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commit 097708f
Merge: 950e625 1a99fa7
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Dec 10 21:43:52 2021 +0000

    Merge pull request epiforecasts#444 from epiforecasts/Bisaloo-patch-1

    Fix website URL

commit 1a99fa7
Author: Hugo Gruson <Bisaloo@users.noreply.github.com>
Date:   Fri Dec 3 17:04:19 2021 +0000

    Fix website URL

commit 950e625
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Dec 3 16:37:48 2021 +0000

    Update NEWS.md

commit b93e19d
Merge: f6c9759 007b535
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Dec 3 16:36:05 2021 +0000

    Merge pull request epiforecasts#437 from epiforecasts/fewer-deps

    Reduce the number of `Imports`

commit f6c9759
Merge: 4509d81 ac3e63e
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Dec 3 16:33:49 2021 +0000

    Merge pull request epiforecasts#439 from epiforecasts/pr-checklist-news

    Update pr-checklist.yaml to include news nudge

commit 4509d81
Merge: 04009e7 b24f2b6
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Dec 3 16:33:08 2021 +0000

    Merge pull request epiforecasts#429 from epiforecasts/alternate-switzerland

    New data source for Switzerland - fix for epiforecasts#412

commit b24f2b6
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Wed Dec 1 19:50:08 2021 +0200

    Update all_country_data.rda

commit ed0f6c0
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Wed Dec 1 19:36:35 2021 +0200

    Fixed documentation links to FOPH as source of Switzerland data, updated News

commit 2a7f105
Merge: aea9b96 04009e7
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 15:23:21 2021 +0000

    Merge branch 'master' into alternate-switzerland

commit 04009e7
Merge: d1630f5 68200f9
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 14:27:05 2021 +0000

    Merge pull request epiforecasts#443 from epiforecasts/feature-boostrap-5-in-docs

    Switch to bootstrap 5 for pkgdown

commit 68200f9
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 13:52:07 2021 +0000

    switch to bootstrap 5 for pkgdown

commit d1630f5
Merge: 71d7b1f ddbdb8e
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 13:48:12 2021 +0000

    Merge pull request epiforecasts#442 from epiforecasts/fix-logo

    Fix giant logo by specifying width instead of height

commit ddbdb8e
Merge: a19643f 71d7b1f
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 13:47:52 2021 +0000

    Merge branch 'master' into fix-logo

commit a19643f
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Wed Dec 1 14:30:11 2021 +0100

    Fix giant logo by specifying width instead of height
    fix epiforecasts#440

commit aea9b96
Merge: 0d8a6e5 71d7b1f
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 10:52:16 2021 +0000

    Merge branch 'master' into alternate-switzerland

commit ac3e63e
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 10:42:33 2021 +0000

    Update pr-checklist.yaml

commit 71d7b1f
Merge: 2e5cabc fb10488
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Dec 1 10:21:14 2021 +0000

    Merge pull request epiforecasts#438 from epiforecasts/rm-joss-action

    Remove action re-building JOSS paper

commit 007b535
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Wed Dec 1 10:43:26 2021 +0100

    Run devtools::document()

commit fe79373
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Wed Dec 1 10:43:16 2021 +0100

    Get rid of tidyselect

commit 3f5c115
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Wed Dec 1 10:27:44 2021 +0100

    Remove withr dependency as well

commit fb10488
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Tue Nov 30 19:09:00 2021 +0100

    Remove action re-building JOSS paper

commit 79857e9
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Tue Nov 30 19:03:17 2021 +0100

    Use dplyr::tibble in tests as well

commit d3c150b
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Tue Nov 30 18:59:59 2021 +0100

    Remove broken rlang::.data import
    to prevent it from being understood as a re-export

commit e711456
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Tue Nov 30 12:53:15 2021 +0100

    Run devtools::document()

commit 4032abd
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Tue Nov 30 12:43:43 2021 +0100

    Use stringr everywhere instead of stringi

commit 1c4ede0
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Tue Nov 30 12:34:20 2021 +0100

    Get tibble functions from dplyr

commit a499cc0
Author: Hugo Gruson <hugo.gruson@protonmail.com>
Date:   Tue Nov 30 12:10:05 2021 +0100

    Re-export pipe from dplyr

commit 2e5cabc
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Mon Nov 29 13:43:29 2021 +0000

    Update NEWS.md

commit d1350d9
Merge: 8c77b82 782256c
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Mon Nov 29 13:41:00 2021 +0000

    Merge pull request epiforecasts#436 from epiforecasts/fix-germany

    fix Germany case/death data

commit 782256c
Author: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date:   Mon Nov 29 07:40:01 2021 +0000

    add missing sum

commit 4c7cb8c
Author: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date:   Mon Nov 29 07:19:09 2021 +0000

    fix Germany case/death data

commit 8c77b82
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Tue Oct 12 10:20:55 2021 +0100

    Check package once a week vs daily

commit 0d8a6e5
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Mon Oct 11 22:19:24 2021 +0300

    Fixes to keep lintr happier

commit 4eb12da
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Mon Oct 11 22:05:46 2021 +0300

    Cleaning code added and running. Passes tests.

    Removed AltSwitzerland code, generated data file of sample data and list of data sets.

commit 76e4c44
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Mon Oct 4 22:16:44 2021 +0300

    Moved old Switzerland code to SwitzerlandAlt, written functional 2-stage download method

commit b5b9cbf
Merge: c782b57 91d0f0c
Author: Sam Abbott <s.e.abbott12@gmail.com>
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 <richard.martin@alumni.utoronto.ca>
Date:   Thu Sep 30 09:12:37 2021 +0300

    Rebuilt all country data table and Vietnam documentation

commit 1d6c024
Author: Tri Luu <ilumitr@users.noreply.github.com>
Date:   Thu Sep 30 09:38:37 2021 +0700

    Update stable API URL of Vietnam

commit c782b57
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Tue Sep 28 09:17:04 2021 +0000

    update hex and docker hex deps

commit 73784b7
Merge: c59154d d1232f1
Author: Sam Abbott <s.e.abbott12@gmail.com>
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 <s.e.abbott12@gmail.com>
Date:   Mon Sep 27 11:52:46 2021 +0000

    update description, news and run tests

commit b3af1a6
Merge: 4b26675 c59154d
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Sep 27 11:34:25 2021 +0000

    fix merge issues

commit c59154d
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Sep 27 11:28:14 2021 +0000

    add precommit initialisation to vscode devcontainer

commit c9d5b19
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Sep 27 11:27:07 2021 +0000

    update dockerfile for new deps

commit 8401fc8
Merge: aa85f36 da185c9
Author: Sam Abbott <s.e.abbott12@gmail.com>
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 <contact@samabbott.co.uk>
Date:   Mon Sep 20 11:06:33 2021 +0100

    Update DESCRIPTION

commit 9c35694
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Sun Sep 19 21:23:51 2021 +0300

    lint cleaning

commit 26cd8ad
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Sun Sep 19 21:19:07 2021 +0300

    Remove prefixes in vietnam_codes.R

commit 2c20067
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
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 <richard.martin@alumni.utoronto.ca>
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 <richard.martin@alumni.utoronto.ca>
Date:   Sun Sep 19 18:56:41 2021 +0300

    Merge branch 'json-reader' into pr/413

commit 5681a2c
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Fri Sep 17 22:04:01 2021 +0300

    Fixing final glitches in clean_common

commit 3aeddbe
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Fri Sep 17 21:40:09 2021 +0300

    Closer to a tidy version of cleaning Vietnam data

commit da185c9
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Sep 17 16:51:23 2021 +0100

    Update DESCRIPTION

commit 27f77f1
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Sep 17 16:51:09 2021 +0100

    Update NEWS.md

commit fc0d356
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Sep 17 16:50:56 2021 +0100

    bump news

commit 7bd4fb0
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Thu Sep 16 21:43:23 2021 +0300

    Using JSON reader to download Vietnam code

commit aff8dbd
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Thu Sep 16 20:41:16 2021 +0300

    Add Estonia.yaml

commit cab4d97
Merge: 24bd668 1426e7a
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
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 <richard.martin@alumni.utoronto.ca>
Date:   Thu Sep 16 20:33:41 2021 +0300

    Transfer Estonia code into new clean branch

commit 1426e7a
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Thu Sep 16 20:33:41 2021 +0300

    Transfer Estonia code into new clean branch

commit abf4cdd
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
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 <richard.martin@alumni.utoronto.ca>
Date:   Thu Sep 16 19:57:23 2021 +0300

    Reformatting of code

commit ce5de11
Merge: 0f0cafb 29070dd
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
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 <biocyberman@gmail.com>
Date:   Wed Sep 15 21:36:40 2021 +0200

    Refactor code for PR epiforecasts#413

commit 7ca169a
Author: biocyberman <biocyberman@gmail.com>
Date:   Mon Sep 13 19:09:18 2021 +0200

    Change data source for Vietnam

commit 7edc95c
Author: biocyberman <biocyberman@gmail.com>
Date:   Mon Sep 13 00:31:35 2021 +0200

    Update with cases_death from 5F team

commit cd25e34
Author: biocyberman <biocyberman@gmail.com>
Date:   Thu Sep 2 21:17:11 2021 +0200

    Add empty locations to Unknown

commit abcd78a
Author: biocyberman <biocyberman@gmail.com>
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 <s.e.abbott12@gmail.com>
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 <s.e.abbott12@gmail.com>
Date:   Fri Aug 6 15:01:09 2021 +0100

    Merge branch 'master' into sshh-bot

commit 4a05152
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Aug 6 14:23:10 2021 +0100

    roll back to dev pkgdown

commit a519d49
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Aug 6 14:20:41 2021 +0100

    make bot less bossy

commit 66da16e
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Aug 6 12:43:15 2021 +0100

    use CRAN pkgdown

commit 0baa18c
Merge: 28d70a0 41d2258
Author: Sam Abbott <s.e.abbott12@gmail.com>
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 <s.e.abbott12@gmail.com>
Date:   Thu Jul 15 10:44:02 2021 +0000

    moves doi badges around

commit fe21a13
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 15 10:39:59 2021 +0000

    fixes citation by rebuilding readme

commit 28d70a0
Merge: 2e0bb8b 63b0d55
Author: Sam Abbott <s.e.abbott12@gmail.com>
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 <palmer-2@hotmail.co.uk>
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 <palmer-2@hotmail.co.uk>
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 <s.e.abbott12@gmail.com>
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 <palmer-2@hotmail.co.uk>
Date:   Thu Jul 8 10:06:13 2021 +0100

    fixed Richards last name

commit 8fe326b
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Jul 5 11:32:57 2021 +0000

    update citation

commit d51eabc
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Jul 5 10:29:44 2021 +0000

    CRAN check

commit 7794fb0
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Jul 5 09:11:33 2021 +0000

    CRAN comments

commit 08022ac
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Mon Jul 5 09:11:10 2021 +0000

    spelling

commit 2aa0847
Merge: b7eeeaa 5b0d347
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Sun Jul 4 17:40:32 2021 +0100

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

commit 5b0d347
Author: Arfon Smith <arfon@users.noreply.github.com>
Date:   Sat Jul 3 22:02:29 2021 +0100

    Fixing paper formatting.

commit b7eeeaa
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Fri Jul 2 09:58:07 2021 +0100

    Remove zenodo links and reference

commit 4165c25
Merge: dea9278 a260533
Author: Sam Abbott <s.e.abbott12@gmail.com>
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 <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 16:40:27 2021 +0100

    Update README.md

commit 992da9e
Author: Richard Martin-Nielsen <richard.martin@alumni.utoronto.ca>
Date:   Thu Jul 1 17:34:50 2021 +0300

    Spelling fix in Readme

commit dea9278
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 14:11:35 2021 +0000

    lithuania in news

commit 4e1b981
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:57:05 2021 +0000

    release candidate

commit 1e095cb
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:44:42 2021 +0000

    fix paper bib

commit 1e4ebb5
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:30:46 2021 +0000

    CRAN comments

commit 0e7e837
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:25:54 2021 +0000

    tweak spelling and lint pass

commit 44fddfc
Merge: a8a97a3 2b6fb38
Author: Sam Abbott <s.e.abbott12@gmail.com>
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 <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 12:58:32 2021 +0000

    update news

commit 78cf455
Merge: 242679f a8a97a3
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 13:36:36 2021 +0100

    Merge branch 'master' into final-joss-checks

commit a8a97a3
Merge: 4ad5583 bd5d30c
Author: Sam Abbott <contact@samabbott.co.uk>
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 <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 12:29:38 2021 +0000

    merge master, fix merge, et al

commit 4ad5583
Merge: 9df009d 6dc82c0
Author: Sam Abbott <contact@samabbott.co.uk>
Date:   Thu Jul 1 13:24:18 2021 +0100

    Merge pull request epiforecasts#393 from epiforecasts:devcontainer

    Devcontainer

commit 6dc82c0
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 12:23:59 2021 +0000

    update prec-commit

commit 49deed2
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 11:56:19 2021 +0000

    docker build working

commit ae46da4
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 11:05:19 2021 +0100

    Update check-full.yaml

commit c030f17
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 09:58:13 2021 +0000

    update naming and add docthis

commit 4a07fd1
Author: seabbs <s.e.abbott12@gmail.com>
Date:   Thu Jul 1 09:53:32 2021 +0000

    switch to devcontainer

commit 242679f
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Thu Jul 1 08:24:21 2021 +0100

    updated versioning and made title case

commit 40d0b9d
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Tue Jun 29 19:33:11 2021 +0300

    Add source fields for country and global sources.

commit c60fb7e
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Tue Jun 29 12:13:20 2021 +0100

    updated version to description and news, also made recomended changes

commit 84aa59e
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Mon Jun 28 16:04:26 2021 +0100

    updated news

commit 611bfc7
Author: Joe <palmer-2@hotmail.co.uk>
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 <palmer-2@hotmail.co.uk>
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 <s.e.abbott12@gmail.com>
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 <s.e.abbott12@gmail.com>
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 <palmer-2@hotmail.co.uk>
Date:   Mon Jun 28 13:26:22 2021 +0100

    Merge branch 'master' into hexisticker

commit de74f9b
Author: Joe <palmer-2@hotmail.co.uk>
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 <richard.martin@utoronto.ca>
Date:   Sat Jun 26 22:56:21 2021 +0300

    Render documentation, generate available datasets file, lint

commit bb115ca
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
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 <richard.martin@utoronto.ca>
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 <richard.martin@utoronto.ca>
Date:   Thu Jun 24 22:21:28 2021 +0300

    Build documentation

commit 00fd919
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
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 <richard.martin@alumni.utoronto.ca>
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 <richard.martin@utoronto.ca>
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 <richard.martin@utoronto.ca>
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 <richard.martin@utoronto.ca>
Date:   Tue Jun 22 20:59:40 2021 +0300

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

commit 5a11397
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
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 <richard.martin@utoronto.ca>
Date:   Sun Jun 20 13:59:13 2021 +0300

    Update README.md

commit a6beb0a
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
Date:   Sun Jun 20 13:57:58 2021 +0300

    Add link to regional maps

commit 88f7116
Merge: 57d20c9 a137ddf
Author: Richard Martin-Nielsen <richard.martin@utoronto.ca>
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 <richard.martin@utoronto.ca>
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 <richard.martin@utoronto.ca>
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 <palmer-2@hotmail.co.uk>
Date:   Fri Jun 18 09:29:56 2021 +0100

    altered borders to make regional data clearer

commit fa13d32
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Thu Jun 17 13:31:19 2021 +0100

    updated designs

commit 2d91ab1
Merge: 96ee5ad f952cfc
Author: Sam Abbott <s.e.abbott12@gmail.com>
Date:   Wed Jun 16 17:20:51 2021 +0100

    Merge branch 'master' into hexisticker

commit 96ee5ad
Merge: 63f7765 0564367
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Wed Jun 16 13:32:36 2021 +0100

    Merge branch 'master' into hexisticker

commit 63f7765
Author: Joe <palmer-2@hotmail.co.uk>
Date:   Wed Jun 16 13:28:45 2021 +0100

    made draft hexsticker
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@RichardMN
RichardMN committed Jan 29, 2022
1 parent c82f769 commit 7cb3866
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Showing 37 changed files with 181 additions and 213 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/pr-checklist.yaml
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Expand Up @@ -14,4 +14,4 @@ jobs:
issue_number: context.issue.number,
owner: context.repo.owner,
repo: context.repo.repo,
body: '👋 Thanks for opening this pull request! Can you please run through the following checklist before requesting review (ticking as complete or if not relevant). \n\n - [ ] Read our [contribution guidelines](https://github.com/epiforecasts/covidregionaldata/wiki/Contributing) if you have not already done so. \n- [ ] If you have altered an existing class please run the tests locally (using `devtools::load_all(); devtools::test()`) first setting `options(testDownload=TRUE, testSource=class-name)` and report your findings. \n- [ ] If you have added a new data class please run the tests locally for that class (using `devtools::load_all(); devtools::test()`). \n- [ ] Check your code passes our CI checks and review any style and code coverage warnings. \n- [ ] Comment with details if unable to get our CI checks to pass or unable to remove all warnings. \n\nThank you again for the contribution. If making large scale changes consider using our `pre-commit` hooks (see the [contributing guide](https://github.com/epiforecasts/covidregionaldata/wiki/Contributing)) to more easily comply with our guidelines.'})
body: '👋 Thanks for opening this pull request! Can you please run through the following checklist before requesting review (ticking as complete or if not relevant). \n\n - [ ] Read our [contribution guidelines](https://github.com/epiforecasts/covidregionaldata/wiki/Contributing) if you have not already done so. \n- [ ] If you have altered an existing class please run the tests locally (using `devtools::load_all(); devtools::test()`) first setting `options(testDownload=TRUE, testSource=class-name)` and report your findings. \n- [ ] If you have added a new data class please run the tests locally for that class (using `devtools::load_all(); devtools::test()`). \n- [ ] Check your code passes our CI checks and review any style and code coverage warnings. \n- [ ] Comment with details if unable to get our CI checks to pass or unable to remove all warnings. \n- [ ] Update the [news](https://github.com/epiforecasts/covidregionaldata/blob/master/NEWS.md) file with information on your changes (crediting yourself at the same time) \n\nThank you again for the contribution. If making large scale changes consider using our `pre-commit` hooks (see the [contributing guide](https://github.com/epiforecasts/covidregionaldata/wiki/Contributing)) to more easily comply with our guidelines.'})
4 changes: 0 additions & 4 deletions DESCRIPTION
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Expand Up @@ -93,19 +93,15 @@ Imports:
jsonlite,
lifecycle,
lubridate,
magrittr,
memoise,
purrr,
R6,
readxl,
rlang,
stringi,
stringr,
tibble,
tidyr (>= 1.0.0),
tidyselect,
vroom,
withr,
xml2
Suggests:
ggplot2,
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19 changes: 6 additions & 13 deletions NAMESPACE
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Expand Up @@ -48,12 +48,14 @@ importFrom(countrycode,countrycode)
importFrom(countrycode,countryname)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_rows)
importFrom(dplyr,count)
importFrom(dplyr,distinct)
importFrom(dplyr,do)
importFrom(dplyr,ends_with)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,full_join)
Expand All @@ -78,6 +80,7 @@ importFrom(dplyr,summarise)
importFrom(dplyr,tally)
importFrom(dplyr,tibble)
importFrom(dplyr,transmute)
importFrom(dplyr,tribble)
importFrom(dplyr,ungroup)
importFrom(dplyr,vars)
importFrom(httr,GET)
Expand All @@ -95,10 +98,10 @@ importFrom(lubridate,month)
importFrom(lubridate,year)
importFrom(lubridate,ymd)
importFrom(lubridate,ymd_hms)
importFrom(magrittr,"%>%")
importFrom(memoise,cache_filesystem)
importFrom(memoise,memoise)
importFrom(purrr,compact)
importFrom(purrr,keep)
importFrom(purrr,map)
importFrom(purrr,map_chr)
importFrom(purrr,map_lgl)
Expand All @@ -113,17 +116,12 @@ importFrom(rlang,"!!")
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,syms)
importFrom(stringi,stri_replace_all)
importFrom(stringi,stri_trans_general)
importFrom(stringi,stri_trim_both)
importFrom(stringr,str_conv)
importFrom(stringr,str_detect)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_to_sentence)
importFrom(stringr,str_to_title)
importFrom(tibble,add_column)
importFrom(tibble,as_tibble)
importFrom(tibble,tibble)
importFrom(tibble,tribble)
importFrom(stringr,str_trim)
importFrom(tidyr,complete)
importFrom(tidyr,drop_na)
importFrom(tidyr,fill)
Expand All @@ -133,13 +131,8 @@ importFrom(tidyr,pivot_longer)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(tidyr,separate)
importFrom(tidyselect,all_of)
importFrom(tidyselect,ends_with)
importFrom(tidyselect,starts_with)
importFrom(tidyselect,vars_select_helpers)
importFrom(utils,download.file)
importFrom(utils,untar)
importFrom(vroom,vroom)
importFrom(withr,with_envvar)
importFrom(xml2,xml_find_first)
importFrom(xml2,xml_text)
3 changes: 2 additions & 1 deletion NEWS.md
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Expand Up @@ -9,8 +9,9 @@ This release is currently under development

## Other changes

* Change the data source for Switzerland to draw data from the Swiss Federal Office of Public Health (FOPH)
* Updated the package logo to include the newly supported data sets.

* Reduced the number of package dependencies (@bisaloo and @RichardMN)
## Bug fixes

- Fixed a bug in the data sourced from Germany so that instead of treating it as a line list of individuals it is treated as a relatively finely resolved count data which needs to be summed up (by @sbfnk).
Expand Down
11 changes: 5 additions & 6 deletions R/Belgium.R
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Expand Up @@ -57,13 +57,13 @@ Belgium <- R6::R6Class("Belgium",
source_url = "https://epistat.wiv-isp.be/covid/",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble tribble
#' @importFrom dplyr tibble tribble
set_region_codes = function() {
self$codes_lookup$`1` <- tibble::tibble(
self$codes_lookup$`1` <- tibble(
level_1_region_code = c("BE-BRU", "BE-VLG", "BE-WAL"),
level_1_region = c("Brussels", "Flanders", "Wallonia")
)
self$codes_lookup$`2` <- tibble::tribble(
self$codes_lookup$`2` <- tribble(
~level_2_region_code, ~level_2_region, ~level_1_region_code,
"BE-VAN", "Antwerpen", "BE-VLG",
"BE-WBR", "BrabantWallon", "BE-WAL",
Expand All @@ -82,8 +82,7 @@ Belgium <- R6::R6Class("Belgium",

#' @description Downloads data from source and (for Belgium)
#' applies an initial data patch.
#' @importFrom dplyr select mutate filter bind_rows
#' @importFrom tibble tribble
#' @importFrom dplyr select mutate filter bind_rows tribble
download = function() {
# do the actual downloading using the parent download method
super$download()
Expand All @@ -92,7 +91,7 @@ Belgium <- R6::R6Class("Belgium",
# For now, we filter out the broken lines and replace them
# with the following data shim

fixed_lines <- tibble::tribble(
fixed_lines <- tribble(
~DATE, ~PROVINCE, ~REGION, ~AGEGROUP, ~SEX, ~CASES,
"2020-04-22", "Limburg", "Flanders", "50-59", "F", 10,
"2021-02-17", "VlaamsBrabant", "Flanders", "10-19", "M", 12
Expand Down
2 changes: 1 addition & 1 deletion R/Brazil.R
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Expand Up @@ -47,7 +47,7 @@ Brazil <- R6::R6Class("Brazil",
source_url = "https://github.com/wcota/covid19br/blob/master/README.en.md",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tribble
#' @importFrom dplyr tibble
set_region_codes = function() {
self$codes_lookup <- tibble(
state_name = c(
Expand Down
2 changes: 1 addition & 1 deletion R/Canada.R
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Expand Up @@ -44,7 +44,7 @@ Canada <- R6::R6Class("Canada",
source_url = "https://open.canada.ca/data/en/dataset/261c32ab-4cfd-4f81-9dea-7b64065690dc", # nolint

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr tibble
set_region_codes = function() {
canada_codes <- tibble(
code = c(
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1 change: 0 additions & 1 deletion R/Colombia.R
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Expand Up @@ -41,7 +41,6 @@ Colombia <- R6::R6Class("Colombia",
source_url = "https://github.com/danielcs88/colombia_covid-19/",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr mutate
set_region_codes = function() {
self$codes_lookup$`1` <- covidregionaldata::colombia_codes
Expand Down
2 changes: 1 addition & 1 deletion R/Cuba.R
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Expand Up @@ -42,7 +42,7 @@ Cuba <- R6::R6Class("Cuba",


#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr tibble
set_region_codes = function() {
self$codes_lookup$`1` <- tibble(
code = c(
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2 changes: 1 addition & 1 deletion R/Estonia.R
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Expand Up @@ -43,7 +43,7 @@ Estonia <- R6::R6Class("Estonia",


#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr tibble
set_region_codes = function() {
self$codes_lookup$`1` <- tibble(
code = c("EE-37",
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1 change: 0 additions & 1 deletion R/France.R
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Expand Up @@ -50,7 +50,6 @@ France <- R6::R6Class("France",


#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr select
set_region_codes = function() {
self$codes_lookup$`1` <- france_codes %>%
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3 changes: 1 addition & 2 deletions R/Germany.R
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Expand Up @@ -44,8 +44,7 @@ Germany <- R6::R6Class("Germany",


#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr mutate
#' @importFrom dplyr tibble
set_region_codes = function() {
self$codes_lookup$`1` <- tibble(
code = c(
Expand Down
2 changes: 1 addition & 1 deletion R/India.R
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Expand Up @@ -37,7 +37,7 @@ India <- R6::R6Class("India",
source_url = "https://www.covid19india.org",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr tibble
set_region_codes = function() {
self$codes_lookup$`1` <- tibble(
code = c(
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2 changes: 1 addition & 1 deletion R/Italy.R
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Expand Up @@ -42,7 +42,7 @@ Italy <- R6::R6Class("Italy",
source_url = "https://github.com/pcm-dpc/COVID-19/blob/master/README_EN.md",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr tibble
set_region_codes = function() {
self$codes_lookup$`1` <- tibble(
code = c(
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1 change: 0 additions & 1 deletion R/JHU.R
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Expand Up @@ -84,7 +84,6 @@ JHU <- R6::R6Class("JHU", # rename to country name
source_url = "https://github.com/CSSEGISandData/COVID-19/",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
set_region_codes = function() {
self$codes_lookup$`1` <- JHU_codes
},
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8 changes: 3 additions & 5 deletions R/Lithuania.R
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Expand Up @@ -184,8 +184,7 @@ Lithuania <- R6::R6Class("Lithuania",
#' @description Common data cleaning for both levels
#'
# nolint start
#' @importFrom dplyr mutate group_by summarise if_else filter select bind_rows rename left_join everything across lead
#' @importFrom tidyselect all_of
#' @importFrom dplyr mutate group_by summarise if_else filter select bind_rows rename left_join everything across lead all_of
#' @importFrom lubridate as_date
# nolint end
clean_common = function() {
Expand Down Expand Up @@ -244,7 +243,7 @@ Lithuania <- R6::R6Class("Lithuania",
# or qualitative)
sum_cols <- names(select(
self$data$raw$main,
"population":tidyselect::last_col()
"population":dplyr::last_col()
))
sum_cols <- sum_cols[!grepl("prc|map_colors", sum_cols)]

Expand Down Expand Up @@ -345,7 +344,6 @@ Lithuania <- R6::R6Class("Lithuania",
#' provided by the source at the level 2 (municipality) regional level.
#'
#' @importFrom dplyr group_by summarise ungroup full_join across if_else
#' @importFrom tidyselect vars_select_helpers
clean_level_1 = function() {
self$data$clean <- self$data$clean %>%
group_by(
Expand All @@ -354,7 +352,7 @@ Lithuania <- R6::R6Class("Lithuania",
) %>%
summarise(
across(
tidyselect::vars_select_helpers$where(is.numeric),
where(is.numeric),
sum
)
) %>%
Expand Down
1 change: 0 additions & 1 deletion R/Mexico.R
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Expand Up @@ -54,7 +54,6 @@ Mexico <- R6::R6Class("Mexico",
source_url = "https://datos.covid-19.conacyt.mx",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr select
set_region_codes = function() {
self$codes_lookup$`1` <- covidregionaldata::mexico_codes %>%
Expand Down
1 change: 0 additions & 1 deletion R/Netherlands.R
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Expand Up @@ -46,7 +46,6 @@ Netherlands <- R6::R6Class("Netherlands",
source_url = "https://data.rivm.nl/covid-19/",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
set_region_codes = function() {

},
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2 changes: 1 addition & 1 deletion R/SouthAfrica.R
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Expand Up @@ -41,7 +41,7 @@ SouthAfrica <- R6::R6Class("SouthAfrica",
source_url = "https://github.com/dsfsi/covid19za",

#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
#' @importFrom dplyr tibble
set_region_codes = function() {
self$codes_lookup$`1` <- tibble(
code = c(
Expand Down

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