fhircrackr (version 2.3.0)

fhir_table_description: Create fhir_table_description object

Description

A fhir_table_description holds the information fhir_crack() needs to flatten (aka crack) FHIR resources from a FHIR bundle. There should be one fhir_table_description per resource type as fhir_crack() will create one data.frame/data.table per resource type in a bundle. See Details.

Usage

fhir_table_description(
  resource,
  cols = fhir_columns(),
  sep = ":::",
  brackets = character(),
  rm_empty_cols = FALSE,
  format = "compact",
  keep_attr = FALSE,
  style = deprecated()
)

Value

An object of class fhir_table_description.

Arguments

resource

A character vector of length one or fhir_resource_type object indicating which resource type should be extracted.

cols

Optional. A fhir_columns object or something that can be coerced to one, like a (named) character vector, a (named) list containing xpath expressions, or a fhir_xpath_expression object. See fhir_columns() and the examples. If this argument is omitted, an empty fhir_columns object will be supplied. This means that in the call to fhir_crack(), all available elements are extracted in put in automatically named columns.

sep

A character of length one containing the separator string used for separating multiple entries in cells when format = "compact". ignored when format = "wide". Defaults to ":::".

brackets

A character of length one or two used for the indices of multiple entries. The first one is the opening bracket and the second one the closing bracket. Vectors of length one will be recycled. Defaults to character(0), i.e. no brackets, meaning that multiple entries won't be indexed.

rm_empty_cols

A logical of length one indicating whether empty columns should be removed from the resulting table or not. Defaults to FALSE.

format

A character of length one indicating whether the resulting table should be cracked to a "wide" or "compact" format. "wide" means multiple entries will be distributed over several columns with indexed names. "compact" means multiple entries will be pasted into one cell/column separated by sep . Defaults to "compact".

keep_attr

A logical of length one indicating whether the attribute name of the respective element (@value in most cases) should be attached to the name of the variable in the resulting table. Defaults to FALSE.

style

Details

A fhir_table_description consists of the following elements:

• The resource element: Defines the resource type (e.g. Patient or Observation). See fhir_resource_type().

• The cols element: Contains the column names and XPath expressions defining the columns to extract. If this element is empty, fhir_crack() will extract all available elements of the resource and name the columns automatically. See fhir_columns().

• The sep element: A character of length one containing the separator string used for separating multiple entries in cells.

• The brackets element: A character of length one or two used for the indices of multiple entries. The first one is the opening bracket and the second one the closing bracket. Vectors of length one will be recycled. Defaults to character(0), i.e. no brackets, meaning that multiple entries won't be indexed.

• The rm_empty_cols element: A logical of length one indicating whether empty columns should be removed in the resulting table or not. Defaults to FALSE.

• The format element: A character of length one indicating whether the resulting table should be cracked to a wide or compact format. wide means multiple entries will be distributed over several columns with indexed names. compact means multiple entries will be pasted into one cell/column separated by sep . Defaults to compact.

• The keep_attr element: A logical of length one indicating whether the attribute name of the respective element (@value in most cases) should be attached to the name of the variable in the resulting table. Defaults to FALSE.

A full fhir_table_description looks for example like this:

fhir_resource_type: Patient
fhir_columns:
column name | xpath expression
------------------------
name        | name/family
gender      | gender
id          | id
sep:           ':::'
brackets:      '[', ']'
rm_empty_cols: FALSE
format:        'compact'
keep_attr:     FALSE

Examples

# a minimal table description
fhir_table_description(
    resource = "Patient"
)

# named list for cols
fhir_table_description(
    resource = "Patient",
    cols     = list(
        id     = "id",
        name   = "name/family",
        gender = "gender"
    )
)

#unnamed character for cols, colnames are generated automatically
fhir_table_description(
    resource = "Patient",
    cols     = c(
        "id",
        "name/family",
        "gender"
    )
)

# named character for cols, and overwritten default for other arguments
fhir_table_description(
    resource = "Patient",
    cols = c(
        id            = "id",
        name          = "name/family",
        gender        = "gender"
    ),
    brackets      = c("[", "]"),
    rm_empty_cols = TRUE,
    format        = "wide"
)

# no column arguments is given -> creates a column for all available elements
fhir_table_description(
    resource = "Patient",
    sep           = " <~> ",
    brackets      = c("<<<", ">>>"),
    rm_empty_cols = FALSE,
    format        = "wide"
)