Function reference • ICU data with R

Data loading Data can be loaded from cofigured data sources, either in the form of data concepts or by directly querying one of the underlying tables. Depending on what route is taken for loading, data is returned either as `data.table` or as one of the `ricu`-provided tabular data types `id_tbl` or `ts_tbl`.
Concept loading Data concepts in `ricu` provide an abstraction that allows to define how a clinical concept (such as heart rate) can be retrieved from a data source. Once defined, concepts can be loaded in a data source agnostic and concise manner.
`load_concepts()`	Load concept data
`new_cncpt()` `is_cncpt()` `init_cncpt()` `new_concept()` `concept()` `is_concept()` `as_concept()`	Data Concepts
`new_itm()` `is_itm()` `init_itm()` `new_item()` `item()` `as_item()` `is_item()`	Data items
`load_dictionary()` `concept_availability()` `explain_dictionary()`	Load concept dictionaries
Callback functions To provided the required flexibility for defining data concepts, individual items can specify callback functions that are used for post-processing steps for loaded data. Some function fatories are provided for creating simple callback functions and more involved scenarios, such as a SOFA score concept require specialized functions, which might even expose function arguments which can be used to fine-tune the concept bahavior.
`transform_fun()` `binary_op()` `comp_na()` `set_val()` `apply_map()` `convert_unit()`	Item callback utilities
`msg_progress()` `fmt_msg()`	Message signaling nested with progress reporting
`pafi()` `safi()` `vent_ind()` `gcs()` `urine24()` `vaso60()` `vaso_ind()` `supp_o2()` `avpu()` `bmi()` `norepi_equiv()`	Concept callback functions
`sofa_score()` `sofa_resp()` `sofa_coag()` `sofa_liver()` `sofa_cardio()` `sofa_cns()` `sofa_renal()`	SOFA score label
`sep3()` `delta_cummin()` `delta_start()` `delta_min()`	Sepsis 3 label
`susp_inf()`	Suspicion of infection label
`sirs_score()` `qsofa_score()` `news_score()` `mews_score()`	SIRS score label
Query loading Tables can be queried directly by creating an R expression that evaluates to a logical vector indicating which rows to load. The expression is evaluated within the data context, powered by the non-standard evaluation framework provided by `rlang`.
`load_id()` `load_ts()` `load_win()`	Load data as `id_tbl` or `ts_tbl` objects
`load_src()` `load_difftime()`	Low level functions for loading data
Tabular ICU data Inheriting from `data.table`, `ricu` provides classes intended to simplify handling of tabular ICU data. For dynamic (i.e. time-varying) data (such as vital sign data), `ts_tbl` is used and for static data (for example an admission diagnonsis), `id_tbl` objects are used. Alongside these data structures, several utility functions are provided.
`id_tbl()` `is_id_tbl()` `as_id_tbl()` `ts_tbl()` `is_ts_tbl()` `as_ts_tbl()` `win_tbl()` `is_win_tbl()` `as_win_tbl()` `as.data.table(<id_tbl>)` `as.data.frame(<id_tbl>)` `validate_tbl()`	Tabular ICU data classes
`id_vars()` `id_var()` `id_col()` `index_var()` `index_col()` `dur_var()` `dur_col()` `dur_unit()` `meta_vars()` `data_vars()` `data_var()` `data_col()` `interval()` `time_unit()` `time_step()` `time_vars()`	ICU class meta data utilities
`rename_cols()` `rm_cols()` `change_interval()` `change_dur_unit()` `rm_na()` `sort(<id_tbl>)` `is_sorted()` `duplicated(<id_tbl>)` `anyDuplicated(<id_tbl>)` `unique(<id_tbl>)` `is_unique()` `aggregate(<id_tbl>)` `dt_gforce()` `replace_na()`	ICU class data utilities
`expand()` `collapse()` `has_no_gaps()` `has_gaps()` `is_regular()` `fill_gaps()` `remove_gaps()` `slide()` `slide_index()` `hop()`	Time series utility functions
`change_id()` `upgrade_id()` `downgrade_id()`	Switch between id types
`stay_windows()`	Stays
Data source setup For a data source to be usable via `ricu`, a JSON-based configuration is required and some preprocessing is carried out by `ricu` as an initial setup step by `import_src()` and for data sets hosted on Physionet, a downloader is available as `download_src()`. As a final step, making data available to `ricu`, `attach_src()` is automatically called for configured data sources at package loading.
`data`	ICU datasets
`download_src()`	Data download utilities
`import_src()` `import_tbl()`	Data import utilities
`attach_src()` `detach_src()` `setup_src_env()`	Data attach utilities
`setup_src_data()`	Data setup
`load_src_cfg()`	Load configuration for a data source
`data_dir()` `src_data_dir()` `auto_attach_srcs()` `config_paths()` `get_config()` `set_config()`	File system utilities
Utilities
`secs()` `mins()` `hours()` `days()` `weeks()`	Utilities for `difftime`
`min_or_na()` `max_or_na()` `is_val()` `not_val()` `is_true()` `is_false()` `last_elem()` `first_elem()`	Utility functions
`write_psv()` `read_psv()`	Read and write utilities

Reference

Data loading

Concept loading

Callback functions

Query loading

Tabular ICU data

Data source setup

Utilities