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Feature missing reference dates preprocessing #106

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merged 54 commits into from
Jul 8, 2022

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@seabbs seabbs commented Jul 7, 2022

This PR is a partial replacement for #64 and includes work on the preprocessing components of #43 (i.e missing data).

adrian-lison and others added 30 commits May 13, 2022 14:18
Moved the whole observations block to have all required variables assigned before
We need the "group" column for internal processing. Maybe we should use a more seldom keyword.
Solving #99 (rename group variable to be more unique) for the preprocessing functions touched by this PR
@seabbs seabbs marked this pull request as ready for review July 8, 2022 09:22
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seabbs commented Jul 8, 2022

To do:

  • Add tests for enw_missing_reference
  • Add tests for enw_complete_dates
  • Update saved examples
  • Add news item

@epinowcast epinowcast deleted a comment from codecov bot Jul 8, 2022
@seabbs seabbs linked an issue Jul 8, 2022 that may be closed by this pull request
@epinowcast epinowcast deleted a comment from codecov bot Jul 8, 2022
@seabbs seabbs requested a review from adrian-lison July 8, 2022 11:47
@epinowcast epinowcast deleted a comment from codecov bot Jul 8, 2022
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codecov bot commented Jul 8, 2022

Codecov Report

Merging #106 (194862e) into develop (3dc4ac0) will increase coverage by 1.13%.
The diff coverage is 79.24%.

❗ Current head 194862e differs from pull request most recent head d314b7f. Consider uploading reports for the commit d314b7f to get more accurate results

@@             Coverage Diff             @@
##           develop     #106      +/-   ##
===========================================
+ Coverage    63.16%   64.29%   +1.13%     
===========================================
  Files           12       12              
  Lines          961     1042      +81     
===========================================
+ Hits           607      670      +63     
- Misses         354      372      +18     
Impacted Files Coverage Δ
R/model-tools.R 38.37% <ø> (ø)
R/model.R 30.52% <0.00%> (-3.00%) ⬇️
R/utils.R 65.71% <ø> (ø)
R/preprocess.R 95.63% <98.82%> (+0.95%) ⬆️

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LGTM (self-review)

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seabbs commented Jul 8, 2022

@adrian-lison planning on merging this today as really need to get something ticked off ahead of the weekend!

I think everything is pretty much doing what we want and have put quite a few tests in place to catch potential issues. Note that running the example script + README was really needed to make sure nothing had changed so at some point we really need to get some more of the code downstream of preprocessing into unit testing.

If you have a chance to kick the tires a bit that would be great though potentially could wait for the next big PR (i.e redesigning the interface) which will slam through over the next few days.

I am also getting quite a few requests for the missing data model (i.e 2 😆 ) so it would be cool to get this in asap. I still need to fix the merge issues and make the reorgs we discussed for the stan code but perhaps we can start planning what to do about the post-processing?

@seabbs seabbs merged commit 47eae4a into develop Jul 8, 2022
@seabbs seabbs deleted the feature-missing-reference-dates-preprocessing branch July 8, 2022 14:25
@seabbs seabbs mentioned this pull request Jul 22, 2022
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