Software

CoordinateCleaner

CoordinateCleaner is an R-package to automatically flag georeferencing problems commonly found in biological collections, for instance, invalid coordinates, coordinates in the sea, coordinates assigned to country centroids, capitals or biodiversity institutions, imprecise dating in fossils and identify if records which have undergone decimal rounding. CoordinateCleaner is available via CRAN or GitHub and has a detailed documentation and tutorials. See here our paper describing the method.


Infomap Bioregions

Infomap Bioregions, web application for delimiting biogeographical regions based on species occurrence data. Species distributions may be provided as georeferenced point occurrences or range maps, and can be of local, regional or global scale. Infomap Bioregions uses a network delimitation algorithm based on information theory and adaptive resolution to account for incomplete species distribution data. You can find more details on the Infomap Bioregions website and the describing paper.


SpeciesgeocodeR

SpeciesgeocodeR is an R-package to facilitate the use of “big data” species distribution information (e.g. millions of occurrence records) in biogeography. The package includes functions to classify species occurrence records into discrete areas in a format ready-to-use with common software used for ancestral area reconstruction, to estimate ranges and range sizes from occurrence records. The latest version of speciesgeocodeR is available from GitHub. There are a lot of tutorials available here, and the method is described in this paper. There is also a Python version called SpeciesGeoCoder.


SampBias

Sampbias is a method and tool to 1) visualize the distribution of occurrence records and species in any user-provided dataset, 2) quantify the biasing effect of geographic features related to human accessibility, such as proximity to cities, rivers or roads, and 3) create publication-level graphs of these biasing effects in space. Find the SampBias R-package here, the shiny web application here and a detailed description here.


PyRate

PyRate is a Python program to estimate speciation, extinction, and preservation rates from fossil occurrence data using probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process. I contributed to the developement of the DES-model (Dispersal-Extintion-Sampling) implemented in PyRate. The DES-model estimates biogeographic parameters (dispersal, extinction and speciation) using fossil occurrences instead of phylogenetic trees.  Check out PyRate here and the description of the DES-model here.

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