Ecological toolbox for QGIS - collecting ideas

[Anne Ghisla-2]

Hi all, and sorry for cross-posting,

during QGIS hackfest the idea of an ecological toolbox has popped up,
thanks mainly to Johannes Signer.
Among currently available standalone bundles, we thought about Hawth's
tools [0] and some other Arc* plugins; other tools, like Conefar [1]
and Circuitscape [2], are dedicated GIS clones and could not cover all
analysis requirements, therefore obliging the user to switch among
different programs.
We'd like to ask ecology researchers, teachers and students what are
the most common analyses you run, and if you'd like to have the
related tools available for QGIS in a toolbox just like for example
GRASS toolbox.

Thanks for feedback, and feel free to forward the message to relevant
people and mailing lists!
Anne Ghisla

[0] http://www.spatialecology.com/htools/tooldesc.php
[1] http://www.conefor.org/
[2] http://www.circuitscape.org/Circuitscape/Welcome.html
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[Agustin Lobo]

I'm not sure if the term "Ecological toolbox" is appropriate, as
few (GIS and not GIS) tools used in Ecology are actually used only
in Ecology and,
actually, most of them were not developed for Ecology.
Anyway, I agree with the essential, that is having the tools to solve
the GIS-related problems faced by people working in Ecology.
Some months ago I actually started a page (never released but
viewable in http://sites.google.com/site/eospansite/mihawthstoolgnu2)
in which I was just listing Hawth's tools with the idea of
writing there how to perform those operations but using open source
or public domain software (excuse for my illiteracy on legal terms).
Unfortunately, I've not been able to find the time for this and
all entries remain unlinked to an answer.

In summary, not sure if this has to be collected as an specific toolbox,
as, for example, many tools will be shared with social scientists, but
for sure the tools have to be available. So I'll be most happy adding my
little grains of sand to that mountain.

Agus


Anne Ghisla wrote:

> Hi all, and sorry for cross-posting,
>
> during QGIS hackfest the idea of an ecological toolbox has popped up,
> thanks mainly to Johannes Signer.
> Among currently available standalone bundles, we thought about Hawth's
> tools [0] and some other Arc* plugins; other tools, like Conefar [1]
> and Circuitscape [2], are dedicated GIS clones and could not cover all
> analysis requirements, therefore obliging the user to switch among
> different programs.
> We'd like to ask ecology researchers, teachers and students what are
> the most common analyses you run, and if you'd like to have the
> related tools available for QGIS in a toolbox just like for example
> GRASS toolbox.
>
> Thanks for feedback, and feel free to forward the message to relevant
> people and mailing lists!
> Anne Ghisla
>
> [0] http://www.spatialecology.com/htools/tooldesc.php
> [1] http://www.conefor.org/
> [2] http://www.circuitscape.org/Circuitscape/Welcome.html
> _______________________________________________
> Qgis-user mailing list
> [hidden email]
> http://lists.osgeo.org/mailman/listinfo/qgis-user
>

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[John C. Tull]

You should see if Tim has some notes on a conversation that he, Peter  
Ersts and I had at one point. We tried to collect these same ideas.  
Perhaps he has something that will be useful.

Cheers,
John

On Nov 7, 2009, at 9:01 AM, Anne Ghisla wrote:

> Hi all, and sorry for cross-posting,
>
> during QGIS hackfest the idea of an ecological toolbox has popped up,
> thanks mainly to Johannes Signer.
> Among currently available standalone bundles, we thought about Hawth's
> tools [0] and some other Arc* plugins; other tools, like Conefar [1]
> and Circuitscape [2], are dedicated GIS clones and could not cover all
> analysis requirements, therefore obliging the user to switch among
> different programs.
> We'd like to ask ecology researchers, teachers and students what are
> the most common analyses you run, and if you'd like to have the
> related tools available for QGIS in a toolbox just like for example
> GRASS toolbox.
>
> Thanks for feedback, and feel free to forward the message to relevant
> people and mailing lists!
> Anne Ghisla
>
> [0] http://www.spatialecology.com/htools/tooldesc.php
> [1] http://www.conefor.org/
> [2] http://www.circuitscape.org/Circuitscape/Welcome.html
> _______________________________________________
> Qgis-user mailing list
> [hidden email]
> http://lists.osgeo.org/mailman/listinfo/qgis-user

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[Darren Norris]

Not sure what you are after - is the idea for Qgis to be a presentation
/ data visualisation tool or to allow analysis to be run from within Qgis?

Anyway, a couple that (I think) would be specifically "ecological" and
are widely applied so may have broad enough appeal / strong user base:

1) niche modelling / habitat suitability
2) Distance sampling ( http://www.ruwpa.st-and.ac.uk/distance/ )

Darren

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[A. Marcia BARBOSA]

Hi everyone,

Great idea. I find the raster comparison tools of the Map Comparison Kit (http://www.riks.nl/mck/) very interesting, though they do require switching among programs, and I'm not sure they can handle very large rasters or be installed on Linux. Would it be possible to include this functionality in QGIS, and make it operate also on GRASS rasters? Maybe after an agreement with the owner and the developer of MCK.

Cheers,
Márcia

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[Paolo Cavallini]

Hi Marcia.
Sorry about my ignorance, but what can this do that GRASS can't?
All the best.

On Sun, 8 Nov 2009 14:30:04 +0000, "A. Marcia BARBOSA"
<[hidden email]> wrote:
> Great idea. I find the raster comparison tools of the Map Comparison Kit
(
> http://www.riks.nl/mck/) very interesting, though they do require
switching
> among programs, and I'm not sure they can handle very large rasters or be
> installed on Linux. Would it be possible to include this functionality in
> QGIS, and make it operate also on GRASS rasters? Maybe after an agreement
> with the owner and the developer of MCK.
--
http://faunalia.it/pc
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[A. Marcia BARBOSA]

It performs a fuzzy comparison of images, mimicking the way human observers compare maps. It takes many aspects into consideration simultaneously. It looks at both local and global similarities, logical coherence and patterns. While other map comparison methods usually focus on single aspects, this one has the flexibility to switch from one aspect to the other. This article explains these features quite well:

H. Visser and T. de Nijs, 2006. The Map Comparison Kit. Environmental Modeling & Software 21, 346-358.

Best,
Márcia

2009/11/8 Paolo Cavallini <[hidden email]>

Hi Marcia.
Sorry about my ignorance, but what can this do that GRASS can't?
All the best.

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[Micha Silver]

Anne Ghisla wrote:

> Hi all, and sorry for cross-posting,
>
> during QGIS hackfest the idea of an ecological toolbox has popped up,
> thanks mainly to Johannes Signer.
> Among currently available standalone bundles, we thought about Hawth's
> tools [0] and some other Arc* plugins; other tools, like Conefar [1]
> and Circuitscape [2], are dedicated GIS clones and could not cover all
> analysis requirements, therefore obliging the user to switch among
> different programs.
> We'd like to ask ecology researchers, teachers and students what are
> the most common analyses you run, and if you'd like to have the
> related tools available for QGIS in a toolbox just like for example
> GRASS toolbox.
>
>  

I'd like to see a simple set of tools for patch analysis: patch density,
perimeter to area ratio, std. dev of patch sizes etc. Similar to what's
available from the GRASS r.le.* modules.
Then that might lead to tools for connectivity analysis, like the
circuitscape example you sited.
Regards,
Micha

> Thanks for feedback, and feel free to forward the message to relevant
> people and mailing lists!
> Anne Ghisla
>
> [0] http://www.spatialecology.com/htools/tooldesc.php
> [1] http://www.conefor.org/
> [2] http://www.circuitscape.org/Circuitscape/Welcome.html
> _______________________________________________
> Qgis-user mailing list
> [hidden email]
> http://lists.osgeo.org/mailman/listinfo/qgis-user
>
> This mail was received via Mail-SeCure System.
>
>
>  

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[Anne Ghisla-2]

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Hi all, and sorry for top and cross posting,

first of all, thanks for feedback and enthusiasm about the topic.
I've tried to collect in this wiki page [0] what came up in the thread,
and I'm looking forward for more contribution!

best regards,
Anne

[0] http://www.qgis.org/wiki/Ecology_Tools

Rainer M Krug ha scritto:

> On Sun, Nov 8, 2009 at 10:00 PM, Micha Silver <[hidden email]> wrote:
>
>> Anne Ghisla wrote:
>>
>>> Hi all, and sorry for cross-posting,
>>>
>>> during QGIS hackfest the idea of an ecological toolbox has popped up,
>>> thanks mainly to Johannes Signer.
>>> Among currently available standalone bundles, we thought about Hawth's
>>> tools [0] and some other Arc* plugins; other tools, like Conefar [1]
>>> and Circuitscape [2], are dedicated GIS clones and could not cover all
>>> analysis requirements, therefore obliging the user to switch among
>>> different programs.
>>> We'd like to ask ecology researchers, teachers and students what are
>>> the most common analyses you run, and if you'd like to have the
>>> related tools available for QGIS in a toolbox just like for example
>>> GRASS toolbox.
>>>
>>>
> I think this is a brilliant idea.  A friend of mine is using Diva GIS for
> teaching, as it has a very good toolbox for ecological GIS work (according
> to him - I haven't used it yet) - but Diva is one reason, why he still needs
> Windows in a virtual machine.
>
> So it might be an option, to look into Diva to see what they have, and
> include those into QGIS.
>
> I like that idea of ecological analysis tools that much, that I would
> suggest an approach which enables the use of these tools from other programs
> as well (I am thinking in particular about R and GRASS). I guess, it would
> be more work, but I think it would be worth.
>
> A set of tools for spatial ecological analysis - like GDAL and OGR are for
> raster and vectors IO - that would be BRILLIANT.
>
> Rainer
>
>
>
>
>> I'd like to see a simple set of tools for patch analysis: patch density,
>> perimeter to area ratio, std. dev of patch sizes etc. Similar to what's
>> available from the GRASS r.le.* modules.
>> Then that might lead to tools for connectivity analysis, like the
>> circuitscape example you sited.
>> Regards,
>> Micha
>>
>>  Thanks for feedback, and feel free to forward the message to relevant
>>> people and mailing lists!
>>> Anne Ghisla
>>>
>>> [0] http://www.spatialecology.com/htools/tooldesc.php
>>> [1] http://www.conefor.org/
>>> [2] http://www.circuitscape.org/Circuitscape/Welcome.html

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[Paolo Craveri]

2009/11/8 Darren Norris <[hidden email]>:
> Not sure what you are after - is the idea for Qgis to be a presentation /
> data visualisation tool or to allow analysis to be run from within Qgis?
>
> Anyway, a couple that (I think) would be specifically "ecological" and are
> widely applied so may have broad enough appeal / strong user base:
>
> 1) niche modelling / habitat suitability
> 2) Distance sampling ( http://www.ruwpa.st-and.ac.uk/distance/ )
>

+1


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Lat. 44° 39' 11.08'' N  Long. 7° 23' 25.26'' E
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[Alex Mandel-2]

Anne Ghisla wrote:

> Hi all, and sorry for cross-posting,
>
> during QGIS hackfest the idea of an ecological toolbox has popped up,
> thanks mainly to Johannes Signer.
> Among currently available standalone bundles, we thought about Hawth's
> tools [0] and some other Arc* plugins; other tools, like Conefar [1]
> and Circuitscape [2], are dedicated GIS clones and could not cover all
> analysis requirements, therefore obliging the user to switch among
> different programs.
> We'd like to ask ecology researchers, teachers and students what are
> the most common analyses you run, and if you'd like to have the
> related tools available for QGIS in a toolbox just like for example
> GRASS toolbox.
>
> Thanks for feedback, and feel free to forward the message to relevant
> people and mailing lists!
> Anne Ghisla
>
> [0] http://www.spatialecology.com/htools/tooldesc.php
> [1] http://www.conefor.org/
> [2] http://www.circuitscape.org/Circuitscape/Welcome.html

For those who have access to Academic Journals, there might be some good
background reading in
http://dx.doi.org/10.1016/j.ecoinf.2009.07.004
Steiniger 2009 Free and open source geographic information tools for
landscape ecology. Ecological Informatics

There are some references to other articles that catalog Landscape
Ecological GIS tools that researchers use (whether or not they exist in
the software)

Anyone have time to read through and make a list of tools?

Alex
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[John C. Tull]

On Nov 21, 2009, at 5:12 PM, Alex Mandel wrote:

> Anne Ghisla wrote:
>> Hi all, and sorry for cross-posting,
>>
>> during QGIS hackfest the idea of an ecological toolbox has popped up,
>> thanks mainly to Johannes Signer.
>> Among currently available standalone bundles, we thought about Hawth's
>> tools [0] and some other Arc* plugins; other tools, like Conefar [1]
>> and Circuitscape [2], are dedicated GIS clones and could not cover all
>> analysis requirements, therefore obliging the user to switch among
>> different programs.
>> We'd like to ask ecology researchers, teachers and students what are
>> the most common analyses you run, and if you'd like to have the
>> related tools available for QGIS in a toolbox just like for example
>> GRASS toolbox.
>>
>> Thanks for feedback, and feel free to forward the message to relevant
>> people and mailing lists!
>> Anne Ghisla
>>
>> [0] http://www.spatialecology.com/htools/tooldesc.php
>> [1] http://www.conefor.org/
>> [2] http://www.circuitscape.org/Circuitscape/Welcome.html
>
> For those who have access to Academic Journals, there might be some good
> background reading in
> http://dx.doi.org/10.1016/j.ecoinf.2009.07.004
> Steiniger 2009 Free and open source geographic information tools for
> landscape ecology. Ecological Informatics

I found it freely available via scholar.google.com at
http://www.geo.unizh.ch/publications/sstein/sstein_freegitools_ecoinf2009.pdf

Regards,
John
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