This is a list of the actors that need to be implemented to complete the
preprocessing of the GARP pipeline. These are actors that would be needed to
take a raw DiGIR query and get it into the form needed to submit to the current
GARP actors.
--DiGIRQuery: actor to query DiGIR for a set of species. This should probably
be done via the ecogrid.
--EnvLayerMetadatExtractor: extracts the metadata from the env layers needed to
get user input. the user's input includes: scaleValue, minSampleSizeThreshold,
SubSampleMethod (choose from medians, quartiles, infinite or manual),
numberOfReplicates (how many times to run the garp algorithm).
--RescaleValues: This actor rescales the presence data values from their current
form to a value between 1 and 254. 0 and 255 are reserved and not used. this
could probably be implemented in java, though i'm not sure of the heterogeneity
of the input files....it might be better to use a gis system if there are a
variety of input formats.
--Clipping: For each species, this actor creates a minimum convex polygon of the
species plots (lats/longs). It then buffers the polygon to n times the area of
the polygon. the environmental layers are then clipped to the size of the new
polygon. This should probably be implemented in a GIS system.
--Sampling: take in a list of species and occurance data. randomly sample the
data into two sets: intrinsic data and extrinsic data. the intrinsic data is
used in the actual garp pipeline, the extrinsic data is used to test the garp
output for ommission and commission error.
--Rescale (general binning utility): Take in a spatial file and rescale to a
specific scale. this probably needs to be implemented in a gis...possibly could
write java to do it.
--SpeciesOccuranceCount: take in a list of species with occurance data that is
adjusted to the same scale. output a vector of species and counts.
--SpeciesSelection: rescale a list of species coverages to a single scale.
select the species that have an occurance count greater than a user defined
threshold. this should output a list of rescaled species (with occurance data)
that have an occurance rate greater than the threshold. This can probably be
implemented in a composite actor using existing (or soon to exist) actors.