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The following GIS extensions or tools allow generating from a spatial layer (either in vector or raster format) the files required as an input to perform the connectivity analyses in Conefor. These extensions generate these input files (node file and connection file) directly in the exact format required by Conefor; therefore, these files can be used as they result from the GIS extensions with no other changes or intermediate processing steps. The three first extensions allow for batch processing of multiple files/layers and calculate the distance between patches as Euclidean (straight-line) distances.
1) New (July 2015): plugin available for the newest QGIS version! Conefor Inputs plugin for QGIS 2.9, 2.10, 2.11 or newer (from vector layers, no commercial license needed since QGIS is a free and open source GIS that can be freely downloaded from www.qgis.org).
The Conefor plugin (QGIS versions 2.9, 2.10, 2.11 or newer) is available in the official QGIS plugin repository and hence it can be searched and installed directly from within QGIS by using the plugin installer (Menu: plugins > manage and install plugins, there search "Conefor"). Alternatively, you can also download the plugin from here.
The plugin generates from a vector layer (different formats can be used) the node and connection files required by Conefor. For using the extension, your vector layer needs to have two fields containing the IDs of the nodes / patches (spatial features, typically polygons) and the attributes of the nodes (not necessarily habitat area, any other attribute of interest could be used). The plugin generates the node and connection files for Conefor, with the connections characterized by the Euclidean (straight-line) distance between patches. This distance can be calculated either from the edges of the patches (the most typical and generally recommended option) of from the centroids of the patches. Batch processing of multiple vector layers is possible. Unlike the ArcGIS extension below, the QGIS plugin includes the option of generating a vector layer with the links (straight lines) among the patch edges or centroids (including the information on the length (distance) along each link); this option however may considerably increase the computational times and hence may be used with caution (note that this is not required as an input for the analyses in Conefor; it may only be of interest for visualization purposes in the GIS). There is also an older version of this plugin that works ony with QGIS 2.2 or 2.4 (not with newer QGIS versions); in case you may be interested you can download this older version from here.
2) Conefor Inputs for ArcGIS (from vector layers, ArcGIS license needed): http://www.jennessent.com/arcgis/conefor_inputs.htm
This version of the Conefor Inputs extension runs in ArcGIS, a commercial software package (therefore, you need an ArcGIS license to be able to use this extension). The extension is available for ArcView 3.x, ArcGIS 9.x and ArcGIS 10.x. The extension generates the node and connection files required by Conefor from a vector layer in ArcGIS. Before using this extension, your vector layer needs to have two fields containing the IDs of the nodes /patches (spatial features, typically polygons) and the attributes of the nodes (not necessarily habitat area, any other attribute of interest could be used). The extension generates the node and connection files, with the connections characterized by the Euclidean (straight-line) distance between patches. This distance can be calculated either from the edges of the patches (the most typical and generally recommended option) of from the centroids of the patches. Batch processing of multiple vector layers is possible. Unlike the QGIS plugin above, the ArcGIS extension includes an option that allows to calculate only the distances among those patches that are separated by less than a maximum specified distance; this may allow reducing processing times in large maps (particularly when the dispersal distance considered is much smaller than the total map extent) and the resultant distance file can be provided as a partial connection file for input in Conefor.
3) Conefor Inputs in Guidos (from raster layers, freeware): http://forest.jrc.ec.europa.eu/download/software/guidos
Guidos is a standalone and freeware software package for raster image processing. Among many other functionalities, Guidos includes a Conefor Inputs extension, which generates the node and connection files required by Conefor from any raster layer file in a variety of raster formats (TIFF and others). The non-habitat pixels in this raster file need to be classified as 0, and the habitat areas as 1. The maximum raster size is 2000 x 2000 pixels. The extension will identify the habitat patches (according either to the 4-neigbourhood or the 8-neigbourhood criteria) and generate a node file in which the area of the patches (number of pixels) is the attribute of the nodes, and a connection file containing the Euclidean (straight-line) distance between every pair of patches (in pixel units). This distance can be calculated either from the edges of the patches (the most typical and generally recommended option) of from the centroids of the patches. A raster file with the IDs of the patches as identified by the extension will also be generated (these IDs will be the same as those in the node and connection file generated by the extension). Batch processing of multiple raster layer files is possible.
4) MatrixGreen tool for ArcGIS (from a vector or raster layer for the nodes and optionally a raster layer for the resistance surface, ArcGIS license needed): http://www.matrixgreen.org
MatrixGreen is a freeware tool (requiring registration to get a copy) for ArcGIS that includes several functionalities for connectivity analyses that run on its own. MatrixGreen includes the possibility of generating the node and connection files required as an input for Conefor, with the connection file optionally including the effective (least-cost) distance between each pair of nodes, providing therefore a useful type of distance measure that is commonly used in landscape ecology and that is different from that provided by the other extensions above.