Dealing with timestamps in R

I have multiple lists of measurements. In each list have the timestramp formated as a string ("2009-12-24 21:00:07.0") and I know that each measurement in the list is separated by 5 seconds. I want to combine all data into a huge data.frame in R. Afterwards I want to be able to easily access the time difference of two measurements so I probably should convert data into something different than characters.

Which format should I use to store the times? Is there some time format in some package that I should use?

You want the (standard) POSIXt type from base R that can be had in 'compact form' as a POSIXct (which is essentially a double representing fractional seconds since the epoch) or as long form in POSIXlt (which contains sub-elements). The cool thing is that arithmetic etc are defined on this -- see help(DateTimeClasses)

Quick example:

R> now <- Sys.time()
R> now
[1] "2009-12-25 18:39:11 CST"
R> as.numeric(now)
[1] 1.262e+09
R> now + 10  # adds 10 seconds
[1] "2009-12-25 18:39:21 CST"
R> as.POSIXlt(now)
[1] "2009-12-25 18:39:11 CST"
R> str(as.POSIXlt(now))
 POSIXlt[1:9], format: "2009-12-25 18:39:11"
R> unclass(as.POSIXlt(now))
$sec
[1] 11.79

$min
[1] 39

$hour
[1] 18

$mday
[1] 25

$mon
[1] 11

$year
[1] 109

$wday
[1] 5

$yday
[1] 358

$isdst
[1] 0

attr(,"tzone")
[1] "America/Chicago" "CST"             "CDT"            
R> 

As for reading them in, see help(strptime)

As for difference, easy too:

R> Jan1 <- strptime("2009-01-01 00:00:00", "%Y-%m-%d %H:%M:%S")
R> difftime(now, Jan1, unit="week")
Time difference of 51.25 weeks
R> 

Lastly, the zoo package is an extremely versatile and well-documented container for matrix with associated date/time indices.