GarpPresampleLayers
org.ecoinformatics.seek.garp.GarpPresampleLayers

GARP is a computer program for predicting species locations based on various spatial data sets of environment variables and known species locations. GARP is an acronym for Genetic Algorithm for Rule Set Production. GARP was originally ceated by David Stockwell. The version in Kepler is based on 'Desktop GARP', http://www.lifemapper.org/desktopgarp/. The GarpPresampleLayers actor carries out the first step in a GARP calculation to be executes as a Kepler workflow. It samples the environment data and known locations to create a 'CellSet' of information to be used in later steps. As input, it takes several file names. One is a summary of spatial grids containing things like environmental data (e.g. temperature, precipitation, etc.) A number of these spatial grids are summarized in an xml file (named *.dxl). The second major input is locations file that contains a list of known spatial locations where the species of interest has been found. This information is 'presampled' to create a CellSet to be used in subsequent pieces of the GARP calculation. There is also an input that should give the file name to be used to store this CellSet data. The output port provides the file name when the file has been actually written. (The output is thus a 'trigger'.) This is a JNI-based actor. It requires the following: linux: libgarp.so windows: garp.dll, libexpat.dll MacOSX - currently not available for the Mac (3/16/2006)

Author(s): Chad Berkeley, Dan Higgins, NCEAS, UC Santa Barbara
Version:


layersetFilename
This input port can be used to supply the file name of the xml file that summarizes all the spatial layers to be used in the GARP calculation. The file name is of the *.dxl format. Examine samples to see the content.

dataPointFileName
This input port can be used to supply the file name of the file that contains the known locations to be used to determine a ruleset for predicting other locations from the spatial environment layers. The file is a text file with one location per line. Each line contains a point location (x,y) with the numeric values of x and separated by a 'tab' character. Typically the (x,y) is (longitude, latitude).

cellSetFileName
input port can be used to supply the file name to be used in saving the cell set information. This information is a sample to be used by GARP in creating the rule set for predicting occurrences.

cellSetFileNameOutput
This output port supplies the file name of the cellSetFile. It has the same name as supplied in the input port, but it is only fired after the data has been calculated. It is thus used as a 'trigger' for the next step in the GARP calculation.



layersetFilenameParameter
This parameter is the file name of the xml file that summarizes all the spatial layers to be used in the GARP calculation. The file name is of the *.dxl format. Examine samples to see the content.

dataPointFileNameParameter
This parameter is the file name of the file that contains the known locations to be used to determine a ruleset for predicting other locations from the spatial environment layers. The file is a text file with one location per line. Each line contains a point location (x,y) with the numeric values of x and y separated by a 'tab' character. Typically the (x,y) is (longitude, latitude).

cellSetFileNameParameter
This parameter is the file name to be used in saving the cell set information. This information is a sample to be used by GARP in creating the rule set for predicting occurrences.