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Overlap function #13

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HarriPettittWade opened this issue Dec 15, 2015 · 22 comments
Closed

Overlap function #13

HarriPettittWade opened this issue Dec 15, 2015 · 22 comments

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@HarriPettittWade
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Hi Andrew,

Is the overlap function included in the standalone SIBER package? I received the following error when trying the original overlap code:

overlap.G1.G2 <- overlap(spx[[1]],spy[[1]],spx[[2]],spy[[2]],steps=1)
Error: could not find function "overlap"

thanks,

Harri
@GeorginaBusst
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Hi Andrew,

I have also found this exact problem and desperately need to calculate the overlap area between two standard ellipses for my PhD thesis. I had performed this before on the old siar but cannot now re-do the analyses. Is there any way to do this in SIBER?

Many thanks,

Georgina

@AndrewLJackson
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hi both

i have added some example code in a new vignette in the development release
on github which you will need to download and install. I haven't tested it
extensively, and its not as user friendly as under siar, but it does the
job.

hope that helps

best wishes

andrew

On 16 August 2016 at 12:29, GeorginaBusst notifications@github.com wrote:

Hi Andrew,

I have also found this exact problem and desperately need to calculate the
overlap area between two standard ellipses for my PhD thesis. I had
performed this before on the old siar but cannot now re-do the analyses. Is
there any way to do this in SIBER?

Many thanks,

Georgina

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@SarinaJ
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SarinaJ commented Nov 6, 2016 •
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Hi,
I am also wanted to use the overlap function and tried the example from the GitHub page (https://github.com/AndrewLJackson/SIBER/blob/master/vignettes/Ellipse-Overlap.R). I stumbled over some inconsistencies, by realizing that I got overlaps of over 1 in some cases. I thought these might help others as well.

  1. Line 88 currently it says m = siber.example$sample.sizes[c.1, e.1],
    as this is part of coords.2 shouldn't this be c.2 and e.2 that are used here?
  2. Line 97 currently says y = coords.2[,2]),
    either it has to say coords.1[,2] here or something has to be changed in one of the next two lines.

If I am wrong please correct me.

Cheers,
Sarina

@marknovak
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Yes, SarinaJ, I believe you're correct for both.

I have an additional issue:

In determining the coordinates for each ellipse (lines 74-93), I get an error message indicating that “small.sample” and “do.plot” are not graphical parameters.

More generally, I can’t figure out how one would even apply the sample-size correction in determining the coordinates of the ellipse. That is, it makes sense to me that one can multiple SEA by (n-1)/(n-2) to get SEAc (i.e. correcting the overall area). However, I don’t see how one would apply the correction to infer the new coordinates (i.e. of the ellipse corresponding to SEAc).

Thanks
-mark

@AndrewLJackson
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hi Sarina

thanks for pointing out those two mistakes. i have fixed them in the vignette on github.

You can get overlaps greater than 1 as they are expressed in units squared, which in isotope spave would be permil^2. They only become less than one if you make them a proportion of something.

mark: im not entirely sure, but i suspect you are running this vignette on an older version of SIBER. Install from github which hopefully has the newer versions of the plotting functions.

@marknovak
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Hi Andrew,
Thanks for the super speedy reply! You must be in the midst of uploading fixes, 'cuz the two errors I reported are indeed gone and the new maxLikOverlap is very convenient (and I now see how the sample size correction is implemented in determining the coordinates).

I do have a follow-up question though:
Looking at the code for maxLikOverlap it appears that the default is for the sample size correction to be performed. Hence, shouldn't the areas given by maxLikOverlap be the same (or similar to) the results of SEAc from groupMetricsML for a given p.interval (incl. NULL)? It looks like they're in between, but generally closer to SEA. Apologies if I'm misunderstanding something basic, but is it simply that applying the (n-1)/(n-2) correction directly to SEA (to get SEAc) is not quite the same as applying it to the eigenvalues? Or is it something to do with the scaling of the sigma before determining the eigenvalues? (Or am I off track completely?)

Thanks!

groupMetricsML(siber.example)
1.1 1.2 1.3 2.1 2.2 2.3
TA 21.924922 10.917715 17.945127 3.0714363 11.476354 1.4818061
SEA 5.783417 3.254484 5.131601 0.8623300 3.458824 0.4430053
SEAc 5.989967 3.370715 5.314872 0.8931275 3.582354 0.4588269

maxLikOverlap("1.2", "1.3", siber.example, p.interval = NULL, n = 100)
area.1 area.2 overlap
3.28548611 5.18048437 0.06872133

maxLikOverlap("1.1", "2.2", siber.example, p.interval = NULL, n = 100)
area.1 area.2 overlap
5.838510 3.491773 0.000000

@AndrewLJackson
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AndrewLJackson commented Feb 21, 2017 via email

@AndrewLJackson
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AndrewLJackson commented Feb 21, 2017 via email

@AndrewLJackson
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AndrewLJackson commented Feb 21, 2017 via email

@marknovak
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You rock, Andrew! Thanks again for the quick and helpful replies.

I have, however, found another bug for you...just a simple typo though! (One that SarinaJ noted, but that seems not to have made it into the new bayesianOverlap function.)

It's in the final section of the function that uses spatstat. You've got coord.2 referenced three times when I think you want the first reference to be coord.1.

thanks


Here's your full function (as currently written) for reference:

> bayesianOverlap
function (ellipse1, ellipse2, ellipses.posterior, draws = 10, 
    p.interval = 0.95, n = 100, do.plot = FALSE) 
{
    if (is.null(draws)) 
        draws = nrow(ellipses.posterior[[1]])
    out <- data.frame(area1 = double(draws), area2 = double(draws), 
        overlap = double(draws))
    for (i in 1:draws) {
        coords.1 <- addEllipse(ellipses.posterior[[ellipse1]][i, 
            5:6], matrix(ellipses.posterior[[ellipse1]][i, 1:4], 
            nrow = 2, ncol = 2), p.interval = p.interval, n = n, 
            do.plot = do.plot, small.sample = FALSE)
        area.1 <- hullArea(coords.1[, 1], coords.1[, 2])
        coords.2 <- addEllipse(ellipses.posterior[[ellipse2]][i, 
            5:6], matrix(ellipses.posterior[[ellipse2]][i, 1:4], 
            nrow = 2, ncol = 2), p.interval = p.interval, n = n, 
            do.plot = do.plot, small.sample = FALSE)
        area.2 <- hullArea(coords.2[, 1], coords.2[, 2])
        overlap <- abs(spatstat::overlap.xypolygon(list(x = coords.1[, 
            1], y = coords.2[, 2]), list(x = coords.2[, 1], y = coords.2[, 
            2])))
        out[i, 1:3] <- c(area.1, area.2, overlap)
    }
    return(out)
}
<environment: namespace:SIBER>

@AndrewLJackson
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AndrewLJackson commented Feb 22, 2017 via email

@AndrewLJackson
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hi Mark. I just pushed a hotfix to the master branch on github. I will have to wait a couple of days to push to CRAN. hopefully thats all the big bugs for now! thanks very much again for the help.

@AndrewLJackson
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all well under v2.1.999

@marknovak
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Works like a charm. Thanks!

@palomapali
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I am having problem with the new overlap code.
I tried in two computer and I get this error all the time. I updated both R and packages and doesn't seem to help. Not sure what to do anymore.

Error: 'overlap.xypolygon' is not an exported object from 'namespace:spatstat'

@Perko84
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Perko84 commented Apr 19, 2017

I'm also having problems running the code from the niche overlap vignette and receive the same Error: 'overlap.xypolygon' is not an exported object from 'namespace:spatstat'

R is up to date (version 3.3.3) and I've also tried stalling spatstat.utils

Any pointers greatly appreciated.
D

@SarinaJ
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SarinaJ commented Apr 21, 2017

I wanted to rerun my script as well as I got some comments back from my supervisors and I got this one as well. The Problem lies within the function of the SIBER package that references back to spatstat directly and as @Perko84 pointed out the function 'overlap.xypolygon' is no longer part of this package but is outsourced to 'spatstat.utils'. When you look at the R code here on GitHub you can find the updated version of the function. I therefore installed the latest development version (see welcome page of SIBER) and it is working again.

@amgarcia70
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Hello there!

I want to estimate the overlap between ONLY two species and express it as a proportion, but I’m not sure if I’m doing right, especially when assigning the denominator in the last step of the script. Could someone please check where (or if) I got wrong? Instead of getting ‘overlap’ in the end of the script I got ‘area.2’.

Thanks in advance for any help!
Alexandre

ellipse1 <- "1.1"
ellipse2 <- "1.2"
sea.overlap <- maxLikOverlap(ellipse1, ellipse2, siber.example,
p.interval = NULL, n = 200)
sea.overlap

area.1 area.2 overlap
3.681389 3.372552 1.858440

ellipse40.overlap <- maxLikOverlap(ellipse1, ellipse2, siber.example,
p.interval = 0.40, n = 200)

ellipse40.overlap

area.1 area.2 overlap
3.761095 3.445572 1.914339

prop.40.over <- ellipse40.overlap[2] / (ellipse40.overlap[1] +
ellipse40.overlap[1] -
ellipse40.overlap[2])

prop.40.over

area.2
0.8452035

@Nesaldi
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Nesaldi commented Jun 7, 2018

Hi Andrew, I want to estimate the overlap between two groups, I was using the "maxLikOverlap" but then i got confused when I saw another example using only "overlap", so I wanted to know if they are the same function...

I hope you can help me, thank you!

@christina-cheung
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Hi, just wondering if the overlap function only works for ellipses? What about convex hulls? Is it possible to calculate the overlapped area between convex hulls? Thanks in advance!

@AndrewLJackson
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AndrewLJackson commented Feb 5, 2020 via email

@christina-cheung
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Thank you for your quick reply!!

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@marknovak @AndrewLJackson @christina-cheung @HarriPettittWade @GeorginaBusst @SarinaJ @palomapali @Perko84 @amgarcia70 @Nesaldi