\contentsline {section}{\numberline {1}Introduction}{2}{section.1}
\contentsline {subsection}{\numberline {1.1}About Graphab}{2}{subsection.1.1}
\contentsline {subsubsection}{\numberline {1.1.1}Authors}{2}{subsubsection.1.1.1}
\contentsline {subsubsection}{\numberline {1.1.2}Terms of use}{2}{subsubsection.1.1.2}
\contentsline {subsection}{\numberline {1.2}System requirements}{2}{subsection.1.2}
\contentsline {subsection}{\numberline {1.3}Installing the software and launching a project}{2}{subsection.1.3}
\contentsline {section}{\numberline {2}Starting a Graphab project }{3}{section.2}
\contentsline {subsection}{\numberline {2.1}Identifying a project}{3}{subsection.2.1}
\contentsline {subsection}{\numberline {2.2}Importing landscape maps and defining nodes }{3}{subsection.2.2}
\contentsline {subsection}{\numberline {2.3}Creating link sets}{5}{subsection.2.3}
\contentsline {subsubsection}{\numberline {2.3.1}Link topology}{5}{subsubsection.2.3.1}
\contentsline {subsubsection}{\numberline {2.3.2}Distance (or link impedance)}{6}{subsubsection.2.3.2}
\contentsline {section}{\numberline {3}Graphs}{7}{section.3}
\contentsline {subsection}{\numberline {3.1}Creating graphs}{7}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Graph clustering}{8}{subsection.3.2}
\contentsline {section}{\numberline {4}Corridors}{9}{section.4}
\contentsline {section}{\numberline {5}Patch capacity}{10}{section.5}
\contentsline {subsection}{\numberline {5.1}Capacity as a function of the neighborhood}{10}{subsection.5.1}
\contentsline {subsection}{\numberline {5.2}Capacity defined from external data}{11}{subsection.5.2}
\contentsline {subsection}{\numberline {5.3}Patch removing}{12}{subsection.5.3}
\contentsline {section}{\numberline {6}Calculating connectivity metrics}{12}{section.6}
\contentsline {subsection}{\numberline {6.1}Metrics family and computing level}{12}{subsection.6.1}
\contentsline {subsection}{\numberline {6.2}Parameters of weighted metrics}{14}{subsection.6.2}
\contentsline {subsubsection}{\numberline {6.2.1}Alpha parameter}{14}{subsubsection.6.2.1}
\contentsline {subsubsection}{\numberline {6.2.2}Beta parameter}{14}{subsubsection.6.2.2}
\contentsline {subsection}{\numberline {6.3}Calculating batch metrics}{15}{subsection.6.3}
\contentsline {subsubsection}{\numberline {6.3.1}Batch graph}{15}{subsubsection.6.3.1}
\contentsline {subsubsection}{\numberline {6.3.2}Batch parameter}{16}{subsubsection.6.3.2}
\contentsline {subsection}{\numberline {6.4}Interpolating metrics}{17}{subsection.6.4}
\contentsline {section}{\numberline {7}Patch addition}{18}{section.7}
\contentsline {section}{\numberline {8}Meta-patch}{19}{section.8}
\contentsline {section}{\numberline {9}Connecting graphs and point data}{20}{section.9}
\contentsline {subsection}{\numberline {9.1}Importing points sets}{20}{subsection.9.1}
\contentsline {subsection}{\numberline {9.2}Inter-point distance matrix}{20}{subsection.9.2}
\contentsline {subsubsection}{\numberline {9.2.1}Raster-based distance}{21}{subsubsection.9.2.1}
\contentsline {subsubsection}{\numberline {9.2.2}Graph-based distance}{21}{subsubsection.9.2.2}
\contentsline {subsection}{\numberline {9.3}Generating random points}{21}{subsection.9.3}
\contentsline {subsection}{\numberline {9.4}Species distribution model}{22}{subsection.9.4}
\contentsline {subsubsection}{\numberline {9.4.1}Weighting for extrapolating metrics to points}{23}{subsubsection.9.4.1}
\contentsline {subsubsection}{\numberline {9.4.2}Estimating the model}{23}{subsubsection.9.4.2}
\contentsline {subsubsection}{\numberline {9.4.3}Using the model}{24}{subsubsection.9.4.3}
\contentsline {section}{\numberline {10}Display}{25}{section.10}
\contentsline {subsection}{\numberline {10.1}Graph properties}{25}{subsection.10.1}
\contentsline {subsection}{\numberline {10.2}Object properties}{25}{subsection.10.2}
\contentsline {section}{\numberline {11}Processing capabilities and limitations}{26}{section.11}
\contentsline {section}{\numberline {12}Metrics}{27}{section.12}
\contentsline {subsection}{\numberline {12.1}Weighted metrics}{29}{subsection.12.1}
\contentsline {subsubsection}{\numberline {12.1.1}Flux}{29}{subsubsection.12.1.1}
\contentsline {subsubsection}{\numberline {12.1.2}Equivalent Probability}{30}{subsubsection.12.1.2}
\contentsline {subsubsection}{\numberline {12.1.3}Probability of Connectivity}{30}{subsubsection.12.1.3}
\contentsline {subsubsection}{\numberline {12.1.4}Interaction Flux (replace FPC)}{31}{subsubsection.12.1.4}
\contentsline {subsubsection}{\numberline {12.1.5}Fractions of delta Probability of Connectivity}{31}{subsubsection.12.1.5}
\contentsline {subsubsection}{\numberline {12.1.6}Betweenness Centrality index}{32}{subsubsection.12.1.6}
\contentsline {subsubsection}{\numberline {12.1.7}Integral Index of Connectivity}{32}{subsubsection.12.1.7}
\contentsline {subsubsection}{\numberline {12.1.8}Current Flow}{33}{subsubsection.12.1.8}
\contentsline {subsection}{\numberline {12.2}Area metrics}{33}{subsection.12.2}
\contentsline {subsubsection}{\numberline {12.2.1}Mean Size of the Components}{33}{subsubsection.12.2.1}
\contentsline {subsubsection}{\numberline {12.2.2}Size of the Largest Component}{33}{subsubsection.12.2.2}
\contentsline {subsubsection}{\numberline {12.2.3}Class Coincidence Probability}{34}{subsubsection.12.2.3}
\contentsline {subsubsection}{\numberline {12.2.4}Expected Cluster Size}{34}{subsubsection.12.2.4}
\contentsline {subsection}{\numberline {12.3}Topological metrics}{34}{subsection.12.3}
\contentsline {subsubsection}{\numberline {12.3.1}Wilks' Lambda}{34}{subsubsection.12.3.1}
\contentsline {subsubsection}{\numberline {12.3.2}Harary Index}{35}{subsubsection.12.3.2}
\contentsline {subsubsection}{\numberline {12.3.3}Graph Diameter}{35}{subsubsection.12.3.3}
\contentsline {subsubsection}{\numberline {12.3.4}Number of Components}{35}{subsubsection.12.3.4}
\contentsline {subsubsection}{\numberline {12.3.5}Node Degree}{36}{subsubsection.12.3.5}
\contentsline {subsubsection}{\numberline {12.3.6}Clustering Coefficient}{36}{subsubsection.12.3.6}
\contentsline {subsubsection}{\numberline {12.3.7}Closeness Centrality}{36}{subsubsection.12.3.7}
\contentsline {subsubsection}{\numberline {12.3.8}Eccentricity}{37}{subsubsection.12.3.8}
\contentsline {subsubsection}{\numberline {12.3.9}Connectivity Correlation}{37}{subsubsection.12.3.9}
