Skip to main content

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

  • Cliff, A.D., and J.K. Ord (1973) Spatial Autocorrelation. London: Pion.

  • Cliff, A.D., and J.K. Ord (1981) Spatial Processes. London: Pion.

  • Dale, M.R T. (1999) Spatial Pattern Analysis in Plant Ecology. Cambridge: Cambridge University Press.

  • 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.

  • 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.

  • Falsetti, A.B., and R.R. Sokal (1993) Genetic structure of human populations in the British Isles. Annals of Human Biology 20:215-229.

  • 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.

  • Gabriel, K.R., and R.R. Sokal (1969) A new statistical approach to geographic variation analysis. Systematic Zoology 18:259-278.

  • Galiano, E.F. (1982) Détection et mesure de l'hétérogénéité spatiale des espèces dans les pâturages. Acta OEcologia / OEcologia Plantarum 3:269-278.

  • Geary, R.C. (1954) The contiguity ratio and statistical mapping. Incorporated Statistician 5:115-145.

  • Moran, P.A.P. (1950) Notes on continuous stochastic phenomena. Biometrika 37:17-23.

  • Hill, M.O. (1973) The intensity of spatial pattern in plant communities. Journal of Ecology 61:225-235.

  • Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27:209-220.

  • Mantel, N., and R.S. Valand (1970) A technique of nonparametric multivariate analysis. Biometrics 26:547-558.

  • Oden, N.L., and R.R. Sokal (1986) Directional autocorrelation: An extension of spatial correlograms to two dimensions. Systematic Zoology 35:608-617.

  • Rosenberg, M.S. (2000) The bearing correlogram: A new method of analyzing directional spatial autocorrelation. Geographical Analysis 32:267-278.

  • Rosenberg, M.S. (2001) PASSAGE. Pattern Analysis, Spatial Statistics and Geographic Exegesis. Version 1.

  • 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

  • Sokal, R.R., and N.L. Oden (1978) Spatial autocorrelation in biology 1. Methodology. Biological Journal of the Linnean Society 10:199-228.

  • 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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyssage-0.0.1.tar.gz (59.2 kB view details)

Uploaded Source

Built Distribution

pyssage-0.0.1-py3-none-any.whl (74.6 kB view details)

Uploaded Python 3

File details

Details for the file pyssage-0.0.1.tar.gz.

File metadata

  • Download URL: pyssage-0.0.1.tar.gz
  • Upload date:
  • Size: 59.2 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.3.0 pkginfo/1.6.1 requests/2.25.1 setuptools/51.1.1 requests-toolbelt/0.9.1 tqdm/4.55.1 CPython/3.9.0

File hashes

Hashes for pyssage-0.0.1.tar.gz
Algorithm Hash digest
SHA256 ccae1b78ef650470bd4cf0eecdeebe6f9c20b6345133dc95fb794782d8892416
MD5 15c9f20b165c817078739da2f052ee9e
BLAKE2b-256 25227a716142a18f805b066333cf69199047cbba08c582df6c7afe71b21d318a

See more details on using hashes here.

File details

Details for the file pyssage-0.0.1-py3-none-any.whl.

File metadata

  • Download URL: pyssage-0.0.1-py3-none-any.whl
  • Upload date:
  • Size: 74.6 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.3.0 pkginfo/1.6.1 requests/2.25.1 setuptools/51.1.1 requests-toolbelt/0.9.1 tqdm/4.55.1 CPython/3.9.0

File hashes

Hashes for pyssage-0.0.1-py3-none-any.whl
Algorithm Hash digest
SHA256 6945277db0ba39996124778584b26c5559137361ec81b2923f8babfa7376d7de
MD5 0efe4d38cdd23651d2df8083bdab07be
BLAKE2b-256 4388a9f931080482cd9b0dd46f4cfdf9db46beace399810a52bd1f31ddd9343b

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page