From 2f2c015598330e6c51f1af721d84879c77e31749 Mon Sep 17 00:00:00 2001 From: Joe Date: Mon, 28 Jun 2021 15:48:20 +0100 Subject: [PATCH 1/6] updated title to be same as the paper, author list looks the same as paper --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index a3590fd0..c0f4986a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: covidregionaldata -Title: Subnational Data for the COVID-19 Outbreak +Title: covidregionaldata: Subnational data for COVID-19 epidemiology Version: 0.9.2.5000 Authors@R: - c(person(given = "Joe", + c(person(given = "Joseph", family = "Palmer", role = "aut", email = "joe.palmer.2019@live.rhul.ac.uk", From 611bfc7e1f375116256584555281e0d9af101de8 Mon Sep 17 00:00:00 2001 From: Joe Date: Mon, 28 Jun 2021 16:02:28 +0100 Subject: [PATCH 2/6] updated citation, left doi blank as not sure what this will be... --- inst/CITATION | 25 +++++++++++++------------ inst/WORDLIST | 4 ++++ 2 files changed, 17 insertions(+), 12 deletions(-) diff --git a/inst/CITATION b/inst/CITATION index 884488b1..306a184a 100644 --- a/inst/CITATION +++ b/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") ) diff --git a/inst/WORDLIST b/inst/WORDLIST index fe06356c..bf00a7dc 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -67,6 +67,8 @@ characterArray characterised Chun CIJ +citEntry +citHeader CJVA ClinicalTrials cloneable @@ -353,6 +355,7 @@ paul paulcampbell Pedersen peoplepopulationandcommunity +personList Petherick PHE piplines @@ -464,6 +467,7 @@ testDownload testSource testthat textquoteright +textVersion theoj Tianhan tibble From 84aa59efa14938f333a8bdcaa946023a5d8cac2a Mon Sep 17 00:00:00 2001 From: Joe Date: Mon, 28 Jun 2021 16:04:26 +0100 Subject: [PATCH 3/6] updated news --- NEWS.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/NEWS.md b/NEWS.md index 31af372f..db06490f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -9,6 +9,8 @@ This release is in development and therefore new features may change without war * Support added for data from the Netherlands provided by RVIM (English: National Institute for Public Health and the Environment). This source provides case, deaths and hospital admission data at the province and municipal levels (by @joseph-palmer). * Support added for data from Switzerland and Liechtenstein collated by Canton Zurich (@OpenZH). This source provides case, deaths and hospital admission data at the canton level (by @RichardMN). * Made package changes recomended in the JOSS review, including additional statements of need to the README, updates to the manuscript (paper.md) and fixes a bug of multiple sources for some countries. We are very grateful for the detailed feedback given by the JOSS reviewers and their help in improving this package. +* Package citation has been updated with the JOSS paper citation. +* Hexsticker has also been added. ## Changes to implemented data sources From c60fb7ec60760c53d03343a766d6350bf1f03b7b Mon Sep 17 00:00:00 2001 From: Joe Date: Tue, 29 Jun 2021 12:13:20 +0100 Subject: [PATCH 4/6] updated version to description and news, also made recomended changes --- DESCRIPTION | 4 ++-- NEWS.md | 6 ++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c0f4986a..69784b23 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: covidregionaldata -Title: covidregionaldata: Subnational data for COVID-19 epidemiology -Version: 0.9.2.5000 +Title: Subnational data for COVID-19 epidemiology +Version: 0.9.3 Authors@R: c(person(given = "Joseph", family = "Palmer", diff --git a/NEWS.md b/NEWS.md index db06490f..81c28794 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# covidregionaldata 0.9.3 + +This release completes all recommendations for the submission to JOSS. + # 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). @@ -9,8 +13,6 @@ This release is in development and therefore new features may change without war * Support added for data from the Netherlands provided by RVIM (English: National Institute for Public Health and the Environment). This source provides case, deaths and hospital admission data at the province and municipal levels (by @joseph-palmer). * Support added for data from Switzerland and Liechtenstein collated by Canton Zurich (@OpenZH). This source provides case, deaths and hospital admission data at the canton level (by @RichardMN). * Made package changes recomended in the JOSS review, including additional statements of need to the README, updates to the manuscript (paper.md) and fixes a bug of multiple sources for some countries. We are very grateful for the detailed feedback given by the JOSS reviewers and their help in improving this package. -* Package citation has been updated with the JOSS paper citation. -* Hexsticker has also been added. ## Changes to implemented data sources From 242679fd76a820667766e8f0b7d620f5b60dd26f Mon Sep 17 00:00:00 2001 From: Joe Date: Thu, 1 Jul 2021 08:24:21 +0100 Subject: [PATCH 5/6] updated versioning and made title case --- DESCRIPTION | 2 +- NEWS.md | 4 ---- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 69784b23..00dd8218 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: covidregionaldata -Title: Subnational data for COVID-19 epidemiology +Title: Subnational Data for COVID-19 Epidemiology Version: 0.9.3 Authors@R: c(person(given = "Joseph", diff --git a/NEWS.md b/NEWS.md index 81c28794..7474ca2a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,5 @@ # covidregionaldata 0.9.3 -This release completes all recommendations for the submission to JOSS. - -# 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). ## New features From 2b6fb387f2c01cb4f9d343edb4874a72716a6ed9 Mon Sep 17 00:00:00 2001 From: seabbs Date: Thu, 1 Jul 2021 12:58:32 +0000 Subject: [PATCH 6/6] update news --- .devcontainer/Dockerfile | 10 +++++----- DESCRIPTION | 2 +- NEWS.md | 7 +++++-- inst/WORDLIST | 33 ++++++++++++++++++++++++++++++--- 4 files changed, 41 insertions(+), 11 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 5060a065..03c558da 100644 --- a/.devcontainer/Dockerfile +++ b/.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 + +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")' \ No newline at end of file +RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")' diff --git a/DESCRIPTION b/DESCRIPTION index 00dd8218..5d8ba1bc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: covidregionaldata Title: Subnational Data for COVID-19 Epidemiology -Version: 0.9.3 +Version: 0.9.2 Authors@R: c(person(given = "Joseph", family = "Palmer", diff --git a/NEWS.md b/NEWS.md index 7474ca2a..d63f21ef 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,8 @@ -# covidregionaldata 0.9.3 +# 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 diff --git a/inst/WORDLIST b/inst/WORDLIST index bf00a7dc..2775d0fe 100644 --- a/inst/WORDLIST +++ b/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 @@ -107,16 +106,20 @@ dd DD de De +debian dec DeclarationsI deps desc +devcontainer devtools DFID DHSC Diaz +dir disaggregated docsearch +docthis documentaion documention documentionr @@ -169,6 +172,7 @@ getRversion GFM ggplot ggspatial +GID Gimma github Github @@ -193,6 +197,7 @@ HDTRA Healy hellewell Hellewell +hexsticker Hexsticker Hiroaki hl @@ -265,7 +270,14 @@ Kreise Kucharski KvZ Landkreis +languageserver LazyData +libcurl +libgdal +libgit +libssl +libxml +libxt LIDP lifecycle Lifecycle @@ -288,6 +300,7 @@ macOS magrittr Majumdar md +mdlincoln Meakin meaking MEDLINE @@ -312,6 +325,7 @@ navbar ncbi ncov nCoV +ncpus NGD nhs nhsregions @@ -322,6 +336,7 @@ nlm NLM Noam nolint +noninteractive nonpharmaceutical nov nr @@ -338,6 +353,7 @@ ONS Ooms OpenDataZH openjournals +openssl ORCID Ordaz org @@ -366,6 +382,7 @@ populationandmigration populationestimates populationestimatesforukenglandandwalesscotlandandnorthernireland positivity +precommit preexisting prioritises programme @@ -394,10 +411,12 @@ reparameterise repo responed RESULTSThe +rf rhul RichardMN RL rlang +rm rmarkdown RME RMGJH @@ -430,6 +449,7 @@ shapefiles sherratt Sherratt Silverman +skipinstalled slowstart sophie SouthAfrica @@ -477,6 +497,7 @@ tidyselect tidyverse Tidyverse TJ +tmp todays toolkits toolset @@ -489,12 +510,15 @@ TWR u ubuntu UCPM +UID uk urldate urls useMemoise +usermod usethis utla +var VignetteBuilder virological Virological @@ -505,6 +529,7 @@ VLG VLI VOC vroom +vscode Wahltinez Wai Waites @@ -540,3 +565,5 @@ zenodo Zenodo Zhilin Zhong +zsh +ZSH