python version of some of the analyses from PASSaGE 2
Project description
PySSaGE
PySSaGE is a collection of python versions of analyses originally part of the PASSaGE (Rosenberg 2001) and PASSaGE 2 (Rosenberg and Anderson 2011) software packages for spatial analysis.
A more throrough explanation of how to use the code is forthcoming.
Analyses
So far the following analyses have been implemented:
Quadrat-Variance
- TTLQV: Two-Term Local Quadrat Variance Analysis (Hill 1973)
- 3TLQV: Three-Term Local Quadrat Variance Analysis (Hill 1973)
- PQV: Paired Quadrat Variance Analysis
- tQV: Triplet Quadrat Variance Analysis (Dale 1999)
- 2NLV: Two-term New Local Variance Analysis (Galiano 1982)
- 3NLV: Three-term New Local Variance Analysis (Galiano 1982)
Distance Calculations
- Euclidean distances/angles from 1, 2, and 3-dimensional points
- Spherical distances/angles from latitudes and longitudes
- Shortest-path/Geodesic distances
- Distances from arrays of data
- Euclidean distances
- Squared Euclidean distances
- Manhattan distances
- Canberra distances
- Hamming distances
- Jaccard distances
- Cosine distances
- Czekanowski distances
- Correlation distances
- Squared correlation distances
- Distance class determination
Connections/Links
- Delaunay/Voronoi Tessellation (Delaunay 1928, 1934)
- Minimum-spanning Tree
- Relative Neighborhood Network
- Gabriel Graph (Gabriel and Sokal 1969)
- Least-diagonal Network (Fraser and van den Driessche 1972)
- Range-based Connections
- k-nearest Neighbors
Correlograms
- Correlograms (Cliff and Ord 1973, 1981; Sokal and Oden 1978)
- Moran's I (Moran 1950)
- Geary's c (Geary 1954)
- Mantel Correlograms (Sokal et al. 1987)
Anisotropy
- Bearing Analysis (Falsetti and Sokal 1993)
- Bearing Correlograms (Rosenberg 2000)
- Windrose Correlograms (Oden and Sokal 1986)
- Windrose Mantel Correlograms
Miscellaneous
- Mantel tests (Mantel 1967; Mantel and Valand 1970)
References
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Cliff, A.D., and J.K. Ord (1973) Spatial Autocorrelation. London: Pion.
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Cliff, A.D., and J.K. Ord (1981) Spatial Processes. London: Pion.
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Dale, M.R T. (1999) Spatial Pattern Analysis in Plant Ecology. Cambridge: Cambridge University Press.
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Delaunay, B. (1928) Sur la sphère vide. Pp. 695-700 in Proceedings of the International Mathematical Congress held in Toronto, August 11-16. Toronto: University of Toronto Press.
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Delaunay, B. (1934) Sur la sphère vide. Bulletin de L'Academie des Sciences de L'URSS Classe des Sciences Mathématiques et Naturelles 7:793-800.
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Falsetti, A.B., and R.R. Sokal (1993) Genetic structure of human populations in the British Isles. Annals of Human Biology 20:215-229.
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Fraser, A.R., and P. van den Driessche (1972) Triangles, density and pattern in point populations. Pp. 277-286 in Proceedings of the 3rd Conference of the Advisory Group of Forest Statisticians. Jouy-en-Josas, France: International Union for Research organization, Institut National de la Recherche Agronomique.
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Gabriel, K.R., and R.R. Sokal (1969) A new statistical approach to geographic variation analysis. Systematic Zoology 18:259-278.
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Galiano, E.F. (1982) Détection et mesure de l'hétérogénéité spatiale des espèces dans les pâturages. Acta OEcologia / OEcologia Plantarum 3:269-278.
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Geary, R.C. (1954) The contiguity ratio and statistical mapping. Incorporated Statistician 5:115-145.
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Moran, P.A.P. (1950) Notes on continuous stochastic phenomena. Biometrika 37:17-23.
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Hill, M.O. (1973) The intensity of spatial pattern in plant communities. Journal of Ecology 61:225-235.
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Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27:209-220.
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Mantel, N., and R.S. Valand (1970) A technique of nonparametric multivariate analysis. Biometrics 26:547-558.
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Oden, N.L., and R.R. Sokal (1986) Directional autocorrelation: An extension of spatial correlograms to two dimensions. Systematic Zoology 35:608-617.
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Rosenberg, M.S. (2000) The bearing correlogram: A new method of analyzing directional spatial autocorrelation. Geographical Analysis 32:267-278.
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Rosenberg, M.S. (2001) PASSAGE. Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 1.
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Rosenberg, M.S., and C.D. Anderson (2011) PASSaGE. Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 2. Methods in Ecology and Evolution 2(3):229–232. DOI: 10.1111/j.2041-210x.2010.00081.x
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Sokal, R.R., and N.L. Oden (1978) Spatial autocorrelation in biology 1. Methodology. Biological Journal of the Linnean Society 10:199-228.
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Sokal, R.R., N.L. Oden, and J.S.F. Barker (1987) Spatial structure in Drosophila buzzatii populations: Simple and directional spatial autocorrelation. American Naturalist 129:122-142.
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