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eds_scikit.emergency.emergency_visit

tag_emergency_visit 

tag_emergency_visit(visit_detail: DataFrame, care_site: Optional[DataFrame] = None, visit_occurrence: Optional[DataFrame] = None, algo: str = 'from_mapping') -> DataFrame

Tag visits that correspond to medical emergency units.

The tagging is done by adding a "IS_EMERGENCY" column to the provided DataFrame.

Some algos can add an additional "EMERGENCY_TYPE" column to the provided DataFrame, providing a more detailled classification.

It works by either tagging each visit detail's care site, or by using the visit_occurrence's "visit_source_value".

PARAMETER DESCRIPTION
visit_detail

TYPE: DataFrame

care_site

Isn't necessary if the algo "from_vo_visit_source_value" is used

TYPE: Optional[DataFrame] DEFAULT: None

visit_occurrence

Is mandatory if the algo "from_vo_visit_source_value" is used

TYPE: Optional[DataFrame] DEFAULT: None

algo

Possible values are:

  • "from_mapping" relies on a list of care_site_source_value extracted by Judith LEBLANC, Ariel COHEN and validated by an ER doctor. The emergency care sites are here further labelled to distinguish the different types of emergency
  • "from_regex_on_care_site_description": relies on a specific list of RegEx applied on the description (= simplified care site name) of each care site.
  • "from_regex_on_parent_UF": relies on a specific list of regular expressions applied on the description (= simplified care site name) of each UF (Unité Fonctionnelle). The obtained tag is then propagated to every UF's children.
  • "from_vo_visit_source_value": relies on the parent visit occurrence of each visit detail: A visit detail will be tagged as emergency if it belongs to a visit occurrence where visit_occurrence.visit_source_value=='urgence'.

TYPE: str DEFAULT: 'from_mapping'

RETURNS DESCRIPTION
care_site

Dataframe with 1 to 2 added columns corresponding to the following concepts:

  • "IS_EMERGENCY"
  • "EMERGENCY_TYPE" (if using algo "from_mapping")

TYPE: DataFrame

Source code in eds_scikit/emergency/emergency_visit.py 
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@algo_checker(algos=ALGOS)
def tag_emergency_visit(
    visit_detail: DataFrame,
    care_site: Optional[DataFrame] = None,
    visit_occurrence: Optional[DataFrame] = None,
    algo: str = "from_mapping",
) -> DataFrame:
    """Tag visits that correspond to **medical emergency units**.

    The tagging is done by adding a `"IS_EMERGENCY"` column to the provided DataFrame.

    Some algos can add an additional `"EMERGENCY_TYPE"` column to the provided DataFrame,
    providing a more detailled classification.

    It works by either [tagging each visit detail's care site][eds_scikit.emergency.emergency_care_site.tag_emergency_care_site],
    or by using the *visit_occurrence*'s `"visit_source_value"`.

    Parameters
    ----------
    visit_detail: DataFrame
    care_site: DataFrame
        Isn't necessary if the algo `"from_vo_visit_source_value"` is used
    visit_occurrence: DataFrame, optional.
        Is mandatory if the algo `"from_vo_visit_source_value"` is used
    algo: str
        Possible values are:

        - [`"from_mapping"`][eds_scikit.emergency.emergency_care_site.from_mapping] relies on a list of `care_site_source_value` extracted
          by Judith LEBLANC, Ariel COHEN and validated by an ER doctor. The emergency care sites
          are here further labelled to distinguish the different types of emergency
        - [`"from_regex_on_care_site_description"`][eds_scikit.emergency.emergency_care_site.from_regex_on_care_site_description]: relies on a specific list of RegEx
          applied on the description (= simplified care site name) of each care site.
        - [`"from_regex_on_parent_UF"`][eds_scikit.emergency.emergency_care_site.from_regex_on_parent_UF]: relies on a specific list of regular expressions
          applied on the description (= simplified care site name) of each UF (Unité Fonctionnelle).
          The obtained tag is then propagated to every UF's children.
        - [`"from_vo_visit_source_value"`][eds_scikit.emergency.emergency_visit.from_vo_visit_source_value]:
        relies on the parent visit occurrence of each visit detail:
          A visit detail will be tagged as emergency if it belongs to a visit occurrence where
          `visit_occurrence.visit_source_value=='urgence'`.


    Returns
    -------
    care_site: DataFrame
        Dataframe with 1 to 2 added columns corresponding to the following concepts:

        - `"IS_EMERGENCY"`
        - `"EMERGENCY_TYPE"` (if using algo `"from_mapping"`)
    """

    if algo == "from_vo_visit_source_value":
        return from_vo_visit_source_value(visit_detail, visit_occurrence)

    else:
        initial_care_site_columns = set(care_site.columns)
        tagged_care_site = tag_emergency_care_site(care_site, algo=algo)
        to_add_columns = list(
            set(tagged_care_site) - initial_care_site_columns | set(["care_site_id"])
        )

        return visit_detail.merge(
            tagged_care_site[to_add_columns], on="care_site_id", how="left"
        )

from_vo_visit_source_value 

from_vo_visit_source_value(visit_detail: DataFrame, visit_occurrence: DataFrame) -> DataFrame

This algo uses the "Type de dossier" of each visit detail's parent visit occurrence. Thus, a visit_detail will be tagged with IS_EMERGENCY=True iff the visit occurrence it belongs to is an emergency-type visit (meaning that visit_occurrence.visit_source_value=='urgence')

Admission through ICU

At AP-HP, when a patient is hospitalized after coming to the ICU, its visit_source_value is set from "urgence" to "hospitalisation complète". So you should keep in mind that this method doesn't tag those visits as ICU.

PARAMETER DESCRIPTION
visit_detail

TYPE: DataFrame

visit_occurrence

TYPE: DataFrame

RETURNS DESCRIPTION
visit_detail

Dataframe with added columns corresponding to the following conceps:

  • "IS_EMERGENCY"

TYPE: DataFrame

Source code in eds_scikit/emergency/emergency_visit.py 
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@concept_checker(concepts=["IS_EMERGENCY"])
def from_vo_visit_source_value(
    visit_detail: DataFrame,
    visit_occurrence: DataFrame,
) -> DataFrame:
    """
    This algo uses the *"Type de dossier"* of each visit detail's parent visit occurrence.
    Thus, a visit_detail will be tagged with `IS_EMERGENCY=True` iff the visit occurrence it belongs to
    is an emergency-type visit (meaning that `visit_occurrence.visit_source_value=='urgence'`)

    !!! aphp "Admission through ICU"
         At AP-HP, when a patient is hospitalized after coming to the ICU, its `visit_source_value`
         is set from `"urgence"` to `"hospitalisation complète"`. So you should keep in mind
         that this method doesn't tag those visits as ICU.

    Parameters
    ----------
    visit_detail: DataFrame
    visit_occurrence: DataFrame

    Returns
    -------
    visit_detail: DataFrame
        Dataframe with added columns corresponding to the following conceps:

        - `"IS_EMERGENCY"`
    """
    vo_emergency = visit_occurrence[["visit_occurrence_id", "visit_source_value"]]
    vo_emergency["IS_EMERGENCY"] = visit_occurrence.visit_source_value == "urgence"

    return visit_detail.merge(
        vo_emergency[["visit_occurrence_id", "IS_EMERGENCY"]],
        on="visit_occurrence_id",
        how="left",
    )
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