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Merge yaib configs #12

Merged
merged 54 commits into from
Apr 3, 2024
Merged

Merge yaib configs #12

merged 54 commits into from
Apr 3, 2024

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manuelburger
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@manuelburger manuelburger commented Mar 26, 2024 •
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TODO:

  • outcomes
  • outcomes: add sic support for death_icu and death_hosp
  • sic support for los_hosp
  • outputs
  • respiratory
  • vitals
  • sic support urine_rate
  • Finish integration of spo2 and sao2 from o2sat for missing datasets
  • Support extraction of patient-id for each dataset

prockenschaub and others added 30 commits April 26, 2023 07:50
@prockenschaub
define SIC data structure
0d7e464
@prockenschaub
add SIC to auto attach
9ffcb4d
@prockenschaub
add SIC loading helpers
2884e3f
@prockenschaub
add callback hooks to postprocess tbls on import
2b39787
@prockenschaub
add callback to deserialise sicdb data_float_h
d459959
@prockenschaub
add missing tbl_callback function
32b8f60
@prockenschaub
add sic_itm inspired by hrd_itm
6afe44c
@prockenschaub
adjust data_float_h config to recent changes
bc41f88
@prockenschaub
add hr and crea as examples for sicdb
b53c592
@prockenschaub
add sex and death concepts for sic
3ca5b04
@prockenschaub
add vitals, labs, height, and weight concepts for sic
9396da5
@prockenschaub
add age and los_icu concepts
e84ea7d
@prockenschaub
add most medication concepts for sic
b9350a1
@prockenschaub
fix preproc for data_float_h
5419ab4 
some values are only taken once during the hour and thus have a cnt=1 and rawdata=NA. The actual data is stored in Val, which otherwise holds the average. Since after expansion, rawdata is the main data field, the value from Val needs to be moved to rawdata in this case.
@dplecko @prockenschaub
add OMR to miiv
078149e
@dplecko @prockenschaub
add miiv omr
e5be7e8
@dplecko @prockenschaub
load_concepts() concepts arg doc fix
c8d0c9b
@dplecko @prockenschaub
load_concepts.integer() src NULL fix
b1e2aed
@manuelburger
Fix sic config
9c3481f
@manuelburger
Properly support full rawdata found in sic
d5d4c07
@manuelburger
Remove print
31d48f7
@manuelburger
Add utility functions proposed by prockenschaub here: https://githu…
eb41aaa 
…b.com/eth-mds/ricu/pull/30/files
@manuelburger
Merge branch 'sicdb' of github.com:prockenschaub/ricu-package into si…
3621a42 
…c-bugfixes
@manuelburger
Fix configs for sic based on prockenschaub
e4c930a
@manuelburger
Merge branch 'main' of github.com:ratschlab/ricu into sic-bugfixes
6ef9b50
@manuelburger
Fix sic configs based on https://github.com/prockenschaub/ricu-pack…
ee48363 
…age/tree/sicdb
@manuelburger
Remove prints and use ricu msg
c2b8c49
@manuelburger
Remove redundant report_probolems
e5061d4
@manuelburger
Add prints and tempdir arg
2c8d763
@manuelburger
Merge branch 'sic-bugfixes' of github.com:ratschlab/ricu into sic-bug…
71672bf 
…fixes
@manuelburger manuelburger linked an issue Mar 26, 2024 that may be closed by this pull request
Merge YAIB configs #9
Closed
@manuelburger
Use apply_map for sic sex
9ebaf7f
@manuelburger
Merge branch 'sic-bugfixes' of github.com:ratschlab/ricu into merge-y…
1650203 
…aib-configs # Please enter a commit message to explain why this merge is necessary,
@mlondschien
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Can you rebase to get a reasonable diff?

@manuelburger
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Can you rebase to get a reasonable diff?

I think right now the diff is fine without the rebase, no?

@manuelburger manuelburger self-assigned this Mar 31, 2024
@mlondschien
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Top! IIUC these are mostly taken from YAIB / icuDG-preprocessing, whose authors I trust more on this than myself. Generally, I would like to see more comments, as all the callbacks are non-trival. But this should be done by the original author, so for anything copy-pasted that's ok.

@manuelburger manuelburger merged commit 0f8362d into main Apr 3, 2024
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@manuelburger manuelburger deleted the merge-yaib-configs branch April 3, 2024 13:28
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Merge YAIB configs
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@manuelburger @mlondschien @prockenschaub @dplecko