[AniMov] Using QGIS for home range

Franco Leandro de Souza flsouza at nin.ufms.br
Fri Feb 12 12:22:31 CET 2010


Dear Clement,
Thank you for your help. So, QGIS does not use R interface for home range 
analyses that is, QGIS is a stand alone tool for this anlayses?
Franco


---------- Original Message -----------
From: animov-request at faunalia.it
To: animov at faunalia.it
Sent: Fri, 12 Feb 2010 12:00:01 +0100
Subject: AniMov Digest, Vol 53, Issue 3

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> Today's Topics:
> 
>    1. LoCoH isopleths intervals... to e.g. 5%? (Henrik Lundqvist)
>    2. Re: Error with kernel LSCV / kernel adj h / NNCH (Anne Ghisla)
>    3. basic use of the R project for home range analyses
>       (Franco Leandro de Souza)
>    4. Re: basic use of the R project for home range analyses
>       (Cl?ment Calenge)
>    5. Re: LoCoH isopleths intervals... to e.g. 5%? (Cl?ment Calenge)
>    6. Re: LoCoH isopleths intervals... to e.g. 5%? (Henrik Lundqvist)
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 11 Feb 2010 18:32:50 +0100
> From: Henrik Lundqvist <h.lundqvist at gmail.com>
> Subject: [AniMov] LoCoH isopleths intervals... to e.g. 5%?
> To: animov at faunalia.it
> Message-ID: 
> <5d355e911002110932x8c9cf2i262877cfdf2aa14 at mail.gmail.com> Content-
> Type: text/plain; charset="utf-8"
> 
> Hi all
> 
> I got a question regarding the k-NNCH or LoCoH funktion in 
> Adehabitat for calculating homeranges. The default setting regaring 
> the isopleths are 10% steps as follows: c(100,90,80,70,60,50,40,30,
> 20,10) Is there a parameter I can change to achieve 5% steps (or 
> other configuration)? I can't find it in the arguments of the 
> function. There seems to be a possibility to set more intervals in 
> the ArcGIS-plugin at: 
http://nature.berkeley.edu/~alyons/locoh/arcgis9/index.html
> 
> I guess I have to engage with the code of NNCH.R, but when I try 
> (the R-guru that I'm not) I get errors.
> 
> Couldn't it be coded as an argument of the function? Would be neat...
> 
> Cheers
> /Henrik Lundqvist
> ___________________________
> Henrik Lundqvist
> h.lundqvist at gmail.com
> henrik.lundqvist at huv.slu.se
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> ------------------------------
> 
> Message: 2
> Date: Thu, 11 Feb 2010 20:34:57 +0200
> From: Anne Ghisla <a.ghisla at gmail.com>
> Subject: Re: [AniMov] Error with kernel LSCV / kernel adj h / NNCH
> To: Animal Movement <animov at faunalia.it>
> Cc: "qgis-user at lists.osgeo.org List" <qgis-user at lists.osgeo.org>
> Message-ID:
> 	<6843cc5e1002111034u72810dd6oebd4211279b71cc1 at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Hi Henrik, Jehol, lists,
> 
> I forward the message to the qgis-user list, if any other Mint user
> has hints to squash this nasty bug...
> 
> I actually have to setup the testing suite :) hope to find time soon.
> 
> cheers
> Anne
> 
> On Mon, Feb 8, 2010 at 12:53 PM, Lunken <h.lundqvist at gmail.com> wrote:
> >
> > Hi all
> >
> > I have the same problem.
> >
> > My config
> >
> > LinuxMint 7 (Ubuntu 9.04)
> > QGIS 1.4.0-Enceladus
> > HomeRange plugin 2.1.4
> > R -base-core 2.10.1-2jaunty0
> > Python 2.6.2
> >
> > Any leads?
> >
> > cheers
> > Henrik Lundqvist, PhD
> > Swedish University of Agricultural Sciences
> > --
> > View this message in context: http://old.nabble.com/Error-with-kernel-
LSCV---kernel-adj-h---NNCH-tp27357248p27498089.html
> > Sent from the AniMov mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > AniMov mailing list
> > AniMov at faunalia.it
> > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> >
> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 11 Feb 2010 15:11:08 -0400
> From: "Franco Leandro de Souza" <flsouza at nin.ufms.br>
> Subject: [AniMov] basic use of the R project for home range analyses
> To: animov at faunalia.it
> Message-ID: <20100211190911.M21387 at nin.ufms.br>
> Content-Type: text/plain;	charset=iso-8859-1
> 
> Dear members,
> I am initialing in R project so, excuse me for some inconvenience 
> and repetition in the questions I will post in this message. I am 
> trying to use this platform to analyze data on animal home range,
>  particularly home range size (e.g. traditional area calculus by 
> minimum convex polygon and kernel). After several tentative by 
> different packages 
> (including ArcView, Home Range, Home Ranger, CalHome?), the tools 
> from R project seems to be interesting for my purposes. However, the 
> things are not so friendly as they are shown. For instance, after 
> install the ?adehabitat? package, I am informed that other packages 
> are necessary for a complete analyze. No problem yet. Things become 
> to be dark when several links are suggested to produce figures: 
> quantum gis and associated files (phyton for instance but the are 
> many other). So, it is like a puzzle and the puzzle pieces are 
> hosted in the hard disk. So, basically I would like to use 
> coordinate data from GPS to produce home range estimates, including 
> figures, and my question is: is there a step by step manual for R 
> project to proceed with such analyses? Thanks for all, Franco
> 
> -- 
> Esta mensagem foi verificada pelo sistema de antiv?rus e
>  acredita-se estar livre de perigo.
> 
> ------------------------------
> 
> Message: 4
> Date: Fri, 12 Feb 2010 09:32:18 +0100
> From: Cl?ment Calenge <clement.calenge at oncfs.gouv.fr>
> Subject: Re: [AniMov] basic use of the R project for home range
> 	analyses
> To: Animal Movement <animov at faunalia.it>
> Message-ID: <4B751212.5070307 at oncfs.gouv.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Dear Franco,
> 
> > So, basically I would like to use coordinate data from GPS to produce 
home 
> > range estimates, including figures, and my question is: is there a step 
by 
> > step manual for R project to proceed with such analyses?
> >
> 
> A good place to start is the Animove "how to": 
> https://wiki.faunalia.it/dokuwiki/doku.php?id=public:animove_howto
> It describes how to install the QGIS plugin for home range 
> estimation. If you want to use adehabitat as such (i.e. without any 
> QGIS interface), you first have to learn how to use R. There are 
> several good manuals available at this URL: http://cran.univ-
> lyon1.fr/other-docs.html The Animove "how to" also describes how to 
> use adehabitat without interface, showing the R code needed for 
> various home range estimation methods. Another good place to start 
> is to type:
> 
> library(adehabitat)
> demo(homerange)
> 
> within R. You can then browse the R code of the demo and look at the 
> help pages of the functions used in the demo.
> Hope this helps,
> 
> Cl?ment Calenge
> 
> -- 
> Cl?ment CALENGE
> Cellule d'appui ? l'analyse de donn?es
> Office national de la chasse et de la faune sauvage
> Saint Benoist - 78610 Auffargis
> tel. (33) 01.30.46.54.14
> 
> ------------------------------
> 
> Message: 5
> Date: Fri, 12 Feb 2010 09:46:20 +0100
> From: Cl?ment Calenge  <clement.calenge at oncfs.gouv.fr>
> Subject: Re: [AniMov] LoCoH isopleths intervals... to e.g. 5%?
> To: Animal Movement <animov at faunalia.it>
> Message-ID: <4B75155C.7070603 at oncfs.gouv.fr>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> Hello Henrik,
> 
> Henrik Lundqvist wrote:
> > I got a question regarding the k-NNCH or LoCoH funktion in Adehabitat 
> > for calculating homeranges.
> > The default setting regaring the isopleths are 10% steps as follows: 
> > c(100,90,80,70,60,50,40,30,20,10)
> > Is there a parameter I can change to achieve 5% steps (or other 
> > configuration)? I can't find it in the arguments of the function. 
> > There seems to be a possibility to set more intervals in the 
> > ArcGIS-plugin at: 
> > http://nature.berkeley.edu/~alyons/locoh/arcgis9/index.html 
> > <http://nature.berkeley.edu/%7Ealyons/locoh/arcgis9/index.html>
> > I guess I have to engage with the code of NNCH.R, but when I try (the 
> > R-guru that I'm not) I get errors.
> > Couldn't it be coded as an argument of the function? Would be neat...
> 
> Actually, the function NNCH returns an object of class "NNCH" 
> containing all possible isopleths that can be built with a given 
> dataset. Then, other functions are used to "extract" given 
> isopleths. For example, if you want to compute the home range size 
> for isopleth 95%, you have to set the argument percent = 95 in the 
> function NNCH.area. Or, if you want the home range sizes for 
> isopleths 100 to 50% by 5% steps, you have to set: percent = 
> rev(seq(50,95, by=5)) in the function NNCH.area. Similarly, if you 
> want to plot the 95% home range, you have to set percent=95 in the 
> function plot.NNCH. etc. Have a look at the argument percent on the 
> help pages of plot.NNCH, and NNCH.area. Hope this helps,
> 
> Cl?ment Calenge
> 
> -- 
> Cl?ment CALENGE
> Cellule d'appui ? l'analyse de donn?es
> Office national de la chasse et de la faune sauvage
> Saint Benoist - 78610 Auffargis
> tel. (33) 01.30.46.54.14
> 
> ------------------------------
> 
> Message: 6
> Date: Fri, 12 Feb 2010 10:05:23 +0100
> From: Henrik Lundqvist <h.lundqvist at gmail.com>
> Subject: Re: [AniMov] LoCoH isopleths intervals... to e.g. 5%?
> To: Animal Movement <animov at faunalia.it>
> Message-ID:
> 	<5d355e911002120105m6d11693fv12ba14d54afac44b at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Thanks Cl?ment, well appreciated
> 
> /Henrik
> 
> ___________________________
> Henrik Lundqvist
> h.lundqvist at gmail.com
> henrik.lundqvist at huv.slu.se
> 
> 2010/2/12 Cl?ment Calenge <clement.calenge at oncfs.gouv.fr>
> 
> > Hello Henrik,
> >
> > Henrik Lundqvist wrote:
> >
> >> I got a question regarding the k-NNCH or LoCoH funktion in Adehabitat 
for
> >> calculating homeranges.
> >> The default setting regaring the isopleths are 10% steps as follows:
> >> c(100,90,80,70,60,50,40,30,20,10)
> >> Is there a parameter I can change to achieve 5% steps (or other
> >> configuration)? I can't find it in the arguments of the function. There
> >> seems to be a possibility to set more intervals in the ArcGIS-plugin at:
> >> http://nature.berkeley.edu/~alyons/locoh/arcgis9/index.html <
> >> http://nature.berkeley.edu/%7Ealyons/locoh/arcgis9/index.html>
> >>
> >> I guess I have to engage with the code of NNCH.R, but when I try (the
> >> R-guru that I'm not) I get errors.
> >> Couldn't it be coded as an argument of the function? Would be neat...
> >>
> >
> > Actually, the function NNCH returns an object of class "NNCH" containing
> > all possible isopleths that can be built with a given dataset. Then, 
other
> > functions are used to "extract" given isopleths. For example, if you 
want to
> > compute the home range size for isopleth 95%, you have to set the 
argument
> > percent = 95 in the function NNCH.area. Or, if you want the home range 
sizes
> > for isopleths 100 to 50% by 5% steps, you have to set: percent =
> > rev(seq(50,95, by=5)) in the function NNCH.area. Similarly, if you want 
to
> > plot the 95% home range, you have to set percent=95 in the function
> > plot.NNCH. etc.
> > Have a look at the argument percent on the help pages of plot.NNCH, and
> > NNCH.area.
> > Hope this helps,
> >
> > Cl?ment Calenge
> >
> > --
> > Cl?ment CALENGE
> > Cellule d'appui ? l'analyse de donn?es
> > Office national de la chasse et de la faune sauvage
> > Saint Benoist - 78610 Auffargis
> > tel. (33) 01.30.46.54.14
> >
> > _______________________________________________
> > AniMov mailing list
> > AniMov at faunalia.it
> > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> >
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