[AniMov] AniMov Digest, Vol 74, Issue 5

dr. V. Maximiliano Giacalone maximiliano.giacalone at iamc.cnr.it
Fri Jan 13 12:39:20 CET 2012


Hello everybody,
I’d like to use the harmonic mean method just to have a “mean position” of 
all my fixes and then estimate the homing movement pattern of my fishes 
after I tagged and released them.
Looking to my data, I can see that all the fixes are close to the refuge 
used by each individual, so I can consider the HM as the representative 
position of fish’ home. Once release, I can calculate distance between fixes 
and the “home” so that I can see that 1) fish moves to home because 2) 
distance decreases over time until a minimum value, then 3) I can appreciate 
how many hour fish spent to reach his home.
None implication or relationship on/with home-range calculation!!

Bye,
Max

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Sent: Friday, January 13, 2012 12:00 PM
To: animov at faunalia.it
Subject: AniMov Digest, Vol 74, Issue 5

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Today's Topics:

   1. Re: site fidelity test and harmonic mean (Anne Ghisla)
   2. Re: site fidelity test and harmonic mean (Paolo Cavallini)
   3. Re: HR analysis, etc. (Roberts, Dan)
   4. Re: HR analysis, etc. (Paolo Cavallini)
   5. Re: HR analysis, etc. (Giovanni Manghi)


----------------------------------------------------------------------

Message: 1
Date: Thu, 12 Jan 2012 15:46:26 +0100
From: Anne Ghisla <a.ghisla at gmail.com>
To: Animal Movement <animov at faunalia.it>
Subject: Re: [AniMov] site fidelity test and harmonic mean
Message-ID: <20120112154626.718a6c73 at galadriel.localdomain>
Content-Type: text/plain; charset="utf-8"

On Mon, 09 Jan 2012 10:34:52 +0000
Giovanni Manghi <giovanni.manghi at gmail.com> wrote:

> Hi,
>
> On Thu, 2012-01-05 at 02:22 -0800, Maximiliano wrote:
> > Hi,
> > does anybody know if there?s an application of Qgis to perform SITE
> > FIDELITY TEST, like in arcview3?
> > I?d like to know if I calculate the harmonic mean of all my fixes
> > and the distance of each fixes from this ?home range? centre?
> > thanks a lot!!
>
>
> don't think there is something ready for QGIS, but it would be a nice
> addon for the Home Range or for the triangulation plugin. Any interest
> in supporting its development?

Hello Maximiliano, Giovanni,

the literature on harmonic mean is quite old: the method dates back to
1980 and the Animal Movements documentation [0] warns about the known
problems in home range estimates.

I won't implement this specific method in HomeRange plugin, as I don't
support the idea of implementing a method that has such known biases.

Also, as HR plugin is a interface to adehabitat, I would ask Cl?ment
Calenge his opinion about adding this method to adehabitat directly.

As an alternative to harmonic means, to individuate the core centres of
the home range, I suggest to calculate homeranges with kernel method and
select the 90% isopleth. (90% is a common value to identify core areas.
However, better run an incremental core area analysis [1] to identify
the correct limit of the core area for each animal). Then, calculate the
center of each core area polygon and use it instead of the harmonic
mean.

This is my suggestion, of course comments and improvements are welcome!

[0]
http://alaska.usgs.gov/science/biology/spatial/gistools/animal_mvmt.php#harm_mean
[1] http://wiki.faunalia.it/dokuwiki/doku.php/public/animove_howto#analyses

Best regards,

Anne
-- 
http://gis.cri.fmach.it/ghisla/
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Message: 2
Date: Thu, 12 Jan 2012 15:46:28 +0100
From: Paolo Cavallini <cavallini at faunalia.it>
To: animov at faunalia.it
Subject: Re: [AniMov] site fidelity test and harmonic mean
Message-ID: <4F0EF244.3060604 at faunalia.it>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Il 12/01/2012 15:46, Anne Ghisla ha scritto:

> I won't implement this specific method in HomeRange plugin, as I don't
> support the idea of implementing a method that has such known biases.

Agreed fully. HM is rubbish.
All the best.
-- 
Paolo Cavallini - Faunalia
www.faunalia.eu
Full contact details at www.faunalia.eu/pc


------------------------------

Message: 3
Date: Thu, 12 Jan 2012 11:20:45 -0500
From: "Roberts, Dan" <Dan.Roberts at MyFWC.com>
To: "cavallini at faunalia.it" <cavallini at faunalia.it>, Animal Movement
<animov at faunalia.it>
Subject: Re: [AniMov] HR analysis, etc.
Message-ID:
<D679AB09BFE3074C8D3961B08B99F965297BF1363B at FWC-TLEX10.fwc.state.fl.us>

Content-Type: text/plain; charset="us-ascii"

I have been using ARCGIS, Spatial Analyst, and Hawthes Tools to analyze fish 
movements in rivers and estuaries. We have been using various home range 
analyses to characterize habitat.  I no longer have access to ARGIS.  Can 
you point me to resources for beginners using ANIMOVE, etc.? Thanks in 
advance for any suggestions.

Waterinterface

------------------------------

Message: 4
Date: Thu, 12 Jan 2012 17:35:40 +0100
From: Paolo Cavallini <cavallini at faunalia.it>
To: "Roberts, Dan" <Dan.Roberts at MyFWC.com>
Cc: Animal Movement <animov at faunalia.it>
Subject: Re: [AniMov] HR analysis, etc.
Message-ID: <4F0F0BDC.9080209 at faunalia.it>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Il 12/01/2012 17:20, Roberts, Dan ha scritto:
> I have been using ARCGIS, Spatial Analyst, and Hawthes Tools to analyze 
> fish movements in rivers and estuaries. We have been using various home 
> range analyses to characterize habitat.  I no longer have access to ARGIS. 
> Can you point me to resources for beginners using ANIMOVE, etc.? Thanks in 
> advance for any suggestions.
>
> Waterinterface

http://www.faunalia.it/animove
https://trac.faunalia.it/animove/wiki/AnimoveHowto

All the best.
-- 
Paolo Cavallini - Faunalia
www.faunalia.eu
Full contact details at www.faunalia.eu/pc


------------------------------

Message: 5
Date: Thu, 12 Jan 2012 18:28:12 +0000
From: Giovanni Manghi <giovanni.manghi at gmail.com>
To: Animal Movement <animov at faunalia.it>
Subject: Re: [AniMov] HR analysis, etc.
Message-ID: <1326392892.2238.16.camel at sibirica>
Content-Type: text/plain; charset="UTF-8"

Hi Robert,


all the steps to put the HR plugin, R and QGIS work together are
described in this screencast and wiki page

http://ubuntuone.com/p/zon/

http://hub.qgis.org/wiki/quantum-gis/HomeRange_plugin


cheers

-- Giovanni --



On Thu, 2012-01-12 at 11:20 -0500, Roberts, Dan wrote:
> I have been using ARCGIS, Spatial Analyst, and Hawthes Tools to analyze 
> fish movements in rivers and estuaries. We have been using various home 
> range analyses to characterize habitat.  I no longer have access to ARGIS. 
> Can you point me to resources for beginners using ANIMOVE, etc.? Thanks in 
> advance for any suggestions.
>
> Waterinterface
> _______________________________________________
> AniMov mailing list
> AniMov at faunalia.it
> http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov




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