How to calculate time elapsed between rows in R - r

Question

I have date and time as separate columns, which i combined into a single column using library(lubridate)
Now i want to create a new column that would calculate the elapsed time between two consecutive rows for each unique ID
I tried diff, however the error i am getting is that the new column has +1 rows compared to original data set
s1$DT<-with(s1, mdy(Date.of.Collection) + hm(MILITARY.TIME))#this worked - #needs the library lubridate
s1$ElapsedTime<-difff(s1$DT)
units(s1$ElapsedTime)<-"hours"
Subject.ID time DT Time elapsed
1 Dose 8/1/2018 8:15 0
1 time point1 8/1/2018 9:56 0.070138889
1 time point2 8/2/2018 9:56 1.070138889
2 Dose 9/4/2018 10:50 0
2 time point1 9/11/2018 11:00 7.006944444
3 Dose 10/1/2018 10:20 0
3 time point1 10/2/2018 14:22 1.168055556
3 time point2 10/3/2018 12:15 2.079861111

Answer 1

From your comment, you don't need a "diff"; in conventional R-speak, a "diff" would be T1-T0, T2-T1, T3-T2, ..., Tn - Tn-1.
For you, one of these will work to give you T1,2,...,n - T0.
Base R
do.call(
rbind,
by(patients, patients$Subject.ID, function(x) {
x$elapsed <- x$realDT - x$realDT[1]
units(x$elapsed) <- "hours"
x
})
)
# Subject.ID time1 DT Time elapsed realDT
# 1.1 1 Dose 8/1/2018 8:15 0.000000 hours 2018-08-01 08:15:00
# 1.2 1 time_point1 8/1/2018 9:56 1.683333 hours 2018-08-01 09:56:00
# 1.3 1 time_point2 8/2/2018 9:56 25.683333 hours 2018-08-02 09:56:00
# 2.4 2 Dose 9/4/2018 10:50 0.000000 hours 2018-09-04 10:50:00
# 2.5 2 time_point1 9/11/2018 11:00 168.166667 hours 2018-09-11 11:00:00
# 3.6 3 Dose 10/1/2018 10:20 0.000000 hours 2018-10-01 10:20:00
# 3.7 3 time_point1 10/2/2018 14:22 28.033333 hours 2018-10-02 14:22:00
# 3.8 3 time_point2 10/3/2018 12:15 49.916667 hours 2018-10-03 12:15:00
dplyr
library(dplyr)
patients %>%
group_by(Subject.ID) %>%
mutate(elapsed = `units<-`(realDT - realDT[1], "hours")) %>%
ungroup()
data.table
library(data.table)
patDT <- copy(patients)
setDT(patDT)
patDT[, elapsed := `units<-`(realDT - realDT[1], "hours"), by = "Subject.ID"]
Notes:
The "hours" in the $elapsed column is just an artifact of dealing with a time-difference thing, it should not affect most operations. To get rid of it, make sure you're in the right units ("hours", "secs", ..., see ?units) and use as.numeric.
The only reasons I used as.POSIXct as above are that I'm not a lubridate user, and the data as provided is not in a time format. You shouldn't need it if your Time is a proper time format, in which case you'd use that field instead of my hacky realDT.
On similar lines, if you do calculate realDT and use it, you really don't need both realDT and the pair of DT and Time.
The data I used:
patients <- read.table(header=TRUE, stringsAsFactors=FALSE, text="
Subject.ID time1 DT Time elapsed
1 Dose 8/1/2018 8:15 0
1 time_point1 8/1/2018 9:56 0.070138889
1 time_point2 8/2/2018 9:56 1.070138889
2 Dose 9/4/2018 10:50 0
2 time_point1 9/11/2018 11:00 7.006944444
3 Dose 10/1/2018 10:20 0
3 time_point1 10/2/2018 14:22 1.168055556
3 time_point2 10/3/2018 12:15 2.079861111")
# this is necessary for me because DT/Time here are not POSIXt (they're just strings)
patients$realDT <- as.POSIXct(paste(patients$DT, patients$Time), format = "%m/%d/%Y %H:%M")