_pkgdown.yml

title: ICU data with R

url: https://eth-mds.github.io/ricu

development:
  mode: release

template:
  params:
    bootswatch: flatly

repo:
  url:
    home: https://github.com/eth-mds/ricu
    issue: https://github.com/eth-mds/ricu/issues

reference:
- title: Data loading
  desc: >
    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`.
- subtitle: Concept loading
  desc: >
    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.
  contents:
  - load_concepts
  - concept
  - item
  - load_dictionary
- subtitle: Callback functions
  desc: >
    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.
  contents:
    - transform_fun
    - msg_progress
    - pafi
    - sofa_score
    - sep3
    - susp_inf
    - sirs_score
- subtitle: Query loading
  desc: >
    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`.
  contents:
    - load_id
    - load_ts
    - load_difftime
    - load_src
- title: Tabular ICU data
  desc: >
    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.
  contents:
    - id_tbl
    - id_vars
    - rename_cols
    - expand
    - change_id
    - stay_windows
- title: Data source setup
  desc: >
    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](https://physionet.org), 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.
  contents:
    - data
    - download_src
    - import_src
    - attach_src
    - setup_src_data
    - load_src_cfg
    - data_dir
- title: Utilities
  contents:
    - secs
    - min_or_na
    - write_psv