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)