Example data - mtop/speciesgeocoder GitHub Wiki
This page describes the example data distributed with SpeciesGeoCoder.
polygons.txt
The polygons are stored in the following format:
Name: Latitude1,Longitude1 Latitude2,Longitude2 Latitude3,Longitude3
... with lines starting with the name of the polygon, and followed with a list of latitude and longitude coordinate pairs that represents the nodes in the polygon. Optionally the line can also contain an elevation limit like this:
Name: Latitude1,Longitude1 Latitude2,Longitude2 Latitude3,Longitude3 : > 1000
In this example, only locality records sampled at an elevation > 1000 m. will be coded as present in this polygon. Elevation data from the analysed area has to be provided to SpeciesGeoCoder as geotiff files using the option "--tif". Elevation limits will not be regarded if the "--tif" option is not used.
A tutorial on how to prepare input polygons using QGIS can be found here
localities.csv
SpeciesGeoCoder can read locality data from a tab-separated text file containing three or more columns like this:
#Species name Lat. Longitude Comment
Ivesia aperta 39.82 -120.4 CHSC35943
Ivesia aperta 39.81 -120.39 CHSC88602
The first line has to start with "#", followed by the name of the first column (e.g. "Species name"). The second and third columns contains the actual locality data in the form of longitude and latitude coordinates (WGS84 coordinate system is assumed). These two columns can be in any order, but the header has to clearly indicate which column contains longitude, and which contains latitude data, by abbreviation (e.g. "Lat." or "Lon.") or full names ("Latitude" or "Longitude"). Additional columns will not be read by the program, but can be used to add comments to the file for readability. Additional lines starting with "#" will also be regarded as comments, and excluded from the analysis.
gbif_Ivesia_localities.txt
Locality data downloaded from GBIF can also be used with SpeciesGeocoder. The downloaded data will consist of a zip-archive containing a number of files. One of them will be named "occurrence.txt" and is the file that can be read by the program (I suggest you give it a more informative name before the analysis).
tree.nex
The stochastic mapping algorithm used by SpeciesGeoCoder requires a phylogenetic tree in NEXUS format as input. A tree in the correct format can be exported from e.g. the program Figtree.
30n120w_20101117_gmted_med300.tif
Elevation data in the form of geotif files can be downloaded from a number of repositories (see this page for information on data from which repositories that has been tested with SpeciesGeoCoder).