[AniMov] Using QGIS for home range

Clément Calenge clement.calenge at oncfs.gouv.fr
Fri Feb 12 12:28:42 CET 2010


Franco Leandro de Souza wrote:
> 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?
>   

The QGIS plugin does use R (so it needs to be installed, see the how 
to), but does not require the user to do so.
Best regards,

Clément


> 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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>> -- 
>> Esta mensagem foi verificada pelo sistema de antivírus e
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>>     
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>
>   


-- 
Clément CALENGE
Cellule d'appui à l'analyse de données
Office national de la chasse et de la faune sauvage
Saint Benoist - 78610 Auffargis
tel. (33) 01.30.46.54.14



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