[R-sig-Geo] potential BUG in BBMM

[Tyler Dean Rudolph]

In fact I have been in fairly regular communication with Ryan Nielson  
about this, but I don't get the impression he has a lot of time to  
devote to resolving it. So far I have managed to circumvent all the  
potential problems he has suggested, and I have narrowed it down to  
this Fortran loop.  Now he seems of the mind that it is a problem with  
R - which I suppose is possible? - but whether it is the Fortran code,  
R, or something else I don't believe I have the tools to assess the  
problem any further.  I am certainly not imagining the problem, as  
I've mentioned, but if somebody more knowledgeable could at least  
reproduce it we might be somewhere closer to a solution.  In the  
meantime I have suggested that BBMM be used with caution, especially  
in big loops with large data sets, but Ryan hasn't commented on this,  
and at any rate I wouldn't mind getting a third or fourth opinion.

Tyler


On 2010-07-14, at 5:33, Roger Bivand <Roger.Bivand at nhh.no> wrote:

> On Tue, 13 Jul 2010, Tyler Dean Rudolph wrote:
>
>>    I've been constructing utilization distributions for 63 animal  
>> movement
>> trajectories using a Brownian bridge movement model with BBMM.  I  
>> started
>> noticing after running the routine numerous times at different  
>> resolutions
>> that certain UDs would be grossly wrong, meaning instead of  
>> returning a
>> strongly negative exponential distribution of probabilities (UD 
>> $probability)
>> that sums to 1, there might be two big modes in opposite places, or  
>> negative
>> probability values, or simply "NaN" across the board.  I have found  
>> this
>> problem on Mac, Linux, and Windows machines in various versions of R
>> (including the most recent), and I was hoping someone in the R  
>> community
>> would be able to verify this and perhaps speculate on why this is  
>> occurring.
>>
>
> Have you also contacted the package authors directly? They would be  
> the best point of entry here, I think.
>
> Roger
>
>>
>> The problem appears to originate either 1) in the FORTRAN code that
>> estimates BMVar and calculates the BBMM, or 2) in the way R handles  
>> its
>> operation.  I've broken down BBMM into its essential parts, and in  
>> the
>> attached environment are all of the objects necessary to run the  
>> FORTRAN
>> code.  I have set it up in a loop here so it continually estimates  
>> a UD on
>> the same data then and produces a histogram, which I have found to  
>> be most
>> revealing in identifying problems.  If the code stops running it's  
>> because
>> the result was all "NaN".  If you run the loop repeatedly you may  
>> find, as I
>> have, that while the results may initially appear more-or-less  
>> consistent,
>> at other moments they will change, sometimes gradually, and sometimes
>> quickly.  If you are looking at it and it is not changing, I  
>> encourage you
>> to remove all objects, close and reopen R, reload the workspace and  
>> run the
>> same loop again.  If you do this numerous times you should  
>> eventually see
>> unusual results, meaning inconsistent estimation, or wacky  
>> probability
>> distributions, or "NaN".
>>
>>
>> ### 
>> ### 
>> ### 
>> ### 
>> ####################################################################
>>
>> ##  Run the Fortran routine repeatedly with identical data
>> ##  - all required objects are in workspace "BBMM_BUG.RData" -
>>
>> require(BBMM)
>>
>> par(mfrow=c(2,2))
>>
>>
>> repeat {
>>       ans <- .Fortran("BBMM", as.integer(n.locs), as.integer 
>> (grid.size),
>>       as.double(time.lag), as.double(T.Total), as.double(x),
>>       as.double(y), as.double(BMvar), as.double(location.error),
>>       as.double(area.grid$x), as.double(area.grid$y),
>> as.double(time.step),
>>       as.double(probability), PACKAGE = "BBMM")
>>
>>   if(!sum(ans[[12]])=="NaN") { hist(ans[[12]]) } else { break }
>> }
>> ### 
>> ### 
>> ### 
>> ### 
>> #####################################################################
>>
>>
>>
>> Tyler
>>
>
> -- 
> Roger Bivand
> Economic Geography Section, Department of Economics, Norwegian  
> School of
> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> e-mail: Roger.Bivand at nhh.no
>