Merge pull request epiforecasts#392 from epiforecasts/final-joss-checks

Final joss checks

.devcontainer/Dockerfile

@@ -34,14 +34,14 @@ RUN install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \
         git2r \
     && rm -rf /tmp/downloaded_packages
 
-# [Optional] Uncomment this section to install additional OS packages.
-# RUN apt-get update \
-#     && export DEBIAN_FRONTEND=noninteractive \
-#     && apt-get -y install --no-install-recommends <your-package-list-here>
+
+RUN apt-get update \
+     && export DEBIAN_FRONTEND=noninteractive \
+     && apt-get -y install --no-install-recommends libgdal-dev
 
 # install dependencies
 COPY DESCRIPTION /tmp/package/DESCRIPTION
 RUN Rscript -e "devtools::install_dev_deps('/tmp/package')"
 
 # add docthis
-RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")'
+RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: covidregionaldata
-Title: Subnational Data for the COVID-19 Outbreak
-Version: 0.9.2.5000
+Title: Subnational Data for COVID-19 Epidemiology
+Version: 0.9.2
 Authors@R:
-    c(person(given = "Joe",
+    c(person(given = "Joseph",
              family = "Palmer",
              role = "aut",
              email = "[email protected]",

NEWS.md

@@ -1,6 +1,8 @@
 # covidregionaldata 0.9.2
 
-This release is in development and therefore new features may change without warning (though we will seek to keep this to a minimum).
+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. 
+
+Thanks to @joseph-palmer, @RichardMN, and @kathsherratt for contributions towards this release.
 
 ## New features
 
@@ -19,6 +21,7 @@ This release is in development and therefore new features may change without war
 * Testing of classes updated to allow for at least one of `common_data_urls` or `level_data_urls` to be present. The previous default which forced the presence of `common_data_urls` meant that several classes had to define an empty field (by @joseph-palmer).
 * Tests on data sets are now included as a method in `DataClass`. `test_regional-datasets` now calls the test function for all classes at each level. Data set specific tests (such as for NHS regions in the UK) are included as a `specific_tests` function within the country class, which is called by the parent (DataClass) `test` after performing standard checks. This allows all the code about a country to be defined in its own class. In addition, users can run tests interactively by calling the test method (e.g. `$test()`;) (by @joseph-palmer)
 * A function to create a template class and automatically add a github workflow file has been added. This makes adding a new data source for a country even easier as now you can call the function `make_new_data_source()` with the country / source name to add and it will set up the basic structure for you. There is also now a github check to make sure all new sources have a workflow set up (by @joseph-palmer).
+* Adds `source_` fields to all data sets to help users properly attribute their data sources (by @RichardMN).
 
 ## Bug fixes
 

inst/CITATION

@@ -1,21 +1,22 @@
 citHeader("To cite covidregionaldata in publications use:")
 
 citEntry(entry = "Article",
-  title        = "covidregionaldata: Subnational Data for the COVID-19 Outbreak",
-  author       = personList(as.person("Sam Abbott"), 
-    as.person("Katharine Sherratt"), as.person("Joe Palmer"),
+  title        = "covidregionaldata: Subnational data for COVID-19 epidemiology",
+  author       = personList(as.person("Joseph Palmer"),
+    as.person("Katharine Sherratt"),
     as.person("Richard Martin-Nielsen"), as.person("Jonnie Bevan"),
-     as.person("Hamish Gibbs"), as.person("Sebastian Funk")),
-  journal      = "-",
-  year         = "2020",
-  volume       = "-",
-  number       = "-",
-  pages        = "-",
+     as.person("Hamish Gibbs"), as.person("Sebastian Funk"),
+     as.person("Sam Abbott")),
+  journal      = "Journal of Open Source Software",
+  year         = "2021",
+  volume       = "6",
+  number       = "62",
+  pages        = "3290",
   doi          = "10.5281/zenodo.3957539",
 
   textVersion  =
-  paste("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, ",
+  paste("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: 10.5281/zenodo.3957539")
 )

inst/WORDLIST

@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-=======
->>>>>>> master
 AAAS
 abbott
 AbbottSam
@@ -31,9 +28,11 @@ apr
 apskritis
 archivePrefix
 Ardia
+ARG
 arXiv
 arxivId
 aut
+autoremove
 Averick
 Bache
 BB
@@ -67,6 +66,8 @@ characterArray
 characterised
 Chun
 CIJ
+citEntry
+citHeader
 CJVA
 ClinicalTrials
 cloneable
@@ -105,16 +106,20 @@ dd
 DD
 de
 De
+debian
 dec
 DeclarationsI
 deps
 desc
+devcontainer
 devtools
 DFID
 DHSC
 Diaz
+dir
 disaggregated
 docsearch
+docthis
 documentaion
 documention
 documentionr
@@ -167,6 +172,7 @@ getRversion
 GFM
 ggplot
 ggspatial
+GID
 Gimma
 github
 Github
@@ -191,6 +197,7 @@ HDTRA
 Healy
 hellewell
 Hellewell
+hexsticker
 Hexsticker
 Hiroaki
 hl
@@ -263,7 +270,14 @@ Kreise
 Kucharski
 KvZ
 Landkreis
+languageserver
 LazyData
+libcurl
+libgdal
+libgit
+libssl
+libxml
+libxt
 LIDP
 lifecycle
 Lifecycle
@@ -286,6 +300,7 @@ macOS
 magrittr
 Majumdar
 md
+mdlincoln
 Meakin
 meaking
 MEDLINE
@@ -310,6 +325,7 @@ navbar
 ncbi
 ncov
 nCoV
+ncpus
 NGD
 nhs
 nhsregions
@@ -320,6 +336,7 @@ nlm
 NLM
 Noam
 nolint
+noninteractive
 nonpharmaceutical
 nov
 nr
@@ -336,6 +353,7 @@ ONS
 Ooms
 OpenDataZH
 openjournals
+openssl
 ORCID
 Ordaz
 org
@@ -353,6 +371,7 @@ paul
 paulcampbell
 Pedersen
 peoplepopulationandcommunity
+personList
 Petherick
 PHE
 piplines
@@ -363,6 +382,7 @@ populationandmigration
 populationestimates
 populationestimatesforukenglandandwalesscotlandandnorthernireland
 positivity
+precommit
 preexisting
 prioritises
 programme
@@ -391,10 +411,12 @@ reparameterise
 repo
 responed
 RESULTSThe
+rf
 rhul
 RichardMN
 RL
 rlang
+rm
 rmarkdown
 RME
 RMGJH
@@ -427,6 +449,7 @@ shapefiles
 sherratt
 Sherratt
 Silverman
+skipinstalled
 slowstart
 sophie
 SouthAfrica
@@ -464,6 +487,7 @@ testDownload
 testSource
 testthat
 textquoteright
+textVersion
 theoj
 Tianhan
 tibble
@@ -473,6 +497,7 @@ tidyselect
 tidyverse
 Tidyverse
 TJ
+tmp
 todays
 toolkits
 toolset
@@ -485,12 +510,15 @@ TWR
 u
 ubuntu
 UCPM
+UID
 uk
 urldate
 urls
 useMemoise
+usermod
 usethis
 utla
+var
 VignetteBuilder
 virological
 Virological
@@ -501,6 +529,7 @@ VLG
 VLI
 VOC
 vroom
+vscode
 Wahltinez
 Wai
 Waites
@@ -536,3 +565,5 @@ zenodo
 Zenodo
 Zhilin
 Zhong
+zsh
+ZSH