Squashed commit of the following:

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

.Rbuildignore

@@ -28,3 +28,5 @@ SMG.md
 ^inst/paper$
 ^inst/examples$
 ^\.devcontainer$
+^CRAN-SUBMISSION$
+^\.covrignore$

.covrignore

@@ -0,0 +1,25 @@
+R/Brazil.R
+R/Belgium.R
+R/Canada.R
+R/Colombia.R
+R/Covid19DataHub.R
+R/Cuba.R
+R/ECDC.R
+R/Estonia.R
+R/France.R
+R/Germany.R
+R/Google.R
+R/India.R
+R/Italy.R
+R/JHU.R
+R/JRC.R
+R/Lithuania.R
+R/Mexico.R
+R/Netherlands.R
+R/SouthAfrica.R
+R/Switzerland.R
+R/UK.R
+R/USA.R
+R/WHO.R
+R/test-DataClass.R
+R/get_linelist.R

.github/workflows/Belgium.yaml

@@ -7,34 +7,17 @@ name: Belgium
 
 jobs:
   Belgium:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Brazil.yaml

@@ -7,34 +7,17 @@ name: Brazil
 
 jobs:
   Brazil:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Canada.yaml

@@ -7,34 +7,18 @@ name: Canada
 
 jobs:
   Canada:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Colombia.yaml

@@ -7,34 +7,17 @@ name: Colombia
 
 jobs:
   Colombia:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Covid19DataHub.yaml

@@ -7,34 +7,17 @@ name: Covid19DataHub
 
 jobs:
   Covid19DataHub:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Cuba.yaml

@@ -7,34 +7,17 @@ name: Cuba
 
 jobs:
   Cuba:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/ECDC.yaml

@@ -7,34 +7,17 @@ name: ECDC
 
 jobs:
   ECDC:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Estonia.yaml

@@ -7,34 +7,17 @@ name: Estonia
 
 jobs:
   Estonia:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/France.yaml

@@ -7,34 +7,17 @@ name: France
 
 jobs:
   France:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .