Constellation contains a set of functions for applying multidimensional, time window based logic to time series data frames of arbitrary length. Constellation was developed to enable rapid and flexible identification of series of events that occur in hospitalized patients. The functions have been abstracted for general purpose use with time series data. Constellation extends and provides a friendly API to rolling joins and overlap joins implemented in data.table. Three datasets (labs, vitals, and orders) with randomly synthesized time series data for a cohort of 100 patients are included to facilitate testing of functions.
There are five functions included in constellation to build complex features from time series data:
value_change() identify increases or decreases in a
value within a given time windowconstellate() identify time stamps when a series of
events occurs within a given time windowconstellate_criteria() identify which events occur
within a given time window for every measurement time stampbundle() identify which events occur within a given
time window of a given eventincidents() identify distinct, incident episodes that
must be separated in time by a minimum of a given time windowThe constellate_criteria() and bundle()
function are similar, but the bundle() function is anchored
around a specific event table. The bundle() function
identifies events that occur within a given time window of a
specific event data frame that is supplied to the
function. On the other hand, the constellate_criteria()
function identifies events that occur within a given time window of
any event data frame that is supplied to the function.
The first data frame passed to the bundle() function is
used as an anchor to search through the subsequent data frames passed to
the function. The order of data frames is significant and passing
different data frames as the first argument will generate different
results. On the other hand, the order in which you pass data frames to
the constellate_criteria() function is insignificant.
Passing data frames in different orders will generate equivalent
results.
Constellation can be used to build point-based scores for time series
data (via constellate_criteria()), identify particular
sequences of events that occur near each other (via
constellate()), identify when specific changes occur for a
given parameter (via value_change()), identify individual
events that occur around a specified time stamp (via
bundle()), and distinguish between eveents that are
separated by a specified time window (via incidents()).
If you are new to constellation, the best place to start is the
vignette("constellation", "identify_sepsis"). You can also
view the sepsis vignette on CRAN.
You can install constellation from CRAN with:
install.packages("constellation")
library(constellation)You can install the development version of constellation from github with:
devtools::install_github("marksendak/constellation")If you have any questions, comments, or feedback, please email mark.sendak@gmail.com.
Below are several variations of finding systolic blood pressure drops of 40 over a 6 hour period.
Examine systolic blood pressure data:
library(constellation)
systolic_bp <- vitals[VARIABLE == "SYSTOLIC_BP"]
systolic_bp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME, format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
head(systolic_bp)
#> PAT_ID RECORDED_TIME VALUE VARIABLE
#> 1: 108546 2010-02-25 05:36:15 110.6677 SYSTOLIC_BP
#> 2: 108546 2010-02-25 08:41:56 116.0423 SYSTOLIC_BP
#> 3: 108546 2010-02-25 10:30:53 119.2235 SYSTOLIC_BP
#> 4: 108546 2010-02-25 11:05:43 102.9899 SYSTOLIC_BP
#> 5: 108546 2010-02-25 11:48:29 122.1348 SYSTOLIC_BP
#> 6: 108546 2010-02-25 12:14:18 119.7529 SYSTOLIC_BPIdentify the first systolic blood pressure drop per patient:
systolic_bp_drop <- value_change(systolic_bp, value = 40, direction = "down",
window_hours = 6, join_key = "PAT_ID", time_var = "RECORDED_TIME",
value_var = "VALUE", mult = "first")
head(systolic_bp_drop)
#> PAT_ID PRIOR_RECORDED_TIME PRIOR_VALUE CURRENT_RECORDED_TIME
#> 1: 108546 2010-02-25 15:45:29 139.9967 2010-02-25 20:42:35
#> 2: 112374 2010-03-09 18:18:13 160.4919 2010-03-09 20:48:09
#> 3: 113163 2010-07-27 15:50:35 170.2034 2010-07-27 19:21:58
#> 4: 124042 2010-11-24 21:34:57 163.8912 2010-11-25 02:03:14
#> 5: 135995 2010-11-21 01:51:09 157.9432 2010-11-21 03:26:00
#> 6: 146478 2010-08-27 16:07:47 179.3603 2010-08-27 21:03:05
#> CURRENT_VALUE
#> 1: 80.07446
#> 2: 107.87212
#> 3: 116.22419
#> 4: 116.66625
#> 5: 111.55469
#> 6: 132.99234Identify the last systolic blood pressure drop per patient:
systolic_bp_drop <- value_change(systolic_bp, value = 40, direction = "down",
window_hours = 6, join_key = "PAT_ID", time_var = "RECORDED_TIME",
value_var = "VALUE", mult = "last")
head(systolic_bp_drop)
#> PAT_ID PRIOR_RECORDED_TIME PRIOR_VALUE CURRENT_RECORDED_TIME
#> 1: 108546 2010-07-01 15:31:31 164.9851 2010-07-01 21:03:04
#> 2: 112374 2010-03-15 15:15:53 164.1634 2010-03-15 17:30:06
#> 3: 113163 2010-07-30 19:12:15 160.1682 2010-07-30 22:33:10
#> 4: 124042 2010-12-04 18:34:18 167.2564 2010-12-04 22:46:57
#> 5: 135995 2010-11-27 04:47:15 127.5603 2010-11-27 06:43:05
#> 6: 146478 2010-09-03 15:14:43 182.1690 2010-09-03 16:18:28
#> CURRENT_VALUE
#> 1: 114.67968
#> 2: 115.95783
#> 3: 111.89387
#> 4: 118.81151
#> 5: 81.90537
#> 6: 138.28222Identify all systolic blood pressure drops per patient:
systolic_bp_drop <- value_change(systolic_bp, value = 40, direction = "down",
window_hours = 6, join_key = "PAT_ID", time_var = "RECORDED_TIME",
value_var = "VALUE", mult = "all")
head(systolic_bp_drop)
#> PAT_ID PRIOR_RECORDED_TIME PRIOR_VALUE CURRENT_RECORDED_TIME
#> 1: 108546 2010-02-25 15:45:29 139.9967 2010-02-25 20:42:35
#> 2: 108546 2010-03-01 15:57:24 136.8654 2010-03-01 16:07:00
#> 3: 108546 2010-03-02 19:59:20 129.0167 2010-03-03 00:46:35
#> 4: 108546 2010-03-02 20:49:00 110.1830 2010-03-03 00:46:35
#> 5: 108546 2010-03-04 00:18:41 137.8095 2010-03-04 04:23:54
#> 6: 108546 2010-03-04 02:13:39 130.3280 2010-03-04 04:23:54
#> CURRENT_VALUE
#> 1: 80.07446
#> 2: 88.88972
#> 3: 69.94551
#> 4: 69.94551
#> 5: 82.16874
#> 6: 82.16874In clinical medicine, there are a subset of conditions that are defined by a sequence of related events that unfold over time. These conditions are described as a “constellation of signs and symptoms.”
Another piece of medical jargon that made it into the package is the
concept of a treatment bundle. The bundle() function was
originally designed to calculate the time stamp at which a group of
treatments is delivered for every patient within a specified amount of
time of developing a condition.
constellation was originally developed to support a machine learning project at the Duke Institute for Health Innovation to predict sepsis.