getTimeSeriesLab separates original data into multiple time windows, and summarize statistical information.
getTimeSeriesLab(
labData,
idColName,
labItemColName,
dateColName,
valueColName,
indexDate = last,
gapDate = NULL,
completeWindows = TRUE
)a file or dataframe of laboratory test data with at least 4 columns about patient ID, lab item, test value and test date, respectively.
the column name that records patient ID in labData.
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.
the column name that records test date in labData. It should be in "YYYYMMDD"/"YYYY-MM-DD" format.
the column name that records test value in labData. Only numeric value is acceptable.
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.
desired period (in days) of each window interval. If NULL, it will be seen as only one single time window.
logical. If TRUE, time window series will be complete in order. If FALSE, a window without lab test will be skipped. Default is TRUE.
A data.table with statistical summary.
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.
ts<-getTimeSeriesLab(labData = labSample,
idColName = SUBJECT_ID,
labItemColName = ITEMID,
dateColName = CHARTTIME,
valueColName = VALUENUM,
indexDate = last,
gapDate = 360,
completeWindows = TRUE)
head(ts)
#> ID ITEMID Window Count Max Min Mean Nearest firstRecord lastRecode
#> 1: 36 50811 -4 4 12.7 10 11.675 12.7 2131-05-04 2131-05-18
#> 2: 36 50811 -3 NA NA NA NA NA <NA> <NA>
#> 3: 36 50811 -2 NA NA NA NA NA <NA> <NA>
#> 4: 36 50811 -1 NA NA NA NA NA <NA> <NA>
#> 5: 36 50861 -4 2 12.0 8 10.000 12.0 2131-04-30 2131-05-17
#> 6: 36 50861 -3 NA NA NA NA NA <NA> <NA>
head(indexTable)
#> # A tibble: 5 x 2
#> ID indexDate
#> <int> <date>
#> 1 36 2134-05-18
#> 2 109 2142-08-29
#> 3 132 2115-12-23
#> 4 143 2155-10-22
#> 5 145 2145-02-20
tsindex<-getTimeSeriesLab(labData = labSample,
idColName = SUBJECT_ID,
labItemColName = ITEMID,
dateColName = CHARTTIME,
valueColName = VALUENUM,
indexDate = indexTable,
gapDate = 360,
completeWindows = TRUE)
head(tsindex)
#> ID ITEMID Window Count Max Min Mean Nearest firstRecord lastRecode
#> 1: 36 50811 -4 4 12.7 10 11.675 12.7 2131-05-04 2131-05-18
#> 2: 36 50811 -3 NA NA NA NA NA <NA> <NA>
#> 3: 36 50811 -2 NA NA NA NA NA <NA> <NA>
#> 4: 36 50811 -1 NA NA NA NA NA <NA> <NA>
#> 5: 36 50811 1 NA NA NA NA NA <NA> <NA>
#> 6: 36 50861 -4 2 12.0 8 10.000 12.0 2131-04-30 2131-05-17