getTS: Obtaining Time-Series Data

In DHLab-TSENG/lab: a package for EHR laboratory data

Obtaining Time-Series Data

Description

getTimeSeriesLab separates original data into multiple time windows, and summarize statistical information.

Usage

getTimeSeriesLab(
  labData,
  idColName,
  labItemColName,
  dateColName,
  valueColName,
  indexDate = last,
  gapDate = NULL,
  completeWindows = TRUE
)

Arguments

labData	a file or dataframe of laboratory test data with at least 4 columns about patient ID, lab item, test value and test date, respectively.
idColName	the column name that records patient ID in labData.
labItemColName	the column name that records lab item in labData. If lab code is combined by multiple columns, then just simply add + operator between column names, e.g., A + B.
dateColName	the column name that records test date in labData. It should be in "YYYYMMDD"/"YYYY-MM-DD" format.
valueColName	the column name that records test value in labData. Only numeric value is acceptable.
indexDate	the specific date that used for cutting time window. It can be first record ("first"), last record ("last"), any single date of interest with "YYYYMMDD"/"YYYY-MM-DD" format, or (indexTable), with ID and indexDate mapping table.
gapDate	desired period (in days) of each window interval. If NULL, it will be seen as only one single time window.
completeWindows	logical. If TRUE, time window series will be complete in order. If FALSE, a window without lab test will be skipped. Default is TRUE.

Details

This function is used for separating lab data into multiple time windows, and it provides overall statistical information: total count, maximun value, minimun value, mean, nearest record to index date of each time window. If indexDate is first, then it will be the earliest test date among all the lab tests.

Value

A data.table with statistical summary.

Examples

ts<-getTimeSeriesLab(labData = labSample,
                idColName = SUBJECT_ID,
                labItemColName = ITEMID,
                dateColName = CHARTTIME,
                valueColName = VALUENUM,
                indexDate = last,
                gapDate = 360,
                completeWindows = TRUE)
head(ts)
head(indexTable)
tsindex<-getTimeSeriesLab(labData = labSample,
                idColName = SUBJECT_ID,
                labItemColName = ITEMID,
                dateColName = CHARTTIME,
                valueColName = VALUENUM,
                indexDate = indexTable,
                gapDate = 360,
                completeWindows = TRUE)
head(tsindex)

DHLab-TSENG/lab documentation built on Sept. 1, 2023, 9:03 p.m.