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Adjust for Netherlands - remove Hospitalisation data - partial fix for #430 #446

Merged
merged 4 commits into from
Feb 5, 2022
Merged

Adjust for Netherlands - remove Hospitalisation data - partial fix for #430 #446

merged 4 commits into from
Feb 5, 2022

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RichardMN
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RIVM seem to have removed the Hospitalisation data from their data. They also note that there are delays in the updating of their data, but for the meantime we may remove the Hospitalisation code (or comment it out) so we still get some Netherlands data from RIVM.

@RichardMN RichardMN linked an issue Jan 29, 2022 that may be closed by this pull request
Upstream data changes break our regional code - Colombia, Cuba, India, United States #430
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@RichardMN RichardMN mentioned this pull request Jan 31, 2022
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@RichardMN RichardMN mentioned this pull request Feb 4, 2022
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@kathsherratt kathsherratt force-pushed the fix-netherlands-430-remove-hospitalisation branch from db4b213 to c048eb8 Compare February 4, 2022 20:40
kathsherratt
kathsherratt approved these changes Feb 4, 2022
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I think the failing checks are due to complete() and otherwise locally (without the tidyr update) this works fine.

seabbs
seabbs approved these changes Feb 5, 2022
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LGTM. I have dropped the commented code to keep with our style guide but can look back at this PR when/if becomes available again. Nice one.

@seabbs seabbs merged commit 579f853 into epiforecasts:master Feb 5, 2022
RichardMN added a commit to RichardMN/covidregionaldata that referenced this pull request Mar 13, 2022
@RichardMN
Squashed commit of the following:
e00e291 
commit f85a90a
Merge: 1c281f9 8d93aa4
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 11 09:59:56 2022 +0000

    Merge pull request epiforecasts#462 from pitmonticone/master

    Fixed a typo in the README file

commit 8d93aa4
Author: Pietro Monticone <[email protected]>
Date:   Thu Feb 10 12:48:47 2022 +0100

    Render updated README.md

commit e49a58b
Author: Pietro Monticone <[email protected]>
Date:   Mon Feb 7 12:47:54 2022 +0100

    Update README.Rmd

    Fix a typo.

commit 1c281f9
Author: Sam Abbott <[email protected]>
Date:   Mon Feb 7 10:40:53 2022 +0000

    Update .covrignore

commit 43f573e
Author: Sam Abbott <[email protected]>
Date:   Mon Feb 7 10:18:21 2022 +0000

    Update .covrignore

commit de1fadb
Author: Sam Abbott <[email protected]>
Date:   Mon Feb 7 10:00:28 2022 +0000

    update commits since badge

commit 1766716
Author: Sam Abbott <[email protected]>
Date:   Mon Feb 7 09:58:36 2022 +0000

    add covrignore

commit 72ada04
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 19:12:38 2022 +0000

    update description

commit 7cceee8
Merge: 79faa57 7b1d329
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:56:37 2022 +0000

    Merge pull request epiforecasts#461 from epiforecasts/bug-460-colombia-failing-tests

    Bug: epiforecasts#460 Colombia failing tests

commit 7b1d329
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:45:33 2022 +0000

    update test data

commit c0c8ab9
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:33:02 2022 +0000

    clean up date processing

commit 79faa57
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:11:25 2022 +0000

    add coverage dep

commit 2b5b6d3
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:08:16 2022 +0000

    fi xcoverage

commit 8b27d8f
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:06:55 2022 +0000

    exclude data classes from coverage reports

commit 97394ef
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 17:57:14 2022 +0000

    update test-coverage.yaml

commit 61ff808
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 17:45:35 2022 +0000

    update all actions

commit 398597e
Merge: 9534602 86c4421
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 17:30:20 2022 +0000

    Merge branch 'master' of https://github.com/epiforecasts/covidregionaldata

commit 9534602
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 17:29:51 2022 +0000

    update Belgium yaml

commit 86c4421
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 13:10:44 2022 +0000

    Update R-CMD-check.yaml

commit 27032ed
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 13:09:49 2022 +0000

    Update test-coverage.yaml

commit 7ee6ee6
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 22:23:20 2022 +0000

    CRAN

commit 2cba860
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 22:14:57 2022 +0000

    drop stringri

commit 6989d72
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 21:40:32 2022 +0000

    update netherlands and prune link issues

commit 9c9b2ad
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:54:02 2022 +0000

    drop vietnam

commit 3187e0f
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:38:22 2022 +0000

    fix CRAN check issue

commit cb20bcf
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:36:15 2022 +0000

    update news

commit 83f48a4
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:34:08 2022 +0000

    CRAN comments updated

commit e8009dd
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:26:40 2022 +0000

    remove static working on CRAN tag

commit 0fc7850
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:23:37 2022 +0000

    updated to non-dev version

commit a580b44
Merge: 3eae8ee 500ae67
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:22:32 2022 +0000

    Merge pull request epiforecasts#433 from RichardMN/fix-colombia-data-430-require-rsocrata

    Alternate fix colombia data 430 which makes RSocrata suggested

commit 500ae67
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:21:54 2022 +0000

    update news

commit 0abf54f
Merge: 9756397 3eae8ee
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:18:37 2022 +0000

    merge master

commit 3eae8ee
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:54:15 2022 +0000

    update news

commit 579f853
Merge: e4b57dd ed1a14d
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:52:11 2022 +0000

    Merge pull request epiforecasts#446 from RichardMN/fix-netherlands-430-remove-hospitalisation

    Adjust for Netherlands - remove Hospitalisation data - partial fix for epiforecasts#430

commit ed1a14d
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:51:28 2022 +0000

    drop commented code

commit 96b5b32
Merge: d1b7997 e4b57dd
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:46:55 2022 +0000

    Merge branch 'master' into fix-netherlands-430-remove-hospitalisation

commit e4b57dd
Merge: 6c43144 4cf4da6
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:44:30 2022 +0000

    Merge pull request epiforecasts#451 from epiforecasts/RichardMN-test-json-2

    Add tests for json_reader function and sample json data

commit 4cf4da6
Merge: 2c6c101 6c43144
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:43:10 2022 +0000

    Merge branch 'master' into RichardMN-test-json-2

commit 6c43144
Merge: eb58d9c d1d64fb
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:42:02 2022 +0000

    Merge pull request epiforecasts#456 from epiforecasts/depreciations

    Depreciations

commit d1d64fb
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:31:35 2022 +0000

    clean up tests

commit e2079d2
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:27:00 2022 +0000

    update package checking

commit 2d31173
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:10:36 2022 +0000

    update news

commit 6700bc2
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:09:37 2022 +0000

    switch get_linelist to depreciate_stop vs warn

commit aff45c6
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:01:41 2022 +0000

    drop dep args from get_regional_data

commit 927d9f1
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:59:39 2022 +0000

    update tests for get_national_data

commit c6c36a3
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:57:17 2022 +0000

    drop the country arg from get_national_data

commit 88b2833
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:54:09 2022 +0000

    drop get_info_covidregionaldata

commit 5266915
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:50:16 2022 +0000

    depreciate get_interventions

commit eb58d9c
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:45:52 2022 +0000

    update news with epiforecasts#448 details

commit 9756397
Merge: b607e1f f54b220
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:29:09 2022 +0000

    Merge branch 'master' into fix-colombia-data-430-require-rsocrata

commit d1b7997
Merge: c048eb8 f54b220
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:28:15 2022 +0000

    Merge branch 'master' into fix-netherlands-430-remove-hospitalisation

commit 2c6c101
Merge: f9672ac f54b220
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:27:59 2022 +0000

    Merge branch 'master' into RichardMN-test-json-2

commit f54b220
Merge: 1ebcc74 9a10f04
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:27:30 2022 +0000

    Merge pull request epiforecasts#448 from RichardMN/fix-vietnam-447-switch-to-stringi

    Refactor Vietnam cleaning code and change string conversion function - fixes epiforecasts#447

commit 9a10f04
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:26:37 2022 +0000

    streamline code

commit ddc6dad
Merge: 8a1b602 1ebcc74
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:20:48 2022 +0000

    Merge branch 'master' into fix-vietnam-447-switch-to-stringi

commit 1ebcc74
Merge: 20c280c 2f8c4d7
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:59:26 2022 +0000

    Merge pull request epiforecasts#453 from epiforecasts/bug-449-tidyr-complete

    Bug epiforecasts#449 tidyr complete

commit 2f8c4d7
Merge: 845b500 20c280c
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:59:20 2022 +0000

    Merge branch 'master' into bug-449-tidyr-complete

commit 845b500
Merge: ab8c599 a6e7fac
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:59:07 2022 +0000

    Merge pull request epiforecasts#455 from epiforecasts/bug-454-countrycode

    Bug 454 countrycode

commit 20c280c
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:55:39 2022 +0000

    use preferably

commit a6e7fac
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:47:33 2022 +0000

    turn off regional testing unless requested

commit 7448db9
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:24:23 2022 +0000

    turn off warning

commit ab8c599
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 16:46:25 2022 +0000

    update news

commit 281f8f8
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 16:44:00 2022 +0000

    update testing data

commit ffdd364
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 16:30:52 2022 +0000

    test processing reversion

commit ee41f59
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 16:16:35 2022 +0000

    use dplyr group_vars

commit c048eb8
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Jan 29 21:48:43 2022 +0200

    Adjustment to check Netherlands works without Hospitalisation data

commit b607e1f
Author: Richard Martin-Nielsen <[email protected]>
Date:   Fri Feb 4 21:43:40 2022 +0200

    Vietnam fix added

commit 190ab71
Author: Richard Martin-Nielsen <[email protected]>
Date:   Fri Feb 4 21:20:43 2022 +0200

    Squashed commit of the following:

    commit 14e112c
    Author: Sam Abbott <[email protected]>
    Date:   Fri Feb 4 15:50:18 2022 +0000

        add github to vscode tools for dev environmenth

    commit a851c75
    Author: Sam Abbott <[email protected]>
    Date:   Fri Feb 4 15:43:07 2022 +0000

        switch to preferably template for website

commit 412d544
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 17:49:37 2022 +0000

    ungroup and then regroup

commit d75476b
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 17:27:44 2022 +0000

    fix fill_empty_dates_with_na test

commit 2e98e5e
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 17:25:31 2022 +0000

    make sure any changes to variable order doesn't impact output

commit b9887be
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 16:48:27 2022 +0000

    make suggested changes

commit f9672ac
Author: Hugo Gruson <[email protected]>
Date:   Fri Feb 4 17:08:14 2022 +0100

    Use less strict tests for JSON input data
    Since we cannot assume it will always be rectangular before the cleaning step

commit 14e112c
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:50:18 2022 +0000

    add github to vscode tools for dev environmenth

commit a851c75
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:43:07 2022 +0000

    switch to preferably template for website

commit e1afd31
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Dec 2 19:18:25 2021 +0200

    Update NEWS with JSON tests

commit 8790ebf
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Oct 3 17:48:12 2021 +0300

    Fixing reference to non-existent dataframe

commit e48e358
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Sep 27 20:26:59 2021 +0300

    Add tests for the download_JSON method

commit c9e9ca8
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Sep 27 20:15:59 2021 +0300

    Add tests for json_reader function and sample json data

commit 07e27d9
Merge: 7a00270 2bec63f
Author: Kath Sherratt <[email protected]>
Date:   Fri Feb 4 15:28:44 2022 +0000

    Merge branch 'master' into fix-colombia-data-430-require-rsocrata

commit 2bec63f
Merge: a13fd4e 6f2753e
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:28:39 2022 +0000

    Merge pull request epiforecasts#450 from epiforecasts/fix-lintr-warnings

    Fix lintr warnings

commit a13fd4e
Merge: 35d6938 fd1219f
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:26:52 2022 +0000

    Merge pull request epiforecasts#445 from DavisVaughan/fix/reliance-on-complete-column-order

    Don't rely on exact column ordering when grouped data is involved

commit 6f2753e
Author: Hugo Gruson <[email protected]>
Date:   Fri Feb 4 16:25:46 2022 +0100

    Fix lintr warnings

    so we don't get nagged with annotations on PRs

commit fd1219f
Merge: 46b22ac 35d6938
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:25:26 2022 +0000

    Merge branch 'master' into fix/reliance-on-complete-column-order

commit 7a00270
Merge: b077c70 35d6938
Author: Kath Sherratt <[email protected]>
Date:   Fri Feb 4 15:23:46 2022 +0000

    Merge branch 'master' into fix-colombia-data-430-require-rsocrata

commit 35d6938
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:22:06 2022 +0000

    Update devcontainer.json

commit 70adf70
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:20:55 2022 +0000

    Create build-image.yaml

commit f29752e
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:19:26 2022 +0000

    Drop docker from full commit

commit 4aa5732
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:15:27 2022 +0000

    Hugo: ctb -> aut (epiforecasts#416)

commit b077c70
Merge: 3e2f873 097708f
Author: kathsherratt <[email protected]>
Date:   Fri Feb 4 15:07:54 2022 +0000

    Merge branch 'master' into pr/433

commit 8a1b602
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Jan 31 22:07:24 2022 +0200

    Add stringi to imports in DESCRIPTION

commit 4506168
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Jan 31 21:57:23 2022 +0200

    Reorg clean_common, switch functions used for string conversion

commit 46b22ac
Author: DavisVaughan <[email protected]>
Date:   Mon Jan 10 10:23:41 2022 -0500

    Don't rely on exact column ordering when grouped data is involved

commit 097708f
Merge: 950e625 1a99fa7
Author: Sam Abbott <[email protected]>
Date:   Fri Dec 10 21:43:52 2021 +0000

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

    Fix website URL

commit 3e2f873
Author: Richard Martin-Nielsen <[email protected]>
Date:   Fri Dec 3 21:01:34 2021 +0200

    Remove work-around for when RSocrata package is not installed

commit 1a99fa7
Author: Hugo Gruson <[email protected]>
Date:   Fri Dec 3 17:04:19 2021 +0000

    Fix website URL

commit 950e625
Author: Sam Abbott <[email protected]>
Date:   Fri Dec 3 16:37:48 2021 +0000

    Update NEWS.md

commit b93e19d
Merge: f6c9759 007b535
Author: Sam Abbott <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Dec 1 19:50:08 2021 +0200

    Update all_country_data.rda

commit ed0f6c0
Author: Richard Martin-Nielsen <[email protected]>
Date:   Wed Dec 1 19:36:35 2021 +0200

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

commit c2de6c8
Author: Richard Martin-Nielsen <[email protected]>
Date:   Wed Dec 1 19:27:29 2021 +0200

    Replace require with requireNamespace in Colombia.R

commit 2a7f105
Merge: aea9b96 04009e7
Author: Sam Abbott <[email protected]>
Date:   Wed Dec 1 15:23:21 2021 +0000

    Merge branch 'master' into alternate-switzerland

commit 04009e7
Merge: d1630f5 68200f9
Author: Sam Abbott <[email protected]>
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 <[email protected]>
Date:   Wed Dec 1 13:52:07 2021 +0000

    switch to bootstrap 5 for pkgdown

commit d1630f5
Merge: 71d7b1f ddbdb8e
Author: Sam Abbott <[email protected]>
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 <[email protected]>
Date:   Wed Dec 1 13:47:52 2021 +0000

    Merge branch 'master' into fix-logo

commit a19643f
Author: Hugo Gruson <[email protected]>
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 <[email protected]>
Date:   Wed Dec 1 10:52:16 2021 +0000

    Merge branch 'master' into alternate-switzerland

commit ac3e63e
Author: Sam Abbott <[email protected]>
Date:   Wed Dec 1 10:42:33 2021 +0000

    Update pr-checklist.yaml

commit 71d7b1f
Merge: 2e5cabc fb10488
Author: Sam Abbott <[email protected]>
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 <[email protected]>
Date:   Wed Dec 1 10:43:26 2021 +0100

    Run devtools::document()

commit fe79373
Author: Hugo Gruson <[email protected]>
Date:   Wed Dec 1 10:43:16 2021 +0100

    Get rid of tidyselect

commit 3f5c115
Author: Hugo Gruson <[email protected]>
Date:   Wed Dec 1 10:27:44 2021 +0100

    Remove withr dependency as well

commit fb10488
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 19:09:00 2021 +0100

    Remove action re-building JOSS paper

commit 79857e9
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 19:03:17 2021 +0100

    Use dplyr::tibble in tests as well

commit d3c150b
Author: Hugo Gruson <[email protected]>
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 <[email protected]>
Date:   Tue Nov 30 12:53:15 2021 +0100

    Run devtools::document()

commit 4032abd
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 12:43:43 2021 +0100

    Use stringr everywhere instead of stringi

commit 1c4ede0
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 12:34:20 2021 +0100

    Get tibble functions from dplyr

commit a499cc0
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 12:10:05 2021 +0100

    Re-export pipe from dplyr

commit 2e5cabc
Author: Sam Abbott <[email protected]>
Date:   Mon Nov 29 13:43:29 2021 +0000

    Update NEWS.md

commit d1350d9
Merge: 8c77b82 782256c
Author: Sam Abbott <[email protected]>
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 <[email protected]>
Date:   Mon Nov 29 07:40:01 2021 +0000

    add missing sum

commit 4c7cb8c
Author: Sebastian Funk <[email protected]>
Date:   Mon Nov 29 07:19:09 2021 +0000

    fix Germany case/death data

commit e14e767
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Nov 28 22:48:40 2021 +0200

    Manual edit of reexports.Rd to get around CMD check fail

commit 3063942
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Nov 28 20:53:52 2021 +0200

    Document changes to Colombia data.

commit 7f84ec8
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Nov 20 20:27:06 2021 +0200

    Document specific download function for Colombia, amend WORDLIST

commit f9087a7
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Nov 20 20:22:58 2021 +0200

    Apply require method for using RSocrata package to allow it to be suggested in DESCRIPTION

commit 6828efd
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Nov 20 18:51:21 2021 +0200

    Revert "Shift to make RSocrata recommended but not required"

    This reverts commit 26a19d0.

commit 26a19d0
Author: Richard Martin-Nielsen <[email protected]>
Date:   Tue Nov 9 20:09:39 2021 +0200

    Shift to make RSocrata recommended but not required

commit d5db53b
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Nov 4 22:48:31 2021 +0200

    Hand edit to add dplyr::n

commit 576085a
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Nov 4 22:47:25 2021 +0200

    Add import of dplyr::n

commit beec592
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Nov 4 22:26:36 2021 +0200

    Add RSocrata to imports

commit f982a25
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Nov 4 22:18:22 2021 +0200

    Colombia fixes

commit 01572c1
Author: Richard Martin-Nielsen <[email protected]>
Date:   Wed Nov 3 22:20:47 2021 +0200

    Initial adjustment for new data source

    Switch to using Socrata api to download case list from Colombian open data source. Aggregation to level 1 not yet working.

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

    Check package once a week vs daily

commit 0d8a6e5
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Oct 11 22:19:24 2021 +0300

    Fixes to keep lintr happier

commit 4eb12da
Author: Richard Martin-Nielsen <[email protected]>
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 <[email protected]>
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 <[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
RichardMN added a commit to RichardMN/covidregionaldata that referenced this pull request Mar 13, 2022
@RichardMN
Squashed commit of the following:
f5002a8 
commit f85a90a
Merge: 1c281f9 8d93aa4
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 11 09:59:56 2022 +0000

    Merge pull request epiforecasts#462 from pitmonticone/master

    Fixed a typo in the README file

commit 8d93aa4
Author: Pietro Monticone <[email protected]>
Date:   Thu Feb 10 12:48:47 2022 +0100

    Render updated README.md

commit e49a58b
Author: Pietro Monticone <[email protected]>
Date:   Mon Feb 7 12:47:54 2022 +0100

    Update README.Rmd

    Fix a typo.

commit 1c281f9
Author: Sam Abbott <[email protected]>
Date:   Mon Feb 7 10:40:53 2022 +0000

    Update .covrignore

commit 43f573e
Author: Sam Abbott <[email protected]>
Date:   Mon Feb 7 10:18:21 2022 +0000

    Update .covrignore

commit de1fadb
Author: Sam Abbott <[email protected]>
Date:   Mon Feb 7 10:00:28 2022 +0000

    update commits since badge

commit 1766716
Author: Sam Abbott <[email protected]>
Date:   Mon Feb 7 09:58:36 2022 +0000

    add covrignore

commit 72ada04
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 19:12:38 2022 +0000

    update description

commit 7cceee8
Merge: 79faa57 7b1d329
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:56:37 2022 +0000

    Merge pull request epiforecasts#461 from epiforecasts/bug-460-colombia-failing-tests

    Bug: epiforecasts#460 Colombia failing tests

commit 7b1d329
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:45:33 2022 +0000

    update test data

commit c0c8ab9
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:33:02 2022 +0000

    clean up date processing

commit 79faa57
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:11:25 2022 +0000

    add coverage dep

commit 2b5b6d3
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:08:16 2022 +0000

    fi xcoverage

commit 8b27d8f
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 18:06:55 2022 +0000

    exclude data classes from coverage reports

commit 97394ef
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 17:57:14 2022 +0000

    update test-coverage.yaml

commit 61ff808
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 17:45:35 2022 +0000

    update all actions

commit 398597e
Merge: 9534602 86c4421
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 17:30:20 2022 +0000

    Merge branch 'master' of https://github.com/epiforecasts/covidregionaldata

commit 9534602
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 17:29:51 2022 +0000

    update Belgium yaml

commit 86c4421
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 13:10:44 2022 +0000

    Update R-CMD-check.yaml

commit 27032ed
Author: Sam Abbott <[email protected]>
Date:   Sun Feb 6 13:09:49 2022 +0000

    Update test-coverage.yaml

commit 7ee6ee6
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 22:23:20 2022 +0000

    CRAN

commit 2cba860
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 22:14:57 2022 +0000

    drop stringri

commit 6989d72
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 21:40:32 2022 +0000

    update netherlands and prune link issues

commit 9c9b2ad
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:54:02 2022 +0000

    drop vietnam

commit 3187e0f
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:38:22 2022 +0000

    fix CRAN check issue

commit cb20bcf
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:36:15 2022 +0000

    update news

commit 83f48a4
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:34:08 2022 +0000

    CRAN comments updated

commit e8009dd
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:26:40 2022 +0000

    remove static working on CRAN tag

commit 0fc7850
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:23:37 2022 +0000

    updated to non-dev version

commit a580b44
Merge: 3eae8ee 500ae67
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:22:32 2022 +0000

    Merge pull request epiforecasts#433 from RichardMN/fix-colombia-data-430-require-rsocrata

    Alternate fix colombia data 430 which makes RSocrata suggested

commit 500ae67
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:21:54 2022 +0000

    update news

commit 0abf54f
Merge: 9756397 3eae8ee
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 20:18:37 2022 +0000

    merge master

commit 3eae8ee
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:54:15 2022 +0000

    update news

commit 579f853
Merge: e4b57dd ed1a14d
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:52:11 2022 +0000

    Merge pull request epiforecasts#446 from RichardMN/fix-netherlands-430-remove-hospitalisation

    Adjust for Netherlands - remove Hospitalisation data - partial fix for epiforecasts#430

commit ed1a14d
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:51:28 2022 +0000

    drop commented code

commit 96b5b32
Merge: d1b7997 e4b57dd
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:46:55 2022 +0000

    Merge branch 'master' into fix-netherlands-430-remove-hospitalisation

commit e4b57dd
Merge: 6c43144 4cf4da6
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:44:30 2022 +0000

    Merge pull request epiforecasts#451 from epiforecasts/RichardMN-test-json-2

    Add tests for json_reader function and sample json data

commit 4cf4da6
Merge: 2c6c101 6c43144
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:43:10 2022 +0000

    Merge branch 'master' into RichardMN-test-json-2

commit 6c43144
Merge: eb58d9c d1d64fb
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:42:02 2022 +0000

    Merge pull request epiforecasts#456 from epiforecasts/depreciations

    Depreciations

commit d1d64fb
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:31:35 2022 +0000

    clean up tests

commit e2079d2
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:27:00 2022 +0000

    update package checking

commit 2d31173
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:10:36 2022 +0000

    update news

commit 6700bc2
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:09:37 2022 +0000

    switch get_linelist to depreciate_stop vs warn

commit aff45c6
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 19:01:41 2022 +0000

    drop dep args from get_regional_data

commit 927d9f1
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:59:39 2022 +0000

    update tests for get_national_data

commit c6c36a3
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:57:17 2022 +0000

    drop the country arg from get_national_data

commit 88b2833
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:54:09 2022 +0000

    drop get_info_covidregionaldata

commit 5266915
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:50:16 2022 +0000

    depreciate get_interventions

commit eb58d9c
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:45:52 2022 +0000

    update news with epiforecasts#448 details

commit 9756397
Merge: b607e1f f54b220
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:29:09 2022 +0000

    Merge branch 'master' into fix-colombia-data-430-require-rsocrata

commit d1b7997
Merge: c048eb8 f54b220
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:28:15 2022 +0000

    Merge branch 'master' into fix-netherlands-430-remove-hospitalisation

commit 2c6c101
Merge: f9672ac f54b220
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:27:59 2022 +0000

    Merge branch 'master' into RichardMN-test-json-2

commit f54b220
Merge: 1ebcc74 9a10f04
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:27:30 2022 +0000

    Merge pull request epiforecasts#448 from RichardMN/fix-vietnam-447-switch-to-stringi

    Refactor Vietnam cleaning code and change string conversion function - fixes epiforecasts#447

commit 9a10f04
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:26:37 2022 +0000

    streamline code

commit ddc6dad
Merge: 8a1b602 1ebcc74
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 18:20:48 2022 +0000

    Merge branch 'master' into fix-vietnam-447-switch-to-stringi

commit 1ebcc74
Merge: 20c280c 2f8c4d7
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:59:26 2022 +0000

    Merge pull request epiforecasts#453 from epiforecasts/bug-449-tidyr-complete

    Bug epiforecasts#449 tidyr complete

commit 2f8c4d7
Merge: 845b500 20c280c
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:59:20 2022 +0000

    Merge branch 'master' into bug-449-tidyr-complete

commit 845b500
Merge: ab8c599 a6e7fac
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:59:07 2022 +0000

    Merge pull request epiforecasts#455 from epiforecasts/bug-454-countrycode

    Bug 454 countrycode

commit 20c280c
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:55:39 2022 +0000

    use preferably

commit a6e7fac
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:47:33 2022 +0000

    turn off regional testing unless requested

commit 7448db9
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 17:24:23 2022 +0000

    turn off warning

commit ab8c599
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 16:46:25 2022 +0000

    update news

commit 281f8f8
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 16:44:00 2022 +0000

    update testing data

commit ffdd364
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 16:30:52 2022 +0000

    test processing reversion

commit ee41f59
Author: Sam Abbott <[email protected]>
Date:   Sat Feb 5 16:16:35 2022 +0000

    use dplyr group_vars

commit c048eb8
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Jan 29 21:48:43 2022 +0200

    Adjustment to check Netherlands works without Hospitalisation data

commit b607e1f
Author: Richard Martin-Nielsen <[email protected]>
Date:   Fri Feb 4 21:43:40 2022 +0200

    Vietnam fix added

commit 190ab71
Author: Richard Martin-Nielsen <[email protected]>
Date:   Fri Feb 4 21:20:43 2022 +0200

    Squashed commit of the following:

    commit 14e112c
    Author: Sam Abbott <[email protected]>
    Date:   Fri Feb 4 15:50:18 2022 +0000

        add github to vscode tools for dev environmenth

    commit a851c75
    Author: Sam Abbott <[email protected]>
    Date:   Fri Feb 4 15:43:07 2022 +0000

        switch to preferably template for website

commit 412d544
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 17:49:37 2022 +0000

    ungroup and then regroup

commit d75476b
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 17:27:44 2022 +0000

    fix fill_empty_dates_with_na test

commit 2e98e5e
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 17:25:31 2022 +0000

    make sure any changes to variable order doesn't impact output

commit b9887be
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 16:48:27 2022 +0000

    make suggested changes

commit f9672ac
Author: Hugo Gruson <[email protected]>
Date:   Fri Feb 4 17:08:14 2022 +0100

    Use less strict tests for JSON input data
    Since we cannot assume it will always be rectangular before the cleaning step

commit 14e112c
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:50:18 2022 +0000

    add github to vscode tools for dev environmenth

commit a851c75
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:43:07 2022 +0000

    switch to preferably template for website

commit e1afd31
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Dec 2 19:18:25 2021 +0200

    Update NEWS with JSON tests

commit 8790ebf
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Oct 3 17:48:12 2021 +0300

    Fixing reference to non-existent dataframe

commit e48e358
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Sep 27 20:26:59 2021 +0300

    Add tests for the download_JSON method

commit c9e9ca8
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Sep 27 20:15:59 2021 +0300

    Add tests for json_reader function and sample json data

commit 07e27d9
Merge: 7a00270 2bec63f
Author: Kath Sherratt <[email protected]>
Date:   Fri Feb 4 15:28:44 2022 +0000

    Merge branch 'master' into fix-colombia-data-430-require-rsocrata

commit 2bec63f
Merge: a13fd4e 6f2753e
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:28:39 2022 +0000

    Merge pull request epiforecasts#450 from epiforecasts/fix-lintr-warnings

    Fix lintr warnings

commit a13fd4e
Merge: 35d6938 fd1219f
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:26:52 2022 +0000

    Merge pull request epiforecasts#445 from DavisVaughan/fix/reliance-on-complete-column-order

    Don't rely on exact column ordering when grouped data is involved

commit 6f2753e
Author: Hugo Gruson <[email protected]>
Date:   Fri Feb 4 16:25:46 2022 +0100

    Fix lintr warnings

    so we don't get nagged with annotations on PRs

commit fd1219f
Merge: 46b22ac 35d6938
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:25:26 2022 +0000

    Merge branch 'master' into fix/reliance-on-complete-column-order

commit 7a00270
Merge: b077c70 35d6938
Author: Kath Sherratt <[email protected]>
Date:   Fri Feb 4 15:23:46 2022 +0000

    Merge branch 'master' into fix-colombia-data-430-require-rsocrata

commit 35d6938
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:22:06 2022 +0000

    Update devcontainer.json

commit 70adf70
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:20:55 2022 +0000

    Create build-image.yaml

commit f29752e
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:19:26 2022 +0000

    Drop docker from full commit

commit 4aa5732
Author: Sam Abbott <[email protected]>
Date:   Fri Feb 4 15:15:27 2022 +0000

    Hugo: ctb -> aut (epiforecasts#416)

commit b077c70
Merge: 3e2f873 097708f
Author: kathsherratt <[email protected]>
Date:   Fri Feb 4 15:07:54 2022 +0000

    Merge branch 'master' into pr/433

commit 8a1b602
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Jan 31 22:07:24 2022 +0200

    Add stringi to imports in DESCRIPTION

commit 4506168
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Jan 31 21:57:23 2022 +0200

    Reorg clean_common, switch functions used for string conversion

commit 46b22ac
Author: DavisVaughan <[email protected]>
Date:   Mon Jan 10 10:23:41 2022 -0500

    Don't rely on exact column ordering when grouped data is involved

commit 097708f
Merge: 950e625 1a99fa7
Author: Sam Abbott <[email protected]>
Date:   Fri Dec 10 21:43:52 2021 +0000

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

    Fix website URL

commit 3e2f873
Author: Richard Martin-Nielsen <[email protected]>
Date:   Fri Dec 3 21:01:34 2021 +0200

    Remove work-around for when RSocrata package is not installed

commit 1a99fa7
Author: Hugo Gruson <[email protected]>
Date:   Fri Dec 3 17:04:19 2021 +0000

    Fix website URL

commit 950e625
Author: Sam Abbott <[email protected]>
Date:   Fri Dec 3 16:37:48 2021 +0000

    Update NEWS.md

commit b93e19d
Merge: f6c9759 007b535
Author: Sam Abbott <[email protected]>
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 <[email protected]>
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 <[email protected]>
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 <[email protected]>
Date:   Wed Dec 1 19:50:08 2021 +0200

    Update all_country_data.rda

commit ed0f6c0
Author: Richard Martin-Nielsen <[email protected]>
Date:   Wed Dec 1 19:36:35 2021 +0200

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

commit c2de6c8
Author: Richard Martin-Nielsen <[email protected]>
Date:   Wed Dec 1 19:27:29 2021 +0200

    Replace require with requireNamespace in Colombia.R

commit 2a7f105
Merge: aea9b96 04009e7
Author: Sam Abbott <[email protected]>
Date:   Wed Dec 1 15:23:21 2021 +0000

    Merge branch 'master' into alternate-switzerland

commit aea9b96
Merge: 0d8a6e5 71d7b1f
Author: Sam Abbott <[email protected]>
Date:   Wed Dec 1 10:52:16 2021 +0000

    Merge branch 'master' into alternate-switzerland

commit ac3e63e
Author: Sam Abbott <[email protected]>
Date:   Wed Dec 1 10:42:33 2021 +0000

    Update pr-checklist.yaml

commit 007b535
Author: Hugo Gruson <[email protected]>
Date:   Wed Dec 1 10:43:26 2021 +0100

    Run devtools::document()

commit fe79373
Author: Hugo Gruson <[email protected]>
Date:   Wed Dec 1 10:43:16 2021 +0100

    Get rid of tidyselect

commit 3f5c115
Author: Hugo Gruson <[email protected]>
Date:   Wed Dec 1 10:27:44 2021 +0100

    Remove withr dependency as well

commit 79857e9
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 19:03:17 2021 +0100

    Use dplyr::tibble in tests as well

commit d3c150b
Author: Hugo Gruson <[email protected]>
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 <[email protected]>
Date:   Tue Nov 30 12:53:15 2021 +0100

    Run devtools::document()

commit 4032abd
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 12:43:43 2021 +0100

    Use stringr everywhere instead of stringi

commit 1c4ede0
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 12:34:20 2021 +0100

    Get tibble functions from dplyr

commit a499cc0
Author: Hugo Gruson <[email protected]>
Date:   Tue Nov 30 12:10:05 2021 +0100

    Re-export pipe from dplyr

commit e14e767
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Nov 28 22:48:40 2021 +0200

    Manual edit of reexports.Rd to get around CMD check fail

commit 3063942
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sun Nov 28 20:53:52 2021 +0200

    Document changes to Colombia data.

commit 7f84ec8
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Nov 20 20:27:06 2021 +0200

    Document specific download function for Colombia, amend WORDLIST

commit f9087a7
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Nov 20 20:22:58 2021 +0200

    Apply require method for using RSocrata package to allow it to be suggested in DESCRIPTION

commit 6828efd
Author: Richard Martin-Nielsen <[email protected]>
Date:   Sat Nov 20 18:51:21 2021 +0200

    Revert "Shift to make RSocrata recommended but not required"

    This reverts commit 26a19d0.

commit 26a19d0
Author: Richard Martin-Nielsen <[email protected]>
Date:   Tue Nov 9 20:09:39 2021 +0200

    Shift to make RSocrata recommended but not required

commit d5db53b
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Nov 4 22:48:31 2021 +0200

    Hand edit to add dplyr::n

commit 576085a
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Nov 4 22:47:25 2021 +0200

    Add import of dplyr::n

commit beec592
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Nov 4 22:26:36 2021 +0200

    Add RSocrata to imports

commit f982a25
Author: Richard Martin-Nielsen <[email protected]>
Date:   Thu Nov 4 22:18:22 2021 +0200

    Colombia fixes

commit 01572c1
Author: Richard Martin-Nielsen <[email protected]>
Date:   Wed Nov 3 22:20:47 2021 +0200

    Initial adjustment for new data source

    Switch to using Socrata api to download case list from Colombian open data source. Aggregation to level 1 not yet working.

commit 0d8a6e5
Author: Richard Martin-Nielsen <[email protected]>
Date:   Mon Oct 11 22:19:24 2021 +0300

    Fixes to keep lintr happier

commit 4eb12da
Author: Richard Martin-Nielsen <[email protected]>
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 <[email protected]>
Date:   Mon Oct 4 22:16:44 2021 +0300

    Moved old Switzerland code to SwitzerlandAlt, written functional 2-stage download method
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@kathsherratt kathsherratt kathsherratt approved these changes

@seabbs seabbs seabbs approved these changes

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Upstream data changes break our regional code - Colombia, Cuba, India, United States
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@RichardMN @seabbs @kathsherratt