concept_dictionary: Load concept dictionaries

In septic-tank/ricu: Intensive Care Unit Data with R

Description

Data concepts can be specified in JSON format as a concept dictionary which can be read and parsed into concept/item objects. Dictionary loading can either be performed on the default included dictionary or on a user- specified custom dictionary. Furthermore, a mechanism is provided for adding concepts and/or data sources to the existing dictionary (see the Details section).

Usage

load_dictionary(
  src = NULL,
  concepts = NULL,
  name = "concept-dict",
  cfg_dirs = NULL
)

Arguments

src	NULL or the name of one or several data sources
concepts	A character vector used to subset the concept dictionary or NULL indicating no subsetting
name	Name of the dictionary to be read
cfg_dirs	File name of the dictionary

Details

A default dictionary is provided at

system.file(
  file.path("extdata", "config", "concept-dict.json"),
  package = "ricu"
)

and can be loaded in to an R session by calling get_config("concept-dict"). The default dictionary can be extended by adding a file concept-dict.json to the path specified by the environment variable RICU_CONFIG_PATH. New concepts can be added to this file and existing concepts can be extended (by adding new data sources). Alternatively, load_dictionary() can be called on non-default dictionaries using the file argument.

In order to specify a concept as JSON object, for example the numeric concept for glucose, is given by

{
  "glu": {
    "unit": "mg/dL",
    "min": 0,
    "max": 1000,
    "description": "glucose",
    "category": "chemistry",
    "sources": {
      "mimic_demo": [
        {
          "ids": [50809, 50931],
          "table": "labevents",
          "sub_var": "itemid"
        }
      ]
    }
  }
}

Using such a specification, constructors for cncpt and itm objects are called either using default arguments or as specified by the JSON object, with the above corresponding to a call like

concept(
  name = "glu",
  items = item(
    src = "mimic_demo", table = "labevents", sub_var = "itemid",
    ids = list(c(50809L, 50931L))
  ),
  description = "glucose", category = "chemistry",
  unit = "mg/dL", min = 0, max = 1000
)

The arguments src and concepts can be used to only load a subset of a dictionary by specifying a character vector of data sources and/or concept names.

Value

A concept object containing several data concepts as cncpt objects.

Examples

if (require(mimic.demo)) {
head(load_dictionary("mimic_demo"))
load_dictionary("mimic_demo", c("glu", "lact"))
}

septic-tank/ricu documentation built on Jan. 30, 2021, 8:40 p.m.