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RichardMN · Jul 5, 2021 · d51eabc · d51eabc
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -65,10 +65,10 @@ Authors@R:
              comment = c(ORCID = "0000-0001-8057-8037")))
 Description: An interface to subnational and national level COVID-19 data
     sourced from both official sources, such as Public Health England in
-    the UK, and from other Covid-19 data collections, including the World
+    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. Designed to streamline Covid-19 data extraction, cleaning, and
+    others. 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

diff --git a/R/shared-methods.R b/R/shared-methods.R
@@ -530,7 +530,7 @@ DataClass <- R6::R6Class(
     #' `specific_tests()`. The snapshots contain the first 1000 rows of data.
     #' For more details see the
     # nolint start
-    #' \href{https://github.com/epiforecasts/covidregionaldata/tree/master/vignettes/testing.Rmd}{'testing' vignette}: \code{vignette(testing)}.
+    #' \href{https://github.com/epiforecasts/covidregionaldata/blob/master/vignettes/testing.Rmd}{'testing' vignette}: \code{vignette(testing)}.
     # nolint end
     #' @param download logical. To download the data (TRUE) or use a snapshot
     #' (FALSE). Defaults to FALSE.

diff --git a/README.Rmd b/README.Rmd
@@ -17,9 +17,9 @@ knitr::opts_chunk$set(
 
 [![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) 
 
-[![status](https://joss.theoj.org/papers/dd6f7acdae3b7136a3ac373ce9a0655c/status.svg)](https://joss.theoj.org/papers/dd6f7acdae3b7136a3ac373ce9a0655c)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.03290/status.svg)](https://doi.org/10.21105/joss.03290)
 
-Interface to subnational and national level COVID-19 data sourced from 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, 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.
+Interface to subnational and national level COVID-19 data sourced from 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, 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.
 
 ## Installation
 
@@ -136,7 +136,7 @@ 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
-[supported countries](https://epiforecasts.io/covidregionaldata/articles/supported-countriees.html) page
+[supported countries](https://epiforecasts.io/covidregionaldata/articles/supported-countries.html) page
 or build the [supported countries vignette](vignettes/supported-countries.Rmd).
 
 For further examples see the [quick start vignette](https://github.com/epiforecasts/covidregionaldata/blob/master/vignettes/quickstart.Rmd). Additional subnational data are supported via the `JHU()` and `Google()` classes. Use the `available_regions()` method once these data have been downloaded and cleaned (see their examples) for subnational data they internally support.

diff --git a/README.md b/README.md
@@ -19,14 +19,14 @@ Welcome](https://img.shields.io/badge/PRs-welcome-yellow.svg)](https://makeapull
 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)
 
-[![status](https://joss.theoj.org/papers/dd6f7acdae3b7136a3ac373ce9a0655c/status.svg)](https://joss.theoj.org/papers/dd6f7acdae3b7136a3ac373ce9a0655c)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.03290/status.svg)](https://doi.org/10.21105/joss.03290)
 
 Interface to subnational and national level COVID-19 data sourced from
 both official sources, such as Public Health England in the UK, and from
-other Covid-19 data collections, including the World Health Organisation
+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
+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
@@ -79,7 +79,7 @@ the temporary directory by default),
 
 ``` r
 start_using_memoise()
-#> Using a cache at: /tmp/RtmpMMiVQw
+#> Using a cache at: /tmp/RtmpvmRzcu
 ```
 
 To stop using `memoise` use,
@@ -104,7 +104,7 @@ 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: 129279 Columns: 8
+#> Rows: 130227 Columns: 8
 #> ── Column specification ────────────────────────────────────────────────────────
 #> Delimiter: ","
 #> chr  (3): Country_code, Country, WHO_region
@@ -116,7 +116,7 @@ nots <- get_national_data()
 #> Cleaning data
 #> Processing data
 nots
-#> # A tibble: 129,401 x 15
+#> # A tibble: 130,349 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
@@ -129,7 +129,7 @@ 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 129,391 more rows, and 8 more variables: deaths_new <dbl>,
+#> # … with 130,339 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>
 ```
@@ -170,7 +170,7 @@ for example by level 1 region in the UK, use:
 ``` r
 uk_nots <- get_regional_data(country = "UK", verbose = FALSE)
 uk_nots
-#> # A tibble: 6,734 x 26
+#> # A tibble: 6,786 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
@@ -183,7 +183,7 @@ 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 6,724 more rows, and 19 more variables: recovered_new <dbl>,
+#> # … with 6,776 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>,
@@ -216,7 +216,7 @@ 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 [supported
-countries](https://epiforecasts.io/covidregionaldata/articles/supported-countriees.html)
+countries](https://epiforecasts.io/covidregionaldata/articles/supported-countries.html)
 page or build the [supported countries
 vignette](vignettes/supported-countries.Rmd).
 

diff --git a/man/DataClass.Rd b/man/DataClass.Rd
diff --git a/man/figures/README-g7_plot-1.png b/man/figures/README-g7_plot-1.png
diff --git a/man/figures/README-uk_plot-1.png b/man/figures/README-uk_plot-1.png
diff --git a/vignettes/slowstart.Rmd b/vignettes/slowstart.Rmd
@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 
 ## Installing and loading the package
 
-The package can either be installed from CRAN, from our [`r-universe`](https://epiforecasts.r-universe.dev/) repository, or from GitHub. See the README for details. Once installed load the package using the following,
+The package can either be installed from CRAN, from our [`r-universe`](https://epiforecasts.r-universe.dev/ui) repository, or from GitHub. See the README for details. Once installed load the package using the following,
 
 ```{r, eval=TRUE}
 library(covidregionaldata)