The pneumococcal incidence diagnostic classifications

The 4 category disjoint classification.

Usage

derive_pneumococcal_categories(df, v, ...)

Arguments

df

the dataframe.

v

the value set. usually precomputed by the augment framework the value set can be explicitly supplied with v = get_value_sets(df)

...

ignored

Value

a dataframe

Details

• pneumo.presentation_class:

  • CAP+/RAD+ - radiologically proved pneumonia

  • CAP+/RAD- - pneumonia without x-ray confirmation

  • NP-LRTI - non-pneumonic lower respiratory tract infection

  • No evidence LRTI - believed to be non-infective at admission, this last group is usually discarded from analysis, however it only really describes people without a clinical diagnosis of LRTI on admission. There could still be undiagnosed infection there, and some of these patients have COVID (possibly without lower respiratory symptoms?).