diff --git a/README.Rmd b/README.Rmd index 59628184..9620ca99 100644 --- a/README.Rmd +++ b/README.Rmd @@ -135,7 +135,7 @@ uk_nots %>% ``` See `get_available_datasets()` for supported regions and subregional levels. -To view what datasets we currently have subnationaldata for, along with their current status, check the +To view what datasets we currently have subnational data for, along with their current status, check the [supported countries](https://epiforecasts.io/covidregionaldata/articles/supported-countries.html) page or build the [supported countries vignette](vignettes/supported-countries.Rmd). diff --git a/README.md b/README.md index ac63f489..20013dd6 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,7 @@ the temporary directory by default), ``` r start_using_memoise() -#> Using a cache at: /tmp/RtmpPgZXiv +#> Using a cache at: /var/folders/68/22ndk9854tq394wl_n1cxzlr0000gn/T//RtmpylL81U ``` To stop using `memoise` use, @@ -103,34 +103,24 @@ 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: 142911 Columns: 8 -#> ── Column specification ──────────────────────────────────────────────────────── -#> Delimiter: "," -#> chr (3): Country_code, Country, WHO_region -#> dbl (4): New_cases, Cumulative_cases, New_deaths, Cumulative_deaths -#> date (1): Date_reported -#> -#> ℹ 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. #> Cleaning 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 -#> 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 -#> # … 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 +#> # A tibble: 182,253 × 15 +#> date un_region who_region country iso_code cases_new cases_total deaths_new deaths_total recovered_new +#> +#> 1 2020-01-03 Asia EMRO Afghan… AF 0 0 0 0 NA +#> 2 2020-01-03 Europe EURO Albania AL 0 0 0 0 NA +#> 3 2020-01-03 Africa AFRO Algeria DZ 0 0 0 0 NA +#> 4 2020-01-03 Oceania WPRO Americ… AS 0 0 0 0 NA +#> 5 2020-01-03 Europe EURO Andorra AD 0 0 0 0 NA +#> 6 2020-01-03 Africa AFRO Angola AO 0 0 0 0 NA +#> 7 2020-01-03 Americas AMRO Anguil… AI 0 0 0 0 NA +#> 8 2020-01-03 Americas AMRO Antigu… AG 0 0 0 0 NA +#> 9 2020-01-03 Americas AMRO Argent… AR 0 0 0 0 NA +#> 10 2020-01-03 Asia EURO Armenia AM 0 0 0 0 NA +#> # … with 182,243 more rows, and 5 more variables: recovered_total , hosp_new , hosp_total , +#> # tested_new , tested_total ``` This can also be filtered for a country of interest, @@ -169,26 +159,25 @@ for example by level 1 region in the UK, use: ``` r uk_nots <- get_regional_data(country = "UK", verbose = FALSE) uk_nots -#> # A tibble: 7,501 × 26 -#> date region region_code cases_new cases_total deaths_new deaths_total -#> -#> 1 2020-01-30 East Mi… E12000004 NA NA NA NA -#> 2 2020-01-30 East of… E12000006 NA NA NA NA -#> 3 2020-01-30 England E92000001 2 2 NA NA -#> 4 2020-01-30 London E12000007 NA NA NA NA -#> 5 2020-01-30 North E… E12000001 NA NA NA NA -#> 6 2020-01-30 North W… E12000002 NA NA NA NA -#> 7 2020-01-30 Norther… N92000002 NA NA NA NA -#> 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 7,491 more rows, and 19 more variables: recovered_new , -#> # recovered_total , hosp_new , hosp_total , tested_new , -#> # tested_total , areaType , cumCasesByPublishDate , -#> # cumCasesBySpecimenDate , newCasesByPublishDate , -#> # newCasesBySpecimenDate , cumDeaths28DaysByDeathDate , -#> # cumDeaths28DaysByPublishDate , newDeaths28DaysByDeathDate , -#> # newDeaths28DaysByPublishDate , … +#> # A tibble: 9,893 × 26 +#> date region region_code cases_new cases_total deaths_new deaths_total recovered_new recovered_total +#> +#> 1 2020-01-11 North Ea… E12000001 NA NA NA NA NA NA +#> 2 2020-01-11 North We… E12000002 NA NA NA NA NA NA +#> 3 2020-01-11 Yorkshir… E12000003 NA NA NA NA NA NA +#> 4 2020-01-11 East Mid… E12000004 NA NA NA NA NA NA +#> 5 2020-01-11 West Mid… E12000005 NA NA NA NA NA NA +#> 6 2020-01-11 East of … E12000006 NA NA NA NA NA NA +#> 7 2020-01-11 London E12000007 NA NA NA NA NA NA +#> 8 2020-01-11 South Ea… E12000008 NA NA NA NA NA NA +#> 9 2020-01-11 South We… E12000009 NA NA NA NA NA NA +#> 10 2020-01-11 England E92000001 NA NA NA NA NA NA +#> # … with 9,883 more rows, and 17 more variables: hosp_new , hosp_total , tested_new , +#> # tested_total , areaType , cumCasesByPublishDate , cumCasesBySpecimenDate , +#> # newCasesByPublishDate , newCasesBySpecimenDate , cumDeaths28DaysByDeathDate , +#> # cumDeaths28DaysByPublishDate , newDeaths28DaysByDeathDate , newDeaths28DaysByPublishDate , +#> # newPillarFourTestsByPublishDate , newPillarOneTestsByPublishDate , +#> # newPillarThreeTestsByPublishDate , newPillarTwoTestsByPublishDate ``` Now we have the data we can create plots, for example the time-series of @@ -210,7 +199,7 @@ uk_nots %>% See `get_available_datasets()` for supported regions and subregional -levels. To view what datasets we currently have subnationaldata for, +levels. To view what datasets we currently have subnational data for, along with their current status, check the [supported countries](https://epiforecasts.io/covidregionaldata/articles/supported-countries.html) page or build the [supported countries @@ -231,9 +220,8 @@ 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: + #> 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: #> 10.21105/joss.03290 #> #> A BibTeX entry for LaTeX users is diff --git a/man/figures/README-g7_plot-1.png b/man/figures/README-g7_plot-1.png index 75fa7c69..0369c12a 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 8a19f88a..d33ddc21 100644 Binary files a/man/figures/README-uk_plot-1.png and b/man/figures/README-uk_plot-1.png differ