_new , #> # deaths_total , recovered_new , recovered_total , #> # hosp_new , hosp_total , tested_new , tested_total ``` @@ -169,7 +169,7 @@ for example by level 1 region in the UK, use: ``` r uk_nots <- get_regional_data(country = "UK", verbose = FALSE) uk_nots -#> # A tibble: 6,539 x 26 +#> # A tibble: 6,474 x 26 #> date region region_code cases_new cases_total deaths_new deaths_total #> #> 1 2020-01-30 East Mi… E12000004 NA NA NA NA @@ -182,7 +182,7 @@ 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 6,529 more rows, and 19 more variables: recovered_new , +#> # … with 6,464 more rows, and 19 more variables: recovered_new , #> # recovered_total , hosp_new , hosp_total , tested_new , #> # tested_total , areaType , cumCasesByPublishDate , #> # cumCasesBySpecimenDate , newCasesByPublishDate , @@ -256,10 +256,10 @@ using the following, [![Development](https://img.shields.io/badge/Wiki-lightblue.svg?style=flat)](https://github.com/epiforecasts/covidregionaldata/wiki/) -This package is the result of work from a number of contributors (see -contributors list -[here](https://epiforecasts.io/covidregionaldata/authors.html)). We -would like to thank the [CMMID COVID-19 working +This package is the result of work from a number of contributors +(see contributors list in the +[here](https://epiforecasts.io/covidregionaldata/authors.html)). +We would like to thank the [CMMID COVID-19 working group](https://cmmid.github.io/groups/ncov-group.html) for inciteful comments and feedback. diff --git a/inst/make_hexsticker.R b/inst/make_hexsticker.R deleted file mode 100644 index 93267dcd..00000000 --- a/inst/make_hexsticker.R +++ /dev/null @@ -1,46 +0,0 @@ -library(hexSticker) -library(ggplot2) -library(dplyr) -library(maps) - -regional_countries <- get_available_datasets() %>% - filter(type == "regional") - -regional_countries_l2 <- regional_countries %>% - filter(!(is.na(level_2_region))) - -world <- map_data("world") - -supported_countries <- mutate( - world, - fill = case_when( - region %in% regional_countries_l2[["class"]] ~ "Level 2", - region %in% regional_countries[["class"]] ~ "Level 1", - TRUE ~ "Unsupported" - ) -) - -covid_map <- ggplot( - supported_countries, aes(long, lat, fill = fill, group = group) -) + - geom_polygon(color = "black", size = 0.05) + - scale_fill_manual( - name = "", - values = c("#0072b2", "#cc79a7", "grey80") - ) + - theme_void() + - theme(legend.position = "none") + - coord_fixed(ratio = 1.7, ylim = c(-55, 80)) - -logo <- sticker( - covid_map, - package = "covidregionaldata", - p_size = 50, s_x = 0.93, s_y = 0.8, s_width = 1.7, s_height = 2, - p_y = 1.45, - p_color = "white", - h_color = "#646770", - h_fill = "#24A7DF", - filename = "man/figures/logo.png", - u_size = 3.5, - dpi = 1000 -) diff --git a/man/figures/README-g7_plot-1.png b/man/figures/README-g7_plot-1.png index aa650904..f1a8b934 100644 Binary files a/man/figures/README-g7_plot-1.png and b/man/figures/README-g7_plot-1.png differ diff --git a/man/figures/README-uk_plot-1.png b/man/figures/README-uk_plot-1.png index ec89db05..0d57407d 100644 Binary files a/man/figures/README-uk_plot-1.png and b/man/figures/README-uk_plot-1.png differ diff --git a/man/figures/logo.png b/man/figures/logo.png deleted file mode 100644 index 976fbb72..00000000 Binary files a/man/figures/logo.png and /dev/null differ