REFERENCES
- Babić , D. , Klein , D. , Lukovits , I. , Nikolić , S. and Trinajstić , N. 2002 . “Resistance-Distance Matrix: A Computational Algorithm and its Application,” . International Journal of Quantum Chemistry , 90 : 166 – 176 .
- Bates , D. and Maechler , M. 2011 . Matrix: Sparse and Dense Matrix Classes and Methods , R package version 0.9996875-3 Available at http://matrix.r-forge.r-project.org
- Besag , J. 1974 . “Spatial Interaction and the Statistical Analysis of Lattice Systems,” . Journal of the Royal Statistical Society, Series B , 36 : 192 – 236 .
- Besag , J. and Kooperberg , C. 1995 . “On Conditional and Intrinsic Autoregressions,” . Biometrika , 82 : 733
- Besag , J. , York , J. and Mollié , A. 1991 . “Bayesian Image Restoration, With Two Applications in Spatial Statistics,” . The Annals of the Institute of Statistical Mathematics , 43 : 1 – 20 .
- Bolin , D. , Lindström , J. , Eklundh , L. and Lindgren , F. 2009 . “Fast Estimation of Spatially Dependent Temporal Vegetation Trends Using Gaussian Markov Random Fields,” . Computational Statistics & Data Analysis , 53 : 2885 – 2896 .
- Broquet , T. , Ray , N. , Petit , E. , Fryxell , J. M. and Burel , F. 2006 . “Genetic Isolation by Distance and Landscape Connectivity in the American Marten (Martes Americana),” . Landscape Ecology , 21 : 877 – 889 .
- Chandra , A. , Raghavan , P. , Ruzzo , W. , Smolensky , R. and Tiwari , P. 1996 . “The Electrical Resistance of a Graph Captures its Commute and Cover Times,” . Computational Complexity , 6 : 312 – 340 .
- Chen , C. , Durand , E. , Forbes , F. and Francois , O. 2007 . “Bayesian Clustering Algorithms Ascertaining Spatial Population Structure: A New Computer Program and a Comparison Study,” . Molecular Ecology Notes , 7 : 747 – 756 .
- Cross , P. , Heisey , D. , Scurlock , B. , Edwards , W. , Ebinger , M. and Brennan , A. 2010 . “Mapping Brucellosis Increases Relative to Elk Density Using Hierarchical Bayesian Models,” . PLoS One , 5 : e10322
- Cushman , S. and Landguth , E. 2010 . “Scale Dependent Inference in Landscape Genetics,” . Landscape Ecology , 25 : 967 – 979 .
- Cushman , S. , McKelvey , K. and Schwartz , M. 2009 . “Use of Empirically Derived Source-Destination Models to Map Regional Conservation Corridors,” . Conservation Biology , 23 : 368 – 376 .
- Cushman , S. A. , McKelvey , K. S. , Hayden , J. and Schwartz , M. K. 2006 . “Gene Flow in Complex Landscapes: Testing Multiple Hypotheses With Causal Modeling,” . The American Naturalist , 168 : 486 – 99 .
- Dorf , R. and Svoboda , J. 2004 . Introduction to Electric Circuits , Hoboken, NJ: Wiley .
- Durand , E. , Jay , F. , Gaggiotti , O. and François , O. 2009 . “Spatial Inference of Admixture Proportions and Secondary Contact Zones,” . Molecular Biology and Evolution , 26 : 1963
- Dyer , R. , Nason , J. and Garrick , R. 2010 . “Landscape Modelling of Gene Flow: Improved Power Using Conditional Genetic Distance Derived From the Topology of Population Networks,” . Molecular Ecology , 19 : 3746 – 3759 .
- Fouss , F. , Pirotte , A. , Renders , J. and Saerens , M. 2007 . “Random-Walk Computation of Similarities Between Nodes of a Graph With application to Collaborative Recommendation,” . IEEE Transactions on Knowledge and Data Engineering , 19 : 355 – 369 .
- Gelman , A. , Carlin , B. P. , Stern , H. and Rubin , D. B. 2004 . Bayesian Data Analysis (2nd ed.) , Princeton, , NJ : Chapman and Hall/CRC .
- Graybill , F. 1983 . Matrices With Applications in Statistics , Belmont, CA : Wadsworth Inc .
- Guillot , G. , Estoup , A. , Mortier , F. and Cosson , J. F. 2005 . “A Spatial Statistical Model for Landscape Genetics,” . Genetics , 170 : 1261 – 1280 .
- Hanks , E. , Hooten , M. , Johnson , D. and Sterling , J. 2011 . “Velocity-Based Movement Modeling for Individual and Population Level Inference,” . PLoS ONE , 6 : e22795
- Harville , D. 2008 . Matrix Algebra From a Statistician’s Perspective , New York : Springer-Verlag .
- Hastie , T. and Tibshirani , R. 1993 . “Varying-Coefficient Models,” . Journal of the Royal Statistical Society, Series B , 55 : 757 – 796 .
- Holsinger , K. and Weir , B. 2009 . “Genetics in Geographically Structured Populations: Defining, Estimating and Interpreting fst,” . Nature Reviews Genetics , 10 : 639 – 650 .
- Hooten , M. and Wikle , C. 2008 . “A Hierarchical Bayesian Non-Linear Spatio-Temporal Model for the Spread of Invasive Species With Application to the Eurasian Collared-Dove,” . Environmental and Ecological Statistics , 15 : 59 – 70 .
- Hooten , M. B. , Johnson , D. S. , Hanks , E. M. and Lowry , J. H. 2010 . “Agent-Based Inference for Animal Movement and Selection,” . Journal of Agricultural, Biological, and Environmental Statistics , 15 : 523 – 538 .
- Hooten , M. B. and Wikle , C. K. 2010 . “Statistical Agent-Based Models for Discrete Spatio-Temporal Systems,” . Journal of the American Statistical Association , 105 : 236 – 248 .
- Jombart , T. 2008 . “Adegenet: A R Package for the Multivariate Analysis of Genetic Markers,” . Bioinformatics , 24 : 1403 – 1405 .
- Jombart , T. 2012 . “A Tutorial for the Spatial Analysis of Principal Components (spca)Using Adegenet 1.3-4,” . Vignette for the R package ‘adegenet’ , Available at http://adegenet.r-forge.r-project.org
- Jombart , T. , Devillard , S. , Dufour , A. B. and Pontier , D. 2008 . “Revealing Cryptic Spatial Patterns in Genetic Variability by a New Multivariate Method,” . Heredity , 101 : 92 – 103 .
- Klein , D. , Palacios , J. , Randic , M. and Trinajstic , N. 2004 . “Random Walks and Chemical Graph Theory,” . Journal of Chemical Information and Computer Sciences , 44 : 1521 – 1525 .
- Klein , D. and Randić , M. 1993 . “Resistance Distance,” . Journal of Mathematical Chemistry , 12 : 81 – 95 .
- Kunegis , J. , Lommatzsch , A. and Bauckhage , C. 2009 . “The Slashdot Zoo: Mining a Social Network With Negative Edges,” . In Proceedings of the 18th International Conference on World Wide Web, ACM 741 – 750 .
- Landguth , E. and Cushman , S. 2010 . “Cdpop: A Spatially Explicit Cost Distance Population Genetics Program,” . Molecular Ecology Resources , 10 : 156 – 161 .
- Legendre , P. and Fortin , M. 2010 . “Comparison of the Mantel Test and Alternative Approaches for Detecting Complex Multivariate Relationships in the Spatial Analysis of Genetic Data,” . Molecular Ecology Resources , 10 : 831 – 844 .
- Lindgren , F. , Rue , H. and Lindström , J. 2011 . “An Explicit Link Between Gaussian Fields and Gaussian Markov Random Fields: The Stochastic Partial Differential Equation Approach,” . Journal of the Royal Statistical Society, Series B , 73 : 423 – 498 .
- Lindström , J. and Lindgren , F. 2008 . A Gaussian Markov Random Field Model for Total Yearly Precipitation Over the African Sahel . Technical Report 8, Centre for Mathematical Sciences, Lund University, Lund Sweden
- Lookingbill , T. , Gardner , R. , Ferrari , J. and Keller , C. 2010 . “Combining a Dispersal Model With Network Theory to Assess Habitat Connectivity,” . Ecological Applications , 20 : 427 – 441 .
- Manel , S. , Schwartz , M. , Luikart , G. and Taberlet , P. 2003 . “Landscape Genetics: Combining Landscape Ecology and Population Genetics,” . Trends in Ecology & Evolution , 18 : 189 – 197 .
- McCullagh , P. 2009 . “Marginal Likelihood for Distance Matrices,” . Statistica Sinica , 19 : 631 – 649 .
- McRae , B. 2006 . “Isolation by Resistance,” . Evolution , 60 : 1551 – 1561 .
- McRae , B. , Dickson , B. , Keitt , T. and Shah , V. 2008 . “Using Circuit Theory to Model Connectivity in Ecology, Evolution, and Conservation,” . Ecology , 89 : 2712 – 2724 .
- McRae , B. H. and Beier , P. 2007 . “Circuit Theory Predicts Gene Flow in Plant and Animal Populations,” . Proceedings of the National Academy of Sciences of the United States of America , 104 : 19885 – 19890 .
- Oksanen , J. , Blanchet , F. G. , Kindt , R. , Legendre , P. , Minchin , P. R. , O’Hara , R. B. , Simpson , G. L. , Solymos , P. , Stevens , M. H. H. and Wagner , H. 2012 . Vegan: Community Ecology Package , R package version 2.0-3 Available at http://vegan.r-forge.r-project.org
- Owen-Smith , N. , Fryxell , J. M. and Merrill , E. H. 2010 . “Foraging Theory Upscaled: The Behavioural Ecology of Herbivore Movement,” . Philosophical Transactions of the Royal Society B: Biological Sciences , 365 : 2267 – 2278 .
- Rayfield , B. , Fortin , M. and Fall , A. 2010 . “The Sensitivity of Least-Cost Habitat Graphs to Relative Cost Surface Values,” . Landscape Ecology , 25 : 519 – 532 .
- R Development Core Team . 2012 . R: A Language and Environment for Statistical Computing , Vienna, Austria : R Foundation for Statistical Computing .
- Rue , H. 2001 . “Fast Sampling of Gaussian Markov Random Fields,” . Journal of the Royal Statistical Society, Series B , 63 : 325 – 338 .
- Rue , H. and Held , L. 2005 . “ Gaussian Markov Random Fields: Theory and Applications ” . In Monographs on Statistics and Applied Probability (Vol. 104) , Boca Raton, , FL : Chapman & Hall .
- Rue , H. , Martino , S. and Chopin , N. 2009 . “Approximate Bayesian Inference for Latent Gaussian Models by Using Integrated Nested Laplace Approximations,” . Journal of the Royal Statistical Society, Series B , 71 : 319 – 392 .
- Saura , S. and Rubio , L. 2010 . “A Common Currency for the Different Ways in Which Patches and Links can Contribute to Habitat Availability and Connectivity in the Landscape,” . Ecography , 33 : 523 – 537 .
- Seber , G. 2008 . A Matrix Handbook for Statisticians (Vol. 746) , Hoboken, NJ: Wiley .
- Shirk , A. , Wallin , D. , Cushman , S. , Rice , C. and Warheit , K. 2010 . “Inferring Landscape Effects on Gene Flow: A New Model Selection Framework,” . Molecular Ecology , 19 : 3603 – 3619 .
- Smouse , P. and Peakall , R. 1999 . “Spatial Autocorrelation Analysis of Individual Multiallele and Multilocus Genetic Structure,” . Heredity , 82 : 561 – 573 .
- Spear , S. , Balkenhol , N. , Fortin , M. , McRae , B. and Scribner , K. 2010 . “Use of Resistance Surfaces for Landscape Genetic Studies: Considerations for Parameterization and Analysis,” . Molecular Ecology , 19 : 3576 – 3591 .
- Spear , S. F. , Peterson , C. R. , Matocq , M. D. and Storfer , A. 2005 . “Landscape Genetics of the Blotched Tiger Salamander (Ambystoma tigrinum melanostictum),” . Molecular Ecology , 14 : 2553 – 2564 .
- Spiegelhalter , D. J. , Best , N. G. , Carlin , B. P. and van der Linde , A. 2002 . “Bayesian Measures of Model Complexity and Fit,” . Journal of the Royal Statistical Society, Series B , 64 : 583 – 639 .
- Storfer , A. , Murphy , M. A. , Evans , J. S. , Goldberg , C. S. , Robinson , S. , Spear , S. F. , Dezzani , R. , Delmelle , E. , Vierling , L. and Waits , L. P. 2007 . “Putting the “Landscape” in Landscape Genetics,” . Heredity , 98 : 128 – 142 .
- Theobald , D. , Crooks , K. and Norman , J. 2011 . “Assessing Effects of Land use on Landscape Connectivity: Loss and Fragmentation of Western us Forests,” . Ecological Applications , 21 : 2445 – 2458 .
- Tizghadam , A. and Leon-Garcia , A. 2010 . “On Traffic-Aware Betweenness and Network Criticality,” . In INFOCOM IEEE Conference on Computer Communications Workshops, IEEE 1 – 6 .
- Tizghadam , A. and Leon-Garcia , A. 2011 . “Robust Network Planning in Nonuniform Traffic Scenarios,” . Computer Communications , 34 : 1436 – 1449 .
- Urban , D. , Minor , E. , Treml , E. and Schick , R. 2009 . “Graph Models of Habitat Mosaics,” . Ecology Letters , 12 : 260 – 273 .
- van Etten , R. J. H. J. 2012 . Raster: Geographic Analysis and Modeling With Raster Data , R package version 1.9-92. Available at http://raster.r-forge.r-project.org
- Volchenkov , D. 2011 . “Random Walks and Flights Over Connected Graphs and Complex Networks,” . Communications in Nonlinear Science and Numerical Simulation , 16 : 21 – 55 .
- Wang , H. and Xia , Y. 2009 . “Shrinkage Estimation of the Varying Coefficient Model,” . Journal of the American Statistical Association , 104 : 747 – 757 .
- Wang , I. , Savage , W. and Bradley Shaffer , H. 2009 . “Landscape Genetics and Least-Cost Path Analysis Reveal Unexpected Dispersal Routes in the California Tiger Salamander (Ambystoma californiense),” . Molecular Ecology , 18 : 1365 – 1374 .
- Wheeler , D. C. and Waller , L. A. 2010 . “Spatial Analysis of Genetic Population Structure in Cougars,” . Technical Report 10-01, Department of Biostatistics and Bioinformatics, Rollins School of Public Health
- Wheeler , D. C. , Waller , L. A. and Biek , R. 2010 . “Spatial Analysis of Feline Immunodeficiency Virus Infection in Cougars,” . Spatial and Spatio-temporal Epidemiology , 1 : 151 – 161 .
- Wikle , C. and Hooten , M. 2010 . “A General Science-Based Framework for Dynamical Spatio-Temporal Models,” . Test , 19 : 417 – 451 .
- Wright , S. 1943 . “Isolation by Distance,” . Genetics , 28 : 114
- Zhu , H. and Klein , D. 1996 . “Graph-Geometric Invariants for Molecular Structures,” . Journal of Chemical Information and Computer Sciences , 36 : 1067 – 1075 .