The PresenceAbsence is a new S3 object class created
and used inside the letsR package. This object class is used to
store information on species distribution within a geographic domain in the form of
a presence-absence matrix. In addition, the PresenceAbsence object also contains
other essential information (e.g. user-defined grid cell system, including resolution,
projection, datum, and extent) necessary for other analysis performed with the package's functions.
Creating a PresenceAbsence object
A PresenceAbsence object can be generated using the following
functions:
- lets.presab
- lets.presab.birds
- lets.presab.points
The PresenceAbsence information
The result is a list object of class PresenceAbsence that includes the
following objects:
- Presence_and_Absence_Matrix: A matrix of species' presence(1) and absence(0)
information. The first two columns contain the longitude (x) and latitude (y) of
the cells' centroid (from the gridded domain used);
- Richness_Raster: A raster containing species richness information across the geographic
domain, which can be used to map the observed geographic gradient in species richness;
- Species_name: A character vector with species' names contained in
the matrix.
Each of the objects can be obtained usign the standard subsetting operators that are
commonly applied to a list object (i.e. '[[' and '$').
letsR functions applied to a PresenceAbsence object
The following functions from the letsR package can be directly applied
to a PresenceAbsence:
- lets.addpoly
- lets.addvar
- lets.distmat
- lets.field
- lets.gridirizer
- lets.iucn
- lets.iucn.ha
- lets.iucn.his
- lets.maplizer
- lets.midpoint
- lets.overlap
- lets.pamcrop
- lets.rangesize
Generic functions applied to a PresenceAbsence object
The following generic functions can be directly applied to
the PresenceAbsence object.
- print (print.PresenceAbsence)
- summary (summary.PresenceAbsence)
- plot (plot.PresenceAbsence)