gmane.science.ecology.animov

Re: QGIS Python plugin progress

Paolo Cavallini — 2013-05-15T12:32:51

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Il 15/05/2013 13:00, Victor Gonzalez ha scritto:


great


Please contact Francesco, the previous developer, and make an
arrangement for him to pass you the ownership.
You will need an osgeo account, and if you need permissions you can
ask Alessandro Pasotti or me.
All the best, and thanks.
- -- 
Paolo Cavallini - Faunalia
www.faunalia.eu
Full contact details at www.faunalia.eu/pc
Nuovi corsi QGIS e PostGIS: http://www.faunalia.it/calendario
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Re: QGIS Python plugin progress

Victor Gonzalez — 2013-05-15T11:00:50

Hi again,

We have made optional input parameters depending on scipy and statsmodels
just as you suggested and we're ready to share a new experimental version.

However, we're not sure how to make the plugin available through the
official qgis plugin repo. I guess we would need to update [1] to add a new
1.3.3 experimental version (and also update the link to the code repo). But
we haven't done it before and it seems like we don't have permissions to do
it. What should we do? I'm attaching the zipped packaged in case you need
it.

Cheers,
Víctor.

[1] http://plugins.qgis.org/plugins/sextante_animove/


2013/5/14 Paolo Cavallini <cavallini-h12OV65+u/41GQ1Ptb7lUw< at >public.gmane.org>

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Re: QGIS Python plugin progress

Paolo Cavallini — 2013-05-14T14:44:40

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Il 14/05/2013 12:52, Victor Gonzalez ha scritto:


Packaging dependencies is evil :)
So, do not worry if not all the options are available to all users: let's develop all
the funcions necessary using the most recent py libraries, and show the user only
what's possible with their system. As soon as the libraries will be available, the
full set of functions will become usable for all.


Fine, thanks.
I suggest you to package the new version and make it available through the official
qgis plugin repo, so to enjoy early testing.
All the best.
- -- 
Paolo Cavallini - Faunalia
www.faunalia.eu
Full contact details at www.faunalia.eu/pc
Nuovi corsi QGIS e PostGIS: http://www.faunalia.it/calendario
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QGIS Python plugin progress

Victor Gonzalez — 2013-05-14T10:52:34

Hi all,

We've made some progress with the Python plugin. Finally, we made a fork
[1] of the previous repository in order to have a more agile development.

We asked in the scipy mailing list about supporting LSCV in scipy and the
answer was that we can use statsmodels [2]. It supports the LSCV bandwidth
estimation. But the problem is that it's supported in a currently developed
version. So maybe we would need to wait for the new release.

Also, we are unsure about how to manage dependencies. We can check if
statsmodels is present, or if scipy is present with a version newer than
0.10 (so we can set the bandwidth value manually) and give different
options depending on the user's system. Another option is to package the
dependencies together with the plugin, but we don't know if there is a
standard procedure to do so in QGIS.

Finally, a new algorithm input parameter (boolean) has been added to
specify if the raster outputs must be added as layers to the project or
not. Thus, you can get all the results or on

Re: HomeRange plugin and rpy2 in Lubuntu, a dead end?

Jorge Arévalo — 2013-05-07T08:12:55

El martes 7 de mayo de 2013 a las 10:06, Anne Ghisla escribió:
Hello,

Ok, that sounds reasonable. Many thanks, Paolo and Anne.

Best regards,
Jorge



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Re: HomeRange plugin and rpy2 in Lubuntu, a dead end?

Anne Ghisla — 2013-05-07T08:06:22

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On Tue, 07 May 2013 08:40:34 +0200
Paolo Cavallini <cavallini-h12OV65+u/41GQ1Ptb7lUw< at >public.gmane.org> wrote:


Hello Jorge, all,

I confirm that the HR plugin is not mantained. I have not time to work
on it soon, and no one stepped in to fix it so far.

Please test the experimental AniMove plugin for Sextante, that is
written in Python, or ask Damiano Preatoni for the batch-processing R
scripts.

Sorry for inconvenience,
Anne



Anne
- -- 
http://wiki.osgeo.org/wiki/User:Aghisla
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Re: HomeRange plugin and rpy2 in Lubuntu, a dead end?

Paolo Cavallini — 2013-05-07T06:40:34

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Il 06/05/2013 18:46, Jorge Arévalo ha scritto:


Hi Jorge,
I think the HR plugin is unmaintained, and the error you found is a consequence of
this. Perhaps you could use an older version of R, but of course this would not be
easy on an updated system. Of course if you need just the results, you could use
directly R+AdeHabitat without the plugin.
Anyone has a cleaner solution?
All the best.
- -- 
Paolo Cavallini - Faunalia
www.faunalia.eu
Full contact details at www.faunalia.eu/pc
Nuovi corsi QGIS e PostGIS: http://www.faunalia.it/calendario
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HomeRange plugin and rpy2 in Lubuntu, a dead end?

Jorge Arévalo — 2013-05-06T16:46:06

Hello,

(sorry, I sent the previous message with an unregistered email. This is the valid one)

I'm working with Victor González in the development of AniMove module for Sextante, and I'd like to test HomeRange plugin. So, I installed it via Plugins Manager. I got this error

"Unable to load the plugin: Unable to load required package rpy2. Please ensure that both R, and the corresponding version of Rpy2 are correctly installed."

But after that, I got the message "Plugin installed successfully".

So, I tried to test the plugin with this csv: http://www.faunalia.it/animov/scripts/sample.csv, and following these instructionshttp://linfiniti.com/2009/11/home-range-plugin-in-qgis/

And I got this error: https://dl.dropboxusercontent.com/u/6599273/errors/qgis/homerange_plugin_error.log

Then, I found this old list message: http://lists.faunalia.it/pipermail/animov/2010-January/000545.html

And tried with

import rpy2.robjects as robjects

Getting this error:

Traceback (most recent call last):
File "<stdin>", l

Re: AniMove plugin for python

Paolo Cavallini — 2013-05-03T13:08:13

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Il 03/05/2013 09:33, Victor Gonzalez ha scritto:


No, because users of other OS could have older scipy; better having a conditional.


Thanks.


Unsure about that - opinions?
Could we have a popup "X maps generated, do you want to load them all?".
Please consider that rasters are optional, many users just want the contour lines
(equiprobability).
All the best, and thanks.
- -- 
Paolo Cavallini - Faunalia
www.faunalia.eu
Full contact details at www.faunalia.eu/pc
Nuovi corsi QGIS e PostGIS: http://www.faunalia.it/calendario
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Re: AniMove plugin for python

Victor Gonzalez — 2013-05-03T07:33:50

Hi again,

The scipy version in osgeo4w is 0.11.0 [1], so I guess we can simply assume
that gaussian_kde.set_bandwidth exists, right?

Regarding the LSCV implementation, I'll ask in the scipy mailing list.

Finally, I asked Víctor Olaya about the algorithm definition and he says
that it's possible to create the different raster outputs, but it's not
possible to define them beforehand. This means that the outputs can be
created and added as layers but since they are not defined, it may cause
some issues, for example, in the graphic modeler. Is that a problem or
should we simply create the outputs without previous definition?

Cheers,
Víctor.

[1] http://download.osgeo.org/osgeo4w/versions.html


2013/5/2 Paolo Cavallini <cavallini-h12OV65+u/41GQ1Ptb7lUw< at >public.gmane.org>

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Re: AniMove plugin for python

Paolo Cavallini — 2013-05-02T09:52:56

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Il 02/05/2013 11:28, Victor Gonzalez ha scritto:


I think you could take the lead, no need for the pull. Francesco?


Please check the one available in osgeo4w. In Debian we have 0.10.1+dfsg2-1.
Maybe you can implement it conditionally, so that it will be available when scipy
will be upgraded.


I would avoid implementing stuff locally, unless it's a relatively simple extension
to numpy/scipy. Always better to try to find another py library, or cooperate
upstream with scipy devs.


Partly: I think there should be a way to add them all. Please check with Victor
Olaya, it would be better to add the function to Sextante core if necessary.

All the best.
- -- 
Paolo Cavallini - Faunalia
www.faunalia.eu
Full contact details at www.faunalia.eu/pc
Nuovi corsi QGIS e PostGIS: http://www.faunalia.it/calendario
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AniMove plugin for python

Victor Gonzalez — 2013-05-02T09:28:58

Hello,

First of all, I want to introduce myself. I am Víctor González and I'll be
working with Jorge Arévalo in the AniMove plugin for python. We are part of
geomati.co and we are very excited for this first collaboration with the
Faunalia and QGIS community.

We already started analyzing the task and we have some questions. First, we
are going to made a fork of the current animove plugin repository [1] and
when we finish we'll do a pull request. Is that ok with you? Anyone has a
better idea?

Regarding the kernel analysis algorithm, we found that the gaussian_kde
class in scipy [2] has a set_bandwidth method in order to set the bandwidth
of the method as a simple scalar. But this is only available from 0.11.0
version. Which version of scipy we assume will be installed in the
distribution?

Also, that gaussian_kde class allows 'scotts' and 'silverman' method to
calculate the bandwidth, but no LSCV or is available. The only way to have
it working is to set the bw_method as a callable and implement the LSC

Re: Using R: AdehabiatHR: passing a different numeric value for the smoothing parameter to different individuals

Iris Dröscher — 2013-04-04T17:47:10

Hi Johannes,

I picked up your idea of combining the UDs of several animals into an
estUDm.

I crosschecked if kerneloverlap and kerneloverlaphr using the so created
estUDm will give the same results.

It works :)

Thank you for your help!
Iris


Message: 2
Date: Thu, 21 Mar 2013 08:55:46 +0100
From: Johannes Signer <j.m.signer-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org>
To: Animal Movement <animov-h12OV65+u/41GQ1Ptb7lUw< at >public.gmane.org>
Subject: Re: [AniMov] Using R: AdehabiatHR: passing a different
        numeric value for the smoothing parameter to different individuals
Message-ID:
        <CAC8qavvHRrPjQKshBxsu5UZv_=K=pcJy975NPhFHKAQbscetjQ-JsoAwUIsXosN+BqQ9rBEUg< at >public.gmane.org>
Content-Type: text/plain; charset="iso-8859-1"

You could calculate a home range for each animal individually.

# Data prep
library(adehabitatHR)
data(puechabonsp)
loc <- puechabonsp$relocs

# Split the the data
loc <- split(loc, loc$Name)

# Calculate home ranges
h <- c(10, 20, 30, 40) # vector with your h values

uds <- lapply

Re: HR QGIS Error

Damiano G. Preatoni — 2013-04-02T11:40:19

In un messaggio del Thursday 28 March 2013, Giovanni Manghi ha scritto:

I confirm what Giovanni wrote: I'm afraid the python-rpy2-R architecture of the 
"old" HR plugin is now obsolete.

A new python-only plugin is heavily worked on (kudos to Francesco!!!).

Since I'mostly involved in HR calculations by-the-ton, I work directly in R, and 
(still!) use the "HR engine" written in R. Again, that script is depending on 
the adehabitat package, that since years has been splitted into 4 different 
packages. A porting to the 'new' adehabitatHR R package is already in progress, 
but this will be "pure R" only.

My 2 eurocents. ;)

PS: the current version of R scripts I use are available on request.
I'm planning to upload on RForge the adehabitatHR port soon.

Re: HR QGIS Error

Giovanni Manghi — 2013-03-28T18:47:07

if you are looking to compute HR within qgis, there is a new plugin
that does not uses R. The plugin that uses R cannot be used anymore,
at least on Windows and at least until a new version od rpy2 for
python 2.7 will be released.

cheers

HR QGIS Error

Dylan Irion — 2013-03-28T13:35:26

Hi list,

I'm having the same 'rpy2.rinterface.RNULLType' object has no attribute 
'r_repr' issues that Manuel Spínola had back in November. Seems the 
issue is being worked on, so I was wondering how I could get in touch 
with Damiano Preatoni for his R script? Cheers.

Kind Regards,
Dylan

AniMove for SEXTANTE vers. 1.3.2

2013-03-25T20:12:48

Hi all,
I fixed the problem of the version in AniMove for SEXTANTE version 1.3.2.
It works fine also in windows system.
Thanks

Francesco

Re: Using R: AdehabiatHR: passing a different numeric value for the smoothing parameter to different individuals

Johannes Signer — 2013-03-21T07:55:46

You could calculate a home range for each animal individually.

# Data prep
library(adehabitatHR)
data(puechabonsp)
loc <- puechabonsp$relocs

# Split the the data
loc <- split(loc, loc$Name)

# Calculate home ranges
h <- c(10, 20, 30, 40) # vector with your h values

uds <- lapply(seq_along(loc), function(x) kernelUD(loc[[x]], h[x]))


# You will end up with a list of UDs (class estUD) one for each animal,
# but not a multiple estUDm, however as far as I can tell estUDm is also
only
# a list of estUD, so you could do (but probably shouldn't)

class(uds) <- "estUDm"

# Then generic functions such as image will work
image(uds)

Hope this helps
Johannes


On Thu, Mar 21, 2013 at 6:11 AM, Iris Dröscher <iris.droescher-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org>wrote:

Using R: AdehabiatHR: passing a different numeric value for the smoothing parameter to different individuals

Iris Dröscher — 2013-03-21T05:11:51

Hello,





I plan to use the root-n bandwidth estimate for my Kernel homerange and
Kernel overlap calculations and this bandwidth estimate varies between
individuals.



How can I pass different numeric values for the smoothing parameters in
AdehabitatHR to different individuals?





A.)



I created a SpatialPointsDataframe (LiMa):





  coordinates      id

1   (237.5, 186.5)  Lizzy

2     (233.5, 188)  Lizzy

3     (230.5, 192)  Lizzy

etc.

127   (207, 190.5) Malcom

128   (207, 190.5) Malcom

129     (214, 176) Malcom

etc.







How could I set a different value for h for each individual (e.g. h=8.2 for
Lizzy, h=9.1 for Malcom)?





I tried the following, which unfortunately does not work:



Kernel  <- kernelUD(LiMa[,1], h=c(8.2, h=9.1))



kerneloverlap(LiMa[,1], method = "UDOI", percent = 95, h=c(8.2, h=9.1))





B.)



Alternatively, I created a SpatialPointsDataframe (LiMa) with an additional
column for the smoothing parameter:



  coordinates      id   h

1   (237.5, 186.5)  Lizzy 8.2

2

Re: AniMove for SEXTANTE 1.3.1

Giovanni Manghi — 2013-03-20T09:54:17

Hi Francesco,
on Linux and Windows I get


Algorithm Kernel Density Estimation started
Traceback (most recent call last): File
"/usr/share/qgis/python/plugins/sextante/core/GeoAlgorithm.py", line
146, in execute self.processAlgorithm(progress) File
"/home/gio/.qgis//python/plugins/sextante_animove/href.py", line 150,
in processAlgorithm
self.to_geotiff(currentPath+'/raster_output/'+raster_name,
xmin,xmax,ymin,ymax,X,Y, Z) File
"/home/gio/.qgis//python/plugins/sextante_animove/href.py", line 240,
in to_geotiff out = driver.Create(fname, len(X), len(Y), 1,
gdal.GDT_Float64) File
"/usr/lib/python2.7/dist-packages/osgeo/gdal.py", line 374, in Create
return _gdal.Driver_Create(self, *args, **kwargs) RuntimeError:
TIFFOpen:/home/gio/.qgis/python/plugins/sextante_animove/raster_output/radio_telemetry_95_01/01/05_2013-03-20:
No such file or directory
Traceback (most recent call last): File
"/usr/share/qgis/python/plugins/sextante/core/GeoAlgorithm.py", line
146, in execute self.processAlgorithm(progress) File
"/home

AniMove for SEXTANTE 1.3.1

2013-03-19T21:45:52

Hi all,
i'm already uploaded a new version of AniMove for SEXTATE plugin version 
1.3.1.
It fixs some crash in windows system.
Please let me know.

Thanks


Francesco