[R] Resampling physiological data using R?

[Charles C. Berry]

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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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> 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