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<p class="MsoNormal"><span lang="EN-US">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Last week I presented a set of three new GRASS-AddOns for analyzing landscape connectivity based on graph-theory at the European Congress of Conservation Biology (ECCB, http://eccb2012.org/) in Glasgow . This set of tools
applies methods documented (a.o.) in the following literature to the input data you might have.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Bunn, A. G., Urban, D. L. & Keitt, T. H. 2000: Landscape connectivity: A conservation application of graph theory. Journal of Environmental Management (2000) 59: 265-278.
<a href="http://www.sciencedirect.com/science/article/pii/S0301479700903736">http://www.sciencedirect.com/science/article/pii/S0301479700903736</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Calabrese, J. M. & Fagan, W. F. 2004</b>: A comparison-shopper's guide to connectivity metrics. Front Ecol Environ 2 (10): 529-536 .
<a href="http://dx.doi.org/10.1890/1540-9295(2004)002%5b0529:ACGTCM%5d2.0.CO;2">http://dx.doi.org/10.1890/1540-9295(2004)002[0529:ACGTCM]2.0.CO;2</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Minor, E. S. & Urban, D. L. 2008: A Graph-Theory Framework for Evaluating Landscape Connectivity and Conservation Planning. Conservation Biology 22 (2): 297-307.
<a href="http://www.uic.edu/labs/minor/minor&urban2008.pdf">http://www.uic.edu/labs/minor/minor&urban2008.pdf</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Zetterberg, A., Mörtberg, U. M. & Balfors, B. 2010: Making graph theory operational for landscape ecological assessments, planning, and design. Landscape and Urban Planning (2010) 95: 181-191.
<a href="http://www.sciencedirect.com/science/article/pii/S0169204610000204">http://www.sciencedirect.com/science/article/pii/S0169204610000204</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Ranius, T. & Roberge, J.-M. 2011: Effects of intensified forestry on the landscape-scale extinction risk of dead wood dependent species. Biodiversity and Conservation 20 (13): 2867-2882.
<a href="http://www.springerlink.com/content/ch9qtv2665h624q4">http://www.springerlink.com/content/ch9qtv2665h624q4</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The input data the tools take are:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">A polygon vector map containing habitat patches (of your species / habitat type in question) and a column for a population proxy (e.g. patch area). (required)<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">A cost raster map (for more information on that see the r.cost-manual) (optional; if no cost raster is provided Euclidean distance is used).<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">Dispersal information<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:72.0pt;text-indent:-18.0pt;mso-list:l0 level2 lfo2">
<![if !supportLists]><span lang="EN-US" style="font-family:"Courier New""><span style="mso-list:Ignore">o<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">A maximum (cost) distance threshold for assumed connectivity<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:72.0pt;text-indent:-18.0pt;mso-list:l0 level2 lfo2">
<![if !supportLists]><span lang="EN-US" style="font-family:"Courier New""><span style="mso-list:Ignore">o<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US">A dispersal kernel (defined by three variables of a negative exponential decay function (see eg. Bunn et al. 2000)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The outputs are connectivity measures on vertex (=patch) level, edge (= the connection between two patches) level, and graph (the entire network) level. With r.connectivity.corridors you can also identify corridors for
the connections (edges) you select, and you can weight their importance based on a column of your choice (e.g. connectivity measures from r.connectivity.network).
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The tools (and documentation) can be found in the GRASS AddOns SVN repository (see: r.connectivity.distance, r.connectivity.network, r.connectivity.corridors in the
<a href="http://grass.osgeo.org/wiki/GRASS_AddOns/">http://grass.osgeo.org/wiki/GRASS_AddOns/</a>). They are UNIX-shell (and one R-) scripts.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Required additional software is: Cran R with at least the packages “igraph” (version 0.6-2) and “nlme” installed. If you want to make use of parallel processing / multi-threading you need also the packages "doMC", "foreach",
"iterators", "codetools", and "multicore". But multithreading is only supported on LINUX. The tools have not been tested on Windows yet, but this will be done in near future.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Any kind of feedback would be very much appreciated!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Stefan<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">P.S.: What do you think, how helpful would an example based on the spearfish dataset be? If you think so, I will add that to the documentation, as soon as the projects which triggered the development of the r.connectivity.*-tools
are published.</span><span lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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