Franco
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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 <[email protected]>
Subject: [AniMov] LoCoH isopleths intervals... to e.g. 5%?
To: [email protected]
Message-ID:
<[email protected]> 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
[email protected]
[email protected]
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Message: 2
Date: Thu, 11 Feb 2010 20:34:57 +0200
From: Anne Ghisla <[email protected]>
Subject: Re: [AniMov] Error with kernel LSCV / kernel adj h / NNCH
To: Animal Movement <[email protected]>
Cc: "[email protected] List" <[email protected]>
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<[email protected]>
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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 <[email protected]> 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
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Message: 3
Date: Thu, 11 Feb 2010 15:11:08 -0400
From: "Franco Leandro de Souza" <[email protected]>
Subject: [AniMov] basic use of the R project for home range analyses
To: [email protected]
Message-ID: <[email protected]>
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
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Message: 4
Date: Fri, 12 Feb 2010 09:32:18 +0100
From: Cl?ment Calenge <[email protected]>
Subject: Re: [AniMov] basic use of the R project for home range
analyses
To: Animal Movement <[email protected]>
Message-ID: <[email protected]>
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 <[email protected]>
Subject: Re: [AniMov] LoCoH isopleths intervals... to e.g. 5%?
To: Animal Movement <[email protected]>
Message-ID: <[email protected]>
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 <[email protected]>
Subject: Re: [AniMov] LoCoH isopleths intervals... to e.g. 5%?
To: Animal Movement <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="utf-8"
Thanks Cl?ment, well appreciated
/Henrik
___________________________
Henrik Lundqvist
[email protected]
[email protected]
2010/2/12 Cl?ment Calenge <[email protected]>
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
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