[R] Resampling physiological data using R?
Charles C. Berry
cberry at tajo.ucsd.edu
Thu Dec 11 22:15:12 CET 2008
On Thu, 11 Dec 2008, tsunhin wong wrote:
> Dear all R users,
>
> I am going to use R to process some of my physiological data about eye.
>
> The problem is the recording machine does not sample in a reliably
> constant rate: the time intervals between data sampled can vary from
> 9msec to ~120msec, while most around in the 15-30msec range.
> The below is a fraction of a single data file of a trial:
>
> Time CursorX CursorY Pupilsize
> 1811543 -1 -1 -1
> 1811563 -1 -1 -1
> 1811584 511 370 4.175665
> 1811603 511 368 4.181973
> 1811624 521 368 4.210732
> 1811644 512 377 4.149632
> 1811664 524 377 4.275845
> 1811684 518 368 4.236212
> 1811703 516 370 4.238384
> 1811725 507 364 4.181157
> 1811744 509 371 4.185016
> 1811764 509 377 4.231987
> 1811784 514 387 4.252449
> 1811802 515 388 4.273726
>
> My goal is to "resample" these data so that the "Time" column
> increments by a regular interval, and the other columns of data are
> the averages (or estimates) at the point in time according to
> available data points.
'resample' is the probably wrong word in a forum in which here are many
statisticians for whom that word has special meaning.
'interpolate' is more appropriate.
Following the _posting guide_, when I do
help.search("interpolate")
I get a number of useful hits. Like
stats::approx Interpolation Functions
Read the help page
?approx
and try
example( approx )
Of course, this is R and there are many other ways to skin this cat like
predict( gam( <...> ), newdata = interpolation.points )
from the mgcv package.
HTH,
Chuck
> I have done something that I use a regular interval that is larger
> than the naturally occurring record machine, i.e. > 120msec for
> example, and acquire an average of the available data points for any
> particular regular time interval.
>
> Now, I need to achieve resampling for smaller regular interval: i.e.
> 5msec intervals, and interpolate / intrapolate the missing data points
> from the available ones.
> i.e. I may have to split up data points into the number of the regular
> intervals that it may occupied in time.
>
> Do you know if there is any package that is doing something similar?
> And because of the size of the data and computational demand (1500
> files each with 2000-8000+ lines), can you suggest me some
> (algorithmically) more efficient way of doing this?
>
> Thanks a lot!
>
> Regards,
>
> John
>
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> and provide commented, minimal, self-contained, reproducible code.
>
Charles C. Berry (858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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