Alexandre Antonelli edited this page Nov 24, 2016 · 62 revisions

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What is SpeciesGeoCoder?

SpeciesGeoCoder is a free software package for coding species occurrences into user-defined units for e.g. biogeographic analyses. The background and goals of the package are described in the following pre-print: http://biorxiv.org/content/early/2014/09/17/009274

How to cite SpeciesGeoCoder?

Töpel, M., Zizka, A., Calió, M.F., Scharn, R., Silvestro, D., Antonelli, A. SpeciesGeoCoder: Fast categorization of species occurrences for analyses of biodiversity, biogeography, ecology and evolution. (2016) Systematic Biology,doi:10.1093/sysbio/syw064

Available for free at: http://sysbio.oxfordjournals.org/content/early/2016/08/26/sysbio.syw064

Which versions are available?

  1. The one available here and written in Python
  2. A web interface that allows the analysis of data online: https://portal.bils.se/tools/speciesgeocoder
  3. A similar package written solely in R: https://cran.rstudio.com/web/packages/speciesgeocodeR/

More details

SpeciesGeoCoder utilises the GDAL library (http://www.gdal.org/) for fast analysis of geoTIFF files, which allows for the easy and fast coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as political units (countries, states), conservation areas, realms, biomes, ecoregions, islands, biodiversity hotspots, and areas of endemism; but they may also be defined as a combination of several criteria, including altitudinal ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and Nexus files that can be directly used in many phylogeny-based applications for ancestral state reconstruction, investigations on biome evolution, and diversification rate analyses.


Installing and running

How to download and install the program, testing it with a simple analysis using the example data.

Tutorials

How to run the program using your data and settings; How to generate or provide pre-defined input polygons in GIS; etc

Example input data

A description of the example files distributed with SpeciesGeoCoder.

Outputs

A description of the primary and optional outputs of SpeciesGeoCoder including:

  • species area coding (primary)
  • result plots (optional)
  • species migrations trough time (optional)

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