plotWindow: Plot Time-Series Window Proportion

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

Plot Time-Series Window Proportion

Description

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

Usage

plotWindowProportion(
  labData,
  idColName,
  labItemColName,
  dateColName,
  indexDate = last,
  gapDate = c(30, 90, 180, 360),
  topN = 10,
  studyPeriodStartDays,
  studyPeriodEndDays
)

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.
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.
studyPeriodStartDays	the expected start date of your study period, calculated by indexDate + studyPeriodStartDays. For example, if studyPeriodStartDays=0, the start date of your study period will be the indexDate.
studyPeriodEndDays	the expected end date of your study period, calculated by indexDate + studyPeriodEndDays. For example, if studyPeriodEndDays=360, the end date of your study period will be the indexDate + 360 days.

Details

This function is used for seperating 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. By Individual means the proportion of individuals do not have any test result, By Window means the proportion of time windows do not have test results.

Examples

windowProportion <- plotWindowProportion(labData = labSample,
                                        idColName = SUBJECT_ID,
                                        labItemColName = ITEMID,
                                        dateColName = CHARTTIME,
                                        indexDate = first,
                                        gapDate = c(30, 90, 180, 360),
                                        studyPeriodStartDays=0,
                                        studyPeriodEndDays=360
                                        )
print(windowProportion$graph)
head(windowProportion$missingData)

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