Plot Time-Series Window Proportion

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

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.

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.

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.

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)
#>      LAB Gap        Method Proportion
#> 1: 50861  30 By Individual          0
#> 2: 50861  30 By Individual          0
#> 3: 50861  30 By Individual          0
#> 4: 50861  30 By Individual          0
#> 5: 50861  30 By Individual          0
#> 6: 50912  30 By Individual          0