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Add Estonia data #414

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Add Estonia data #414

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RichardMN
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Inspired by @biocyberman work on Vietnam I had another look and found usable open data for Estonia.

This provides open data for number of cases and number of tests for Estonia, but there are some quirks.

https://www-terviseamet-ee.translate.goog/et/koroonaviirus/avaandmed?_x_tr_sl=et&_x_tr_tl=en&_x_tr_hl=lt&_x_tr_pto=ajax,se,elem

Estonia lists a number of tests and a number of cases for each county (there are 15) for each result, P or N. The google translation isn't quite clear on how these are differentiated and I've not yet tried resolving this against a different presentation (e.g., aggregates):

A case is considered to be a first positive or first negative test per person, i. repeat tests are not considered. Thus, there can be a maximum of 2 cases per person - one positive, one negative.

With this limitation, this is first go at bringing in the data for tests and cases, as well as calculating a test positivity metric. Comments and advice welcome.

RichardMN and others added 3 commits September 12, 2021 19:46
@RichardMN
Squashed commit of the following:
661bef3 
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
Create estonia-doodles.R
f25b2ee
@RichardMN
Initial full implementation of Estonia in covidregionaldata
09e3c63 
Removed experimental doodles code, added workflow, regenerated data - appears to work.
@RichardMN RichardMN requested a review from seabbs September 15, 2021 17:36
@RichardMN RichardMN added the enhancement New feature or request label Sep 15, 2021
seabbs
seabbs reviewed Sep 16, 2021
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R/Estonia.R
@@ -0,0 +1,86 @@
#' Estonia Class for downloading, cleaning and processing notification data
#' @description Information for downloading, cleaning
#' and processing COVID-19 region data for Estonia
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some more detail on the source would be helpful here.

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Any idea why actions aren’t running on this PR, @seabbs ? Did I break something in the workflow directory? (I seem to have made changes to more files than I thought I had so I may have to clean this PR.)

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Nice work - great to be adding in some more data. The core of this (i.e adding Estonia) looks good and runs for me with sensible results. From the code + explanation your handling of tests seems sensible but I think there might need to be a note in the documentation about this. For most of the datasets, I assume total tests includes negative tests from people who were formerly positive and so this would be the same but unusual to see it stated like this. I think perhaps google is giving an odd definition of case as they seem to be using it for people both positive and negative which is odd!

Missing currently: News update + version bump + logo update.

Before merging might need to fix whatever is happening with the commit history.. is this due to you working on a fork (perhaps just work on a branch in the main repository to avoid this issue)? Not really clear why actions aren't working either but again assume its due to working on an out of date fork? Ick git is tricky.

@RichardMN RichardMN mentioned this pull request Sep 16, 2021
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Closing in favour of #417

I still need to add to news, bump the version and update the map - this might be synchronized with adding Vietnam.

@RichardMN RichardMN closed this Sep 16, 2021
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