Hello all, and sorry for cross-posting, as first result of QGIS hackfest in Vienna, here is a new version of HR plugin with NNCH implementation available. An long-time requested enhancement is coming soon: the separate threading for long running analyses. Therefore, qgis gui will be usable while the plugin works. Stay tuned for updates! regards, Anne Ghisla
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
Dear Community, this time I have a rather difficult problem to solve and I failed so far ... I now hope that there is a solution slumbering somewhere here ... Situation: I have several polygons which represent seperated areas of one 95 % UD-Kernel homerange calculation. Now I need to find the radius of the smallest possible circle that is able to enclose all areas of this homerange. I was already able calculate the centroid of all points inside all included areas of the homerange as the center for the circle. I now need to calculate the maximum distance from the centroid to the most distant bit of margin from any of the polygons. Any ideas about that? I later have to do it for many homeranges that can include several polygons. I did about the same for MCPs before, but it is relatively easy in that case because the margins of MCPs are definded by points/coordinates. So it is simply a calculation of the distance from the centroid to most distant point of the points that enclose the MCP area. In the case of the kernel the margins or contour lines do not usually correspond with point. I hope that any of you has an idea about that ...?! Cheers, Nils
Dear Nils,
> Situation:
> I have several polygons which represent seperated areas of one 95 % UD-Kernel homerange calculation. Now
I need to find the radius of the smallest possible circle that is able to enclose all areas of this
homerange. I was already able calculate the centroid of all points inside all included areas of the
homerange as the center for the circle. I now need to calculate the maximum distance from the centroid to
the most distant bit of margin from any of the polygons. Any ideas about that? I later have to do it for many
homeranges that can include several polygons.
>
The center of the circle is not the centroid. The problem is not
mathematically simple, but computer solutions do exist. You will need
the function miniball from the package BARD to find the minimum
enclosing circle. Let us take an example to make clear how you can
calculate this circle:
library(BARD)
library(adehabitat)
data(puechabon)
## estimate the home-range of the animals
kud <- kernelUD(puechabon$locs[,c("X","Y")], puechabon$locs$Name)
## get the contour of the home-range
ver <- getverticeshr(kud)
plot(ver)
## consider for example Chou, who has two areas
chou <- ver$Chou
(Continue reading)
_______________________________________________ AniMov mailing list AniMov@... http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
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 <micha@...> 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
Hi Anne!
many thanks for the new version of your plugin
I was giving it a try after a long and after having received your
message about the update.
Actually I'm getting the same error (see below) under windows
(qgis-dev via osgeo4w) and under Ubuntu 9.04. Under Ubuntu 9.10 it
seems to work fine.
thanks in advance
ciao!
-- Giovanni --
--------------------------------
An error has occured while executing Python code:
Traceback (most recent call last):
File "C:/Documents and
Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py",
line 76, in
QObject.connect(self.buttonBox, SIGNAL("accepted()"), lambda
mth=mth: self.run(mth))
File "C:/Documents and
Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py",
line 184, in run
output = rwrapper.Rcall(geomData, opt)
File "C:/Documents and
Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py",
line 257, in Rcall
QMessageBox.information(self, "Home range analysis", "R error")
TypeError: argument 1 of QMessageBox.information() has an invalid type
Python version:
2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)]
Python path: ['C:/OSGeo4W/apps/qgis-dev/./python', 'C:/Documents and
Settings/Gio/.qgis//python/plugins',
'C:/OSGeo4W/apps/qgis-dev/./python/plugins',
'C:\\OSGeo4W\\apps\\gdal-16\\pymod', 'C:\\Documents and
Settings\\Gio\\Desktop', 'C:\\OSGeo4W\\bin\\python25.zip',
'C:\\OSGeo4W\\apps\\Python25\\DLLs',
'C:\\OSGeo4W\\apps\\Python25\\lib',
'C:\\OSGeo4W\\apps\\Python25\\lib\\plat-win',
'C:\\OSGeo4W\\apps\\Python25\\lib\\lib-tk',
'C:\\OSGeo4W\\apps\\qgis-dev\\bin', 'C:\\OSGeo4W\\apps\\Python25',
'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages',
'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\win32',
'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\win32\\lib',
'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\Pythonwin',
'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\wx-2.8-msw-unicode',
'C:\\OSGeo4W\\apps\\qgis-dev\\python\\plugins\\fTools\\tools',
'/usr/share/qgis/python']
--------------------------------
Giovanni Manghi ha scritto:
> Hi Anne!
>
> many thanks for the new version of your plugin
>
> I was giving it a try after a long and after having received your
> message about the update.
>
> Actually I'm getting the same error (see below) under windows
> (qgis-dev via osgeo4w) and under Ubuntu 9.04. Under Ubuntu 9.10 it
> seems to work fine.
Hi Giovanni,
sorry for the unclear error, it most probably comes from a missing R
package, likely shapefiles used by NNCH and not by the other methods.
The function I wrote for checking packages fails in raising an error,
you can patch it right now by modifying line 179
MissingPackageMessage + i + ', '
in
MissingPackageMessage = MissingPackageMessage + i + ', '
sorry I can't do it right now but I wouldn't have access to the repo
until next week. For sure, next week I'll upload the patched version for
upgrade by Plugin Installer.
all the best,
Anne
> thanks in advance
>
> ciao!
>
> -- Giovanni --
>
>
> --------------------------------
>
> An error has occured while executing Python code:
>
> Traceback (most recent call last):
> File "C:/Documents and
> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py",
> line 76, in
> QObject.connect(self.buttonBox, SIGNAL("accepted()"), lambda
> mth=mth: self.run(mth))
> File "C:/Documents and
> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py",
> line 184, in run
> output = rwrapper.Rcall(geomData, opt)
> File "C:/Documents and
> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py",
> line 257, in Rcall
> QMessageBox.information(self, "Home range analysis", "R error")
> TypeError: argument 1 of QMessageBox.information() has an invalid type
>
> Python version:
> 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)]
>
> Python path: ['C:/OSGeo4W/apps/qgis-dev/./python', 'C:/Documents and
> Settings/Gio/.qgis//python/plugins',
> 'C:/OSGeo4W/apps/qgis-dev/./python/plugins',
> 'C:\\OSGeo4W\\apps\\gdal-16\\pymod', 'C:\\Documents and
> Settings\\Gio\\Desktop', 'C:\\OSGeo4W\\bin\\python25.zip',
> 'C:\\OSGeo4W\\apps\\Python25\\DLLs',
> 'C:\\OSGeo4W\\apps\\Python25\\lib',
> 'C:\\OSGeo4W\\apps\\Python25\\lib\\plat-win',
> 'C:\\OSGeo4W\\apps\\Python25\\lib\\lib-tk',
> 'C:\\OSGeo4W\\apps\\qgis-dev\\bin', 'C:\\OSGeo4W\\apps\\Python25',
> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages',
> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\win32',
> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\win32\\lib',
> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\Pythonwin',
> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\wx-2.8-msw-unicode',
> 'C:\\OSGeo4W\\apps\\qgis-dev\\python\\plugins\\fTools\\tools',
> '/usr/share/qgis/python']
>
> --------------------------------
Hi Anne, thanks for the quick answer, I'm pretty sure I have installed the "shapefiles" package, in any case 'll try the patch and I'll give you feedback. thanks! On Tue, Nov 10, 2009 at 8:36 PM, Anne Ghisla <a.ghisla@...> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Giovanni Manghi ha scritto: >> Hi Anne! >> >> many thanks for the new version of your plugin >> >> I was giving it a try after a long and after having received your >> message about the update. >> >> Actually I'm getting the same error (see below) under windows >> (qgis-dev via osgeo4w) and under Ubuntu 9.04. Under Ubuntu 9.10 it >> seems to work fine. > > Hi Giovanni, > > sorry for the unclear error, it most probably comes from a missing R > package, likely shapefiles used by NNCH and not by the other methods. > The function I wrote for checking packages fails in raising an error, > you can patch it right now by modifying line 179 > > MissingPackageMessage + i + ', ' > > in > > MissingPackageMessage = MissingPackageMessage + i + ', ' > > sorry I can't do it right now but I wouldn't have access to the repo > until next week. For sure, next week I'll upload the patched version for > upgrade by Plugin Installer. > > all the best, > Anne > >> thanks in advance >> >> ciao! >> >> -- Giovanni -- >> >> >> -------------------------------- >> >> An error has occured while executing Python code: >> >> Traceback (most recent call last): >> File "C:/Documents and >> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py", >> line 76, in >> QObject.connect(self.buttonBox, SIGNAL("accepted()"), lambda >> mth=mth: self.run(mth)) >> File "C:/Documents and >> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py", >> line 184, in run >> output = rwrapper.Rcall(geomData, opt) >> File "C:/Documents and >> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py", >> line 257, in Rcall >> QMessageBox.information(self, "Home range analysis", "R error") >> TypeError: argument 1 of QMessageBox.information() has an invalid type >> >> Python version: >> 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] >> >> Python path: ['C:/OSGeo4W/apps/qgis-dev/./python', 'C:/Documents and >> Settings/Gio/.qgis//python/plugins', >> 'C:/OSGeo4W/apps/qgis-dev/./python/plugins', >> 'C:\\OSGeo4W\\apps\\gdal-16\\pymod', 'C:\\Documents and >> Settings\\Gio\\Desktop', 'C:\\OSGeo4W\\bin\\python25.zip', >> 'C:\\OSGeo4W\\apps\\Python25\\DLLs', >> 'C:\\OSGeo4W\\apps\\Python25\\lib', >> 'C:\\OSGeo4W\\apps\\Python25\\lib\\plat-win', >> 'C:\\OSGeo4W\\apps\\Python25\\lib\\lib-tk', >> 'C:\\OSGeo4W\\apps\\qgis-dev\\bin', 'C:\\OSGeo4W\\apps\\Python25', >> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages', >> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\win32', >> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\win32\\lib', >> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\Pythonwin', >> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\wx-2.8-msw-unicode', >> 'C:\\OSGeo4W\\apps\\qgis-dev\\python\\plugins\\fTools\\tools', >> '/usr/share/qgis/python'] >> >> -------------------------------- > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.9 (MingW32) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iEYEARECAAYFAkr5ztwACgkQzZ3g4YwFFgYsZACfUJBQxle94dEpV53eUSfIPmON > TPkAn0wU7RLzE+doFwRClKdl39ZujdpA > =6s+p > -----END PGP SIGNATURE----- >
Giovanni Manghi ha scritto: > Hi Anne, > > thanks for the quick answer, I'm pretty sure I have installed the > "shapefiles" package, in any case 'll try the patch and I'll give you > feedback. It could be also gpclib - just installed yesterday HR plugin on a Ubuntu 9.10 machine (Tim Sutton's :), see his guide [0] ); he had to install adehabitat, shapefiles, rgdal and gpclib and then all methods worked. Hope that will solve your problem as well! ciao ;) Anne [0] http://linfiniti.com/2009/11/home-range-plugin-in-qgis/ > thanks! > > > > > On Tue, Nov 10, 2009 at 8:36 PM, Anne Ghisla <a.ghisla@...> wrote: > Giovanni Manghi ha scritto: >>>> Hi Anne! >>>> >>>> many thanks for the new version of your plugin >>>> >>>> I was giving it a try after a long and after having received your >>>> message about the update. >>>> >>>> Actually I'm getting the same error (see below) under windows >>>> (qgis-dev via osgeo4w) and under Ubuntu 9.04. Under Ubuntu 9.10 it >>>> seems to work fine. > Hi Giovanni, > > sorry for the unclear error, it most probably comes from a missing R > package, likely shapefiles used by NNCH and not by the other methods. > The function I wrote for checking packages fails in raising an error, > you can patch it right now by modifying line 179 > > MissingPackageMessage + i + ', ' > > in > > MissingPackageMessage = MissingPackageMessage + i + ', ' > > sorry I can't do it right now but I wouldn't have access to the repo > until next week. For sure, next week I'll upload the patched version for > upgrade by Plugin Installer. > > all the best, > Anne > >>>> thanks in advance >>>> >>>> ciao! >>>> >>>> -- Giovanni -- >>>> >>>> >>>> -------------------------------- >>>> >>>> An error has occured while executing Python code: >>>> >>>> Traceback (most recent call last): >>>> File "C:/Documents and >>>> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py", >>>> line 76, in >>>> QObject.connect(self.buttonBox, SIGNAL("accepted()"), lambda >>>> mth=mth: self.run(mth)) >>>> File "C:/Documents and >>>> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py", >>>> line 184, in run >>>> output = rwrapper.Rcall(geomData, opt) >>>> File "C:/Documents and >>>> Settings/Gio/.qgis//python/plugins\HomeRange_plugin\HRplugin_dialog.py", >>>> line 257, in Rcall >>>> QMessageBox.information(self, "Home range analysis", "R error") >>>> TypeError: argument 1 of QMessageBox.information() has an invalid type >>>> >>>> Python version: >>>> 2.5.2 (r252:60911, Feb 21 2008, 13:11:45) [MSC v.1310 32 bit (Intel)] >>>> >>>> Python path: ['C:/OSGeo4W/apps/qgis-dev/./python', 'C:/Documents and >>>> Settings/Gio/.qgis//python/plugins', >>>> 'C:/OSGeo4W/apps/qgis-dev/./python/plugins', >>>> 'C:\\OSGeo4W\\apps\\gdal-16\\pymod', 'C:\\Documents and >>>> Settings\\Gio\\Desktop', 'C:\\OSGeo4W\\bin\\python25.zip', >>>> 'C:\\OSGeo4W\\apps\\Python25\\DLLs', >>>> 'C:\\OSGeo4W\\apps\\Python25\\lib', >>>> 'C:\\OSGeo4W\\apps\\Python25\\lib\\plat-win', >>>> 'C:\\OSGeo4W\\apps\\Python25\\lib\\lib-tk', >>>> 'C:\\OSGeo4W\\apps\\qgis-dev\\bin', 'C:\\OSGeo4W\\apps\\Python25', >>>> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages', >>>> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\win32', >>>> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\win32\\lib', >>>> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\Pythonwin', >>>> 'C:\\OSGeo4W\\apps\\Python25\\lib\\site-packages\\wx-2.8-msw-unicode', >>>> 'C:\\OSGeo4W\\apps\\qgis-dev\\python\\plugins\\fTools\\tools', >>>> '/usr/share/qgis/python'] >>>> >>>> -------------------------------- >>
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