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commit 8c77b82
Author: Sam Abbott <[email protected]>
Date:   Tue Oct 12 10:20:55 2021 +0100

    Check package once a week vs daily

commit b5b9cbf
Merge: c782b57 91d0f0c
Author: Sam Abbott <[email protected]>
Date:   Thu Sep 30 13:01:56 2021 +0100

    Merge pull request epiforecasts#428 from RichardMN/update-Vietnam-url-and-docs

    Update vietnam url and docs

commit 91d0f0c
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 30 09:12:37 2021 +0300

    Rebuilt all country data table and Vietnam documentation

commit 1d6c024
Author: Tri Luu <[email protected]>
Date:   Thu Sep 30 09:38:37 2021 +0700

    Update stable API URL of Vietnam

commit c782b57
Author: seabbs <[email protected]>
Date:   Tue Sep 28 09:17:04 2021 +0000

    update hex and docker hex deps

commit 73784b7
Merge: c59154d d1232f1
Author: Sam Abbott <[email protected]>
Date:   Mon Sep 27 14:11:00 2021 +0100

    Merge pull request epiforecasts#413 from biocyberman/vietnam

    Add subnational data for Vietnam

commit d1232f1
Author: seabbs <[email protected]>
Date:   Mon Sep 27 11:52:46 2021 +0000

    update description, news and run tests

commit b3af1a6
Merge: 4b26675 c59154d
Author: seabbs <[email protected]>
Date:   Mon Sep 27 11:34:25 2021 +0000

    fix merge issues

commit c59154d
Author: seabbs <[email protected]>
Date:   Mon Sep 27 11:28:14 2021 +0000

    add precommit initialisation to vscode devcontainer

commit c9d5b19
Author: seabbs <[email protected]>
Date:   Mon Sep 27 11:27:07 2021 +0000

    update dockerfile for new deps

commit 8401fc8
Merge: aa85f36 da185c9
Author: Sam Abbott <[email protected]>
Date:   Mon Sep 27 11:27:16 2021 +0100

    Merge pull request epiforecasts#417 from epiforecasts/estonia-data

    Add Estonia data

commit 4b26675
Author: Sam Abbott <[email protected]>
Date:   Mon Sep 20 11:06:33 2021 +0100

    Update DESCRIPTION

commit 9c35694
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Sep 19 21:23:51 2021 +0300

    lint cleaning

commit 26cd8ad
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Sep 19 21:19:07 2021 +0300

    Remove prefixes in vietnam_codes.R

commit 2c20067
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Sep 19 20:02:55 2021 +0300

    JSON-reading implementation of Vietnam

    Uses download_json method for downloading. Adjustment to the DataClass tests to deal with tables of lists. Addition of stringi to imported packages, and of fromJSON and jsonlinte to the WORDLIST. Tests run and data stored.

commit f0cec88
Merge: 5f7e82e 5681a2c
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Sep 19 19:02:02 2021 +0300

    Merge branch 'json-reader-vietnam' into pr/413

commit 5f7e82e
Merge: b54bd03 abf4cdd
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Sep 19 18:56:41 2021 +0300

    Merge branch 'json-reader' into pr/413

commit 5681a2c
Author: Richard Martin-Nielsen <[email protected]>
Date:   Fri Sep 17 22:04:01 2021 +0300

    Fixing final glitches in clean_common

commit 3aeddbe
Author: Richard Martin-Nielsen <[email protected]>
Date:   Fri Sep 17 21:40:09 2021 +0300

    Closer to a tidy version of cleaning Vietnam data

commit da185c9
Author: Sam Abbott <[email protected]>
Date:   Fri Sep 17 16:51:23 2021 +0100

    Update DESCRIPTION

commit 27f77f1
Author: Sam Abbott <[email protected]>
Date:   Fri Sep 17 16:51:09 2021 +0100

    Update NEWS.md

commit fc0d356
Author: Sam Abbott <[email protected]>
Date:   Fri Sep 17 16:50:56 2021 +0100

    bump news

commit 7bd4fb0
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 16 21:43:23 2021 +0300

    Using JSON reader to download Vietnam code

commit aff8dbd
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 16 20:41:16 2021 +0300

    Add Estonia.yaml

commit cab4d97
Merge: 24bd668 1426e7a
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 16 20:38:40 2021 +0300

    Merge branch 'estonia-data' of https://github.com/epiforecasts/covidregionaldata into estonia-data

commit 24bd668
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 16 20:33:41 2021 +0300

    Transfer Estonia code into new clean branch

commit 1426e7a
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 16 20:33:41 2021 +0300

    Transfer Estonia code into new clean branch

commit abf4cdd
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 16 20:24:28 2021 +0300

    Initial implementation of a generic json_reader function and download_JSON method

commit b54bd03
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 16 19:57:23 2021 +0300

    Reformatting of code

commit ce5de11
Merge: 0f0cafb 29070dd
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Sep 16 19:29:49 2021 +0300

    Merge branch 'vietnam' of https://github.com/biocyberman/covidregionaldata into pr/413

commit 29070dd
Author: biocyberman <[email protected]>
Date:   Wed Sep 15 21:36:40 2021 +0200

    Refactor code for PR epiforecasts#413

commit 7ca169a
Author: biocyberman <[email protected]>
Date:   Mon Sep 13 19:09:18 2021 +0200

    Change data source for Vietnam

commit 7edc95c
Author: biocyberman <[email protected]>
Date:   Mon Sep 13 00:31:35 2021 +0200

    Update with cases_death from 5F team

commit cd25e34
Author: biocyberman <[email protected]>
Date:   Thu Sep 2 21:17:11 2021 +0200

    Add empty locations to Unknown

commit abcd78a
Author: biocyberman <[email protected]>
Date:   Sat Aug 28 23:29:05 2021 +0200

    Add priliminary support for Vietnam subnational data

commit 0f0cafb
Author: Vang Le-Quy <vlequy@viko01>
Date:   Mon Sep 13 19:09:18 2021 +0200

    Change data source for Vietnam

commit a66539f
Author: Vang Le-Quy <vlequy@viko01>
Date:   Mon Sep 13 00:31:35 2021 +0200

    Update with cases_death from 5F team

commit 4f57d0f
Author: Vang Le-Quy <vlequy@viko01>
Date:   Thu Sep 2 21:17:11 2021 +0200

    Add empty locations to Unknown

commit 8996977
Author: Vang Le-Quy <vlequy@viko01>
Date:   Sat Aug 28 23:29:05 2021 +0200

    Add priliminary support for Vietnam subnational data

commit aa85f36
Merge: 4a05152 63c5638
Author: Sam Abbott <[email protected]>
Date:   Mon Aug 9 10:11:59 2021 +0100

    Merge pull request epiforecasts#407 from epiforecasts/sshh-bot

    Make bot less bossy

commit 63c5638
Merge: a519d49 4a05152
Author: Sam Abbott <[email protected]>
Date:   Fri Aug 6 15:01:09 2021 +0100

    Merge branch 'master' into sshh-bot

commit 4a05152
Author: Sam Abbott <[email protected]>
Date:   Fri Aug 6 14:23:10 2021 +0100

    roll back to dev pkgdown

commit a519d49
Author: Sam Abbott <[email protected]>
Date:   Fri Aug 6 14:20:41 2021 +0100

    make bot less bossy

commit 66da16e
Author: Sam Abbott <[email protected]>
Date:   Fri Aug 6 12:43:15 2021 +0100

    use CRAN pkgdown

commit 0baa18c
Merge: 28d70a0 41d2258
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 15 17:42:44 2021 +0100

    Merge pull request epiforecasts#402 from epiforecasts/fix-readme-citation

    Fixes citation by rebuilding readme

commit 41d2258
Author: seabbs <[email protected]>
Date:   Thu Jul 15 10:44:02 2021 +0000

    moves doi badges around

commit fe21a13
Author: seabbs <[email protected]>
Date:   Thu Jul 15 10:39:59 2021 +0000

    fixes citation by rebuilding readme

commit 28d70a0
Merge: 2e0bb8b 63b0d55
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 15 11:23:14 2021 +0100

    Merge pull request epiforecasts#401 from epiforecasts/create-discord

    added link to discord chat in readme badge

commit 63b0d55
Author: Joe <[email protected]>
Date:   Wed Jul 14 15:59:28 2021 +0100

    updated citation in README, forgot to update covidregionaldata so produced the old one on knit

commit edf7a11
Author: Joe <[email protected]>
Date:   Wed Jul 14 13:25:08 2021 +0100

    added link to discord chat in readme badge

commit 2e0bb8b
Merge: 8fe326b 9f1318e
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 8 15:58:33 2021 +0100

    Merge pull request epiforecasts#396 from epiforecasts/fix-paper-author-names

    fixed Richards last name

commit 9f1318e
Author: Joe <[email protected]>
Date:   Thu Jul 8 10:06:13 2021 +0100

    fixed Richards last name

commit 8fe326b
Author: seabbs <[email protected]>
Date:   Mon Jul 5 11:32:57 2021 +0000

    update citation

commit d51eabc
Author: seabbs <[email protected]>
Date:   Mon Jul 5 10:29:44 2021 +0000

    CRAN check

commit 7794fb0
Author: seabbs <[email protected]>
Date:   Mon Jul 5 09:11:33 2021 +0000

    CRAN comments

commit 08022ac
Author: seabbs <[email protected]>
Date:   Mon Jul 5 09:11:10 2021 +0000

    spelling

commit 2aa0847
Merge: b7eeeaa 5b0d347
Author: Sam Abbott <[email protected]>
Date:   Sun Jul 4 17:40:32 2021 +0100

    Merge pull request epiforecasts#395 from arfon/patch-1

commit 5b0d347
Author: Arfon Smith <[email protected]>
Date:   Sat Jul 3 22:02:29 2021 +0100

    Fixing paper formatting.

commit b7eeeaa
Author: Sam Abbott <[email protected]>
Date:   Fri Jul 2 09:58:07 2021 +0100

    Remove zenodo links and reference

commit 4165c25
Merge: dea9278 a260533
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 1 16:41:12 2021 +0100

    Merge pull request epiforecasts#394 from epiforecasts/RichardMN-patch-1

    Spelling fix in Readme

commit a260533
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 1 16:40:27 2021 +0100

    Update README.md

commit 992da9e
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Jul 1 17:34:50 2021 +0300

    Spelling fix in Readme

commit dea9278
Author: seabbs <[email protected]>
Date:   Thu Jul 1 14:11:35 2021 +0000

    lithuania in news

commit 4e1b981
Author: seabbs <[email protected]>
Date:   Thu Jul 1 13:57:05 2021 +0000

    release candidate

commit 1e095cb
Author: seabbs <[email protected]>
Date:   Thu Jul 1 13:44:42 2021 +0000

    fix paper bib

commit 1e4ebb5
Author: seabbs <[email protected]>
Date:   Thu Jul 1 13:30:46 2021 +0000

    CRAN comments

commit 0e7e837
Author: seabbs <[email protected]>
Date:   Thu Jul 1 13:25:54 2021 +0000

    tweak spelling and lint pass

commit 44fddfc
Merge: a8a97a3 2b6fb38
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 1 13:59:56 2021 +0100

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

    Final joss checks

commit 2b6fb38
Author: seabbs <[email protected]>
Date:   Thu Jul 1 12:58:32 2021 +0000

    update news

commit 78cf455
Merge: 242679f a8a97a3
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 1 13:36:36 2021 +0100

    Merge branch 'master' into final-joss-checks

commit a8a97a3
Merge: 4ad5583 bd5d30c
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 1 13:31:32 2021 +0100

    Merge pull request epiforecasts#388 from RichardMN:source-fields

    Add source text and url fields to classes

commit bd5d30c
Merge: 40d0b9d 4ad5583
Author: seabbs <[email protected]>
Date:   Thu Jul 1 12:29:38 2021 +0000

    merge master, fix merge, et al

commit 4ad5583
Merge: 9df009d 6dc82c0
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 1 13:24:18 2021 +0100

    Merge pull request epiforecasts#393 from epiforecasts:devcontainer

    Devcontainer

commit 6dc82c0
Author: seabbs <[email protected]>
Date:   Thu Jul 1 12:23:59 2021 +0000

    update prec-commit

commit 49deed2
Author: seabbs <[email protected]>
Date:   Thu Jul 1 11:56:19 2021 +0000

    docker build working

commit ae46da4
Author: Sam Abbott <[email protected]>
Date:   Thu Jul 1 11:05:19 2021 +0100

    Update check-full.yaml

commit c030f17
Author: seabbs <[email protected]>
Date:   Thu Jul 1 09:58:13 2021 +0000

    update naming and add docthis

commit 4a07fd1
Author: seabbs <[email protected]>
Date:   Thu Jul 1 09:53:32 2021 +0000

    switch to devcontainer

commit 242679f
Author: Joe <[email protected]>
Date:   Thu Jul 1 08:24:21 2021 +0100

    updated versioning and made title case

commit 40d0b9d
Author: Richard Martin-Nielsen <[email protected]>
Date:   Tue Jun 29 19:33:11 2021 +0300

    Add source fields for country and global sources.

commit c60fb7e
Author: Joe <[email protected]>
Date:   Tue Jun 29 12:13:20 2021 +0100

    updated version to description and news, also made recomended changes

commit 84aa59e
Author: Joe <[email protected]>
Date:   Mon Jun 28 16:04:26 2021 +0100

    updated news

commit 611bfc7
Author: Joe <[email protected]>
Date:   Mon Jun 28 16:02:28 2021 +0100

    updated citation, left doi blank as not sure what this will be...

commit 2f2c015
Author: Joe <[email protected]>
Date:   Mon Jun 28 15:48:20 2021 +0100

    updated title to be same as the paper, author list looks the same as paper

commit 9df009d
Merge: 337f0b1 4f5ee09
Author: Sam Abbott <[email protected]>
Date:   Mon Jun 28 14:30:28 2021 +0100

    Merge pull request epiforecasts#390 from RichardMN/fix-render-available-datasets-389

    Fixed glitch in rendering available datasets file - fixes epiforecasts#389

commit 337f0b1
Merge: bf4b680 07b7e39
Author: Sam Abbott <[email protected]>
Date:   Mon Jun 28 14:27:57 2021 +0100

    Merge pull request epiforecasts#383 from epiforecasts/hexisticker

    made draft hexsticker

commit 07b7e39
Merge: de74f9b bf4b680
Author: Joe <[email protected]>
Date:   Mon Jun 28 13:26:22 2021 +0100

    Merge branch 'master' into hexisticker

commit de74f9b
Author: Joe <[email protected]>
Date:   Mon Jun 28 13:25:45 2021 +0100

    made recomended changes, removed old logos and placed hexsticker in correct location

commit 1de2205
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Jun 26 22:56:21 2021 +0300

    Render documentation, generate available datasets file, lint

commit bb115ca
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Jun 26 22:21:55 2021 +0300

    Fixed handling of NULL in summary table, completed country data

commit 4f5ee09
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Jun 26 21:53:43 2021 +0300

    Fixed glitch in rendering available datasets file, added Switzerland test data

commit df7993b
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Jun 24 22:21:28 2021 +0300

    Build documentation

commit 00fd919
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Jun 24 22:11:42 2021 +0300

    Adjusted summary method, began adding source text and url fields

commit 7cd6f05
Merge: 06a7eb4 ea6a48e
Author: Richard Martin-Nielsen <[email protected]>
Date:   Wed Jun 23 21:08:06 2021 +0300

    Merge pull request epiforecasts#386 from RichardMN/hexisticker-regions

    Hexisticker - with region colouring using natural earth data and mapshaper for geometry manipulation

commit ea6a48e
Author: Richard Martin-Nielsen <[email protected]>
Date:   Wed Jun 23 20:31:08 2021 +0300

    Change outlines to be lines, reorder display, remove commented code

commit ce0214d
Author: Richard Martin-Nielsen <[email protected]>
Date:   Tue Jun 22 21:27:05 2021 +0300

    Outlines added to supported countries, palette adjusted, code reorganised slightly.

commit 2815431
Merge: 5a11397 3b18401
Author: Richard Martin-Nielsen <[email protected]>
Date:   Tue Jun 22 20:59:40 2021 +0300

    Merge remote-tracking branch 'upstream/master' into hexisticker-regions

commit 5a11397
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Jun 21 18:36:31 2021 +0300

    Fixed separation of countries with level 1 and level 2 data

commit 628a22f
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Jun 20 13:59:13 2021 +0300

    Update README.md

commit a6beb0a
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Jun 20 13:57:58 2021 +0300

    Add link to regional maps

commit 88f7116
Merge: 57d20c9 a137ddf
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Jun 20 13:56:19 2021 +0300

    Merge branch 'hexisticker-regions' of https://github.com/RichardMN/covidregionaldata into hexisticker-regions

commit 57d20c9
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Jun 20 13:32:12 2021 +0300

    Initial work to show regions for countries where we have regional data

commit a137ddf
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Jun 20 13:32:12 2021 +0300

    Initial work to show regions for countries where we have regional data

commit 06a7eb4
Author: Joe <[email protected]>
Date:   Fri Jun 18 09:29:56 2021 +0100

    altered borders to make regional data clearer

commit fa13d32
Author: Joe <[email protected]>
Date:   Thu Jun 17 13:31:19 2021 +0100

    updated designs

commit 2d91ab1
Merge: 96ee5ad f952cfc
Author: Sam Abbott <[email protected]>
Date:   Wed Jun 16 17:20:51 2021 +0100

    Merge branch 'master' into hexisticker

commit 96ee5ad
Merge: 63f7765 0564367
Author: Joe <[email protected]>
Date:   Wed Jun 16 13:32:36 2021 +0100

    Merge branch 'master' into hexisticker

commit 63f7765
Author: Joe <[email protected]>
Date:   Wed Jun 16 13:28:45 2021 +0100

    made draft hexsticker
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RichardMN committed Oct 31, 2021
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24 changes: 19 additions & 5 deletions .devcontainer/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -34,14 +34,28 @@ RUN install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \
git2r \
&& rm -rf /tmp/downloaded_packages

# add development dependencies
RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")'

# add linux libraries for dependencies
RUN apt-get update \
&& export DEBIAN_FRONTEND=noninteractive \
&& apt-get -y install --no-install-recommends libgdal-dev libudunits2-dev
&& apt-get -y install --no-install-recommends libgdal-dev \
libudunits2-dev libharfbuzz-dev libfribidi-dev \
libjq-dev libprotobuf-dev protobuf-compiler

# add dependencies for logo making
RUN install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \
hexSticker \
showtext \
maps \
sf \
rnaturalearth \
rmapshaper \
&& rm -rf /tmp/downloaded_packages
RUN Rscript -e 'devtools::install_github("ropensci/rnaturalearthdata")'
RUN Rscript -e 'devtools::install_github("ropensci/rnaturalearthhires")'

# install dependencies
# install package 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")'
7 changes: 5 additions & 2 deletions .devcontainer/devcontainer.json
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Expand Up @@ -23,14 +23,17 @@
"extensions": [
"ikuyadeu.r",
"reditorsupport.r-lsp",
"shan.code-settings-sync"
"shan.code-settings-sync",
"searking.preview-vscode",
"tht13.html-preview-vscode",
"formulahendry.code-runner"
],

// Use 'forwardPorts' to make a list of ports inside the container available locally.
// "forwardPorts": [],

// Use 'postCreateCommand' to run commands after the container is created.
// "postCreateCommand": "R --version",
"postCreateCommand": "Rscript -e 'precommit::use_precommit()'",

// Uncomment to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker.
// "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/check-full.yaml
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Expand Up @@ -7,7 +7,7 @@ name: R-CMD-check
branches:
- master
schedule:
- cron: '0 0 * * *'
- cron: '0 0 * * 1'
pull_request:
branches:
- '*'
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17 changes: 10 additions & 7 deletions NEWS.md
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@@ -1,11 +1,15 @@
# covidregionaldata 0.9.3

This release is currrently under development
This release is currently under development

## New data sets

- Support for level 1 region data in Estonia (thanks to @RichardMN). See `?Estonia` for details.
- Support for level 1 region data in Vietnam (thanks to @biocyberman). See `?Vietname` for details.
* Support for level 1 region data in Estonia (thanks to @RichardMN). See `?Estonia` for details.
* Support for level 1 region data in Vietnam (thanks to @biocyberman). See `?Vietnam` for details.

## Other changes

* Updated the package logo to include the newly supported data sets.

# covidregionaldata 0.9.2

Expand Down Expand Up @@ -80,13 +84,13 @@ Thanks to @joseph-palmer, @RichardMN, and @kathsherratt for major contributions
## Technical improvements

* `get_regional_data()` and `get_national_data()` now use R6 method dispatch. This is an internal change and so should have minimal user impact for users of the `get_` functions. However, all datasets are now available to be used as R6 methods (see `get_available_datasets`) which may allow for more modular use cases. These classes can also be initialised using `initialise_dataclass()` which is used internally by both `get_regional_data()` and `get_national_data()`.
* Unit testing has been separated from data downloading which is now tested individually by data set. This allows for contributors to more easily assess the impact of their additions and also allows us to publish data status updates for each data sets (see the README: https://github.com/epiforecasts/covidregionaldata#readme).
* Unit testing has been separated from data downloading which is now tested individually by data set. This allows for contributors to more easily assess the impact of their additions and also allows us to publish data status updates for each data sets (see the README: <https://github.com/epiforecasts/covidregionaldata#readme>).

## Deprecated functions

* `get_available_datasets()` replaces `get_info_covidregionaldata()` to view available data. `get_info_covidregionaldata()` is deprecated.
* `get_interventions_data()` is deprecated. These data no longer update as of December 2020. Check for alternatives at https://supertracker.spi.ox.ac.uk/policy-trackers/
* `get_linelist` is deprecated. Linelist stopped updating June 2020. Up to date linelist data are now behind a login: access at https://global.health/. We are working on a solution for accessing with `covidregionaldata`.
* `get_interventions_data()` is deprecated. These data no longer update as of December 2020. Check for alternatives at <https://supertracker.spi.ox.ac.uk/policy-trackers/>
* `get_linelist` is deprecated. Linelist stopped updating June 2020. Up to date linelist data are now behind a login: access at <https://global.health/>. We are working on a solution for accessing with `covidregionaldata`.

## Data changes since 0.8.3

Expand All @@ -99,7 +103,6 @@ Thanks to @joseph-palmer, @RichardMN, and @kathsherratt for major contributions
* UK level 2 "ltla_code" is now "local_authority_code".
* `get_available_datasets()` now return an origin column rather than a country column and a type column rather than a get_data_function to better reflect the types of data supported.


# covidregionaldata 0.8.3

## New data sets
Expand Down
12 changes: 6 additions & 6 deletions R/Vietnam.R
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Expand Up @@ -4,7 +4,7 @@
#' @description Information for downloading, cleaning
#' and processing covid-19 region data for Vietnam.
#'
#' @source \url{https://covid.ncsc.gov.vn}
#' @source \url{https://covid19.ncsc.gov.vn}
#' @export
#' @concept dataset
#' @family subnational
Expand All @@ -29,10 +29,10 @@ Vietnam <- R6::R6Class("Vietnam",
#' @field common_data_urls List of named links to raw data.
common_data_urls = list(
# nolint start
"case_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=case_by_time",
"death_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=death_by_time",
"recovered_by_time" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces?filter_type=recovered_by_time",
"provinces" = "https://covid.ncsc.gov.vn/api/v3/covid/provinces"
"case_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=case_by_time",
"death_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=death_by_time",
"recovered_by_time" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces?filter_type=recovered_by_time",
"provinces" = "https://covid19.ncsc.gov.vn/api/v3/covid/provinces"
# nolint end
),
#' @field source_data_cols existing columns within the raw data
Expand All @@ -44,7 +44,7 @@ Vietnam <- R6::R6Class("Vietnam",
"Public COVID-19 for Vietnam, curated by NCSC's COVID-19 team",
#' @field source_url Website address for explanation/introduction of the
#' data
source_url = "https://covid.ncsc.gov.vn",
source_url = "https://covid19.ncsc.gov.vn",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
Expand Down
41 changes: 19 additions & 22 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ the temporary directory by default),

``` r
start_using_memoise()
#> Using a cache at: /tmp/RtmprTOAdV
#> Using a cache at: /tmp/RtmpPgZXiv
```

To stop using `memoise` use,
Expand All @@ -105,7 +105,7 @@ 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: 132483 Columns: 8
#> Rows: 142911 Columns: 8
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (3): Country_code, Country, WHO_region
Expand All @@ -117,20 +117,20 @@ nots <- get_national_data()
#> Cleaning data
#> Processing data
nots
#> # A tibble: 132,483 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
#> 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 & 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 132,473 more rows, and 8 more variables: deaths_new <dbl>,
#> # A tibble: 142,911 × 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
#> 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 <dbl>,
#> # deaths_total <dbl>, recovered_new <dbl>, recovered_total <dbl>,
#> # hosp_new <dbl>, hosp_total <dbl>, tested_new <dbl>, tested_total <dbl>
```
Expand Down Expand Up @@ -171,7 +171,7 @@ for example by level 1 region in the UK, use:
``` r
uk_nots <- get_regional_data(country = "UK", verbose = FALSE)
uk_nots
#> # A tibble: 6,916 x 26
#> # A tibble: 7,501 × 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
Expand All @@ -184,16 +184,13 @@ 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 6,906 more rows, and 19 more variables: recovered_new <dbl>,
#> # … with 7,491 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>,
#> # newCasesBySpecimenDate <dbl>, cumDeaths28DaysByDeathDate <dbl>,
#> # cumDeaths28DaysByPublishDate <dbl>, newDeaths28DaysByDeathDate <dbl>,
#> # newDeaths28DaysByPublishDate <dbl>, newPillarFourTestsByPublishDate <lgl>,
#> # newPillarOneTestsByPublishDate <dbl>,
#> # newPillarThreeTestsByPublishDate <dbl>,
#> # newPillarTwoTestsByPublishDate <dbl>
#> # newDeaths28DaysByPublishDate <dbl>, …
```

Now we have the data we can create plots, for example the time-series of
Expand Down
15 changes: 11 additions & 4 deletions inst/make_hexsticker.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,13 @@ library(sf)
library(rnaturalearth)
library(rmapshaper)

# This code may fail if you do not have two more packages installed.
# They are not on CRAN, but can likely be installed with the following
# lines:
# devtools::install_github("ropensci/rnaturalearthdata") # nolint
# devtools::install_github("ropensci/rnaturalearthhires") # nolint
# Alternatively use the provided development dockerfile (optionally via VScode)

# font setup
font_add_google("Zilla Slab Highlight", "useme")

Expand Down Expand Up @@ -62,10 +69,10 @@ regional_outlines <- ms_lines(
gsub(" \\(.*\\)", "", regional_countries$origin, perl = TRUE),
"United States", "United Kingdom"
),
returnclass = "sf"
returnclass = "sf",
scale = 50
),
keep = 0.1,
scale = 50
keep = 0.1
)
)

Expand All @@ -79,7 +86,7 @@ covid_map <- ggplot() +
data = regional_outlines,
aes(colour = factor(RANK)), size = 0.1
) +
coord_sf(crs = "ESRI:54016") +
coord_sf(crs = 54016) +
scale_fill_fermenter(palette = "RdBu") +
theme_void() +
scale_colour_manual(name = "", values = c("black", "black", "black")) +
Expand Down
2 changes: 1 addition & 1 deletion man/Vietnam.Rd
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2 changes: 1 addition & 1 deletion man/all_country_data.Rd
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