Update data-sources.json

Allow passing a directory containing jsons to data-sources arg

* Separate entries in the concept dict by category.

* Use underscore in blood_gas.

* Add picdb.json.

* Some fewer rows.

* Add "easy" entries to concept dicts.

* Add 'sub_var': 'itemid'

* Add some 'defaults' values.

* Get rid of surgery vital signs.

* load_difftime and id_win_helper for picdb.

* Add picdb to startup datasets

* Update row counts: chartevents, labevents

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Co-authored-by: Manuel Burger <manuel.burger@inf.ethz.ch>

* Add picdb ca and cai.

* Add sbp and dbp.

* Add tco2

* Add 1002 - 'pulse' to HR.

* fio2

* Add ph.

* po2

* Add sex.

* age.

* death

* height: get rid of biopsy variable.

* weight: get rid of labevents entry

* alb

* alt

* ast

* bili and bilidir.

* ck

* ckmb and cl

* fix conversion ckmb

* Add conversion to crea.

* glu add conversion.

* mg

* na

* phos

* tnt

* Fix outcome json.

* samp

* Add working `picdb_sampling`

* Fix unit conversion on `alb`

---------

Co-authored-by: Manuel Burger <manuel.burger@inf.ethz.ch>

* define SIC data structure

* add SIC to auto attach

* add SIC loading helpers

* add callback hooks to postprocess tbls on import

* add callback to deserialise sicdb data_float_h

* add missing tbl_callback function

* add sic_itm inspired by hrd_itm

* adjust data_float_h config to recent changes

* add hr and crea as examples for sicdb

* add sex and death concepts for sic

* add vitals, labs, height, and weight concepts for sic

* add age and los_icu concepts

* add most medication concepts for sic

* fix preproc for data_float_h

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.

* add OMR to miiv

* add miiv omr

* load_concepts() concepts arg doc fix

* load_concepts.integer() src NULL fix

* Fix sic config

* Properly support full rawdata found in sic

* Remove print

* Add utility functions proposed by `prockenschaub` here: https://github.com/eth-mds/ricu/pull/30/files

* Fix configs for `sic` based on `prockenschaub`

* Fix `sic` configs based on https://github.com/prockenschaub/ricu-package/tree/sicdb

* Remove prints and use ricu msg

* Remove redundant `report_probolems`

* Add prints and tempdir arg

* Cleanup prints

* Fix blood_gas config

* Fix sic table config

* Use finer resolution rawdata where available

* Pass tbl callback correctly

* Fix missing callback application

* Apply callback before split_write

* Config updates:
- Fix sic bugs
- Slack temp range

* Fix configs

* Fix callback

* Use `apply_map` for `sic` `sex`

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Co-authored-by: prockenschaub <rockenschaub.patrick@gmail.com>
Co-authored-by: Drago <www.plecko@gmail.com>

* Test ci.

* Add qpdf.

* Try message=False

* Set env variables above.

* global message=F, warning=F

* Try conda

* add environment.yml.

* Add some dependencies.

* Add r-knitr to env.yaml.

* install knitr manually.

* Add r-covr and r-units to env.yaml.

* Test R location

* execute command in shell

* Execute steps in shell

* Add pdflatex to environment

* check pdflatex

* add texlive env

* move

* don't check for pdflatex

* Add texlive to env

* Remove texlive action

* Update env

* Upd env

* Add tinytex install

* force tiny tex

* Update env and install demos

* Fix typo

* No need to make docs

* Add codetools to env

* Suppress manual check

* add qpdf

* Add picdb data-env doclines

* Don't check doc size

* run roxygen

* Add qpdf

* Add env var

* Add env var to check step

* Edit

* Change to r-qpdf

* Add qpdf

* remove force

* remove env var

* grep exclude pdf size warning

* don't cache conda env

* Add caching back

* ch sh

* Revert

* Delete coverage.yaml, pkgdown.yaml

* Add comment to check.yaml, only run this on ubuntu.

* cleanup environment.yamls.

* cleanup environment.yamls 2.

* mimic-demo is on conda-forge.

* yaml -> yml.

* r-mimic-demo -> r-mimic.demo

---------

Co-authored-by: Manuel Burger <manuel.burger@inf.ethz.ch>