[R] SDMTools package - calculating overlap?

David Winsemius dwinsemius at comcast.net
Mon Jul 18 16:41:03 CEST 2011

On Jul 18, 2011, at 10:11 AM, Ana Kolar wrote:

> Yes, indeed! I believe I should integrate differences of min of both  
> functions, no? I'm not quite sure how this should be done in R  
> therefore I was wondering if there are some build in functions that  
> do this job already. If not I would appreciate any help of how  
> should it be done otherwise.

?integrate   # would seem to be the glaringly obvious help query

> Toy example of data is here:
> a <- matrix(runif(30))
> b <- matrix(runif(30))

That's not a well-defined example of functions even if we take the  
index to be the x value. Presumably you have some sort of value in  
mind for "a" at an x-value of 1.5 but it is not clear from what you  
have presented.


A function takes inputs (on some continuous measurement scale) and  
returns results. Perhaps you should be seeking some local mathematical/ 
statistical consulting resource.


> I tried to calculate this overlap with "Istat" function but am not  
> sure that it does the job right! This is the example:
> library(SDMTools)
> a <- matrix(runif(30))
> b <- matrix(runif(30))
> Istat(a,b)
> Many thanks for your response, David!
> Ana
> From: David Winsemius <dwinsemius at comcast.net>
> To: Ana Kolar <annakolar at yahoo.com>
> Cc: R <r-help at r-project.org>
> Sent: Monday, 18 July 2011, 15:45
> Subject: Re: [R] SDMTools package - calculating overlap?
> On Jul 18, 2011, at 9:40 AM, Ana Kolar wrote:
> > Dear R users,
> >
> > Any idea of how to calculate an area of an overlap between two  
> functions? The only R build in function that I found is I Similarity  
> Statistic for Quantifying Niche Overlap and I am really not sure if  
> this function is producing exactly what I am interested in since I  
> was plotting functions and often got confused results (for example:  
> got high value for the overlap of one pair and low for the other  
> pair, while from the plot it looked like the first pair was  
> overlapping better.) Can anyone please explain what's the reason  
> behind such a behaviour? And does anyone has a suggestion of what  
> function could be used for a calculation of an overlap area? The  
> problem with 'Istat' function is also that it requires both data  
> sets to have the same length, while I would be more interested in a  
> function that enables overlap calculation even if data sets have  
> different length. Looking forward to hearing from you! Have a good  
> day. Ana
> Shouldn't you be integrating their difference (or the absolute value  
> of their differences depending on your definition of "overlap"). I  
> fail in understanding your example. Where is/are the function(s)?
> >
> > library(SDMTools)
> > a <- matrix(runif(30))
> > b <- matrix(runif(30))
> > Istat(a,b)
> >     [[alternative HTML version deleted]]
> --
> David Winsemius, MD
> West Hartford, CT

David Winsemius, MD
West Hartford, CT

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