extractPathology: Extract pathology reports

In davidcoffey/Nexus: For clinical data mining of the Caisis and Diamonds databases

Description

Extracts pathology reports from the Caisis database and returns a data frame.

Usage

extractPathology(connection, patients = NULL, parsePlasmacells = FALSE,
  n = -1)

Arguments

connection	ODBC connection object returned by dbConnect.
patients	A character vector of patient medical record numbers. If no limit is desired then set as NULL.
parsePlasmacells	A Boolean indicating whether unabstracted plasma cell precentrages should be abstracted from PathNotes column.
n	Number of records to retrieve. Use n = -1 to retrieve all records.

Details

For columns reporting the precentatage of plasma cells, a new column is created with the numeric value only. Less or greater than symbols are removed and the median is reported for ranges. N/As are converted to 0.

Value

Returns a data frame with pathology reports from the Caisis database.

davidcoffey/Nexus documentation built on March 10, 2020, 4:54 p.m.