PresenceAbsence: PresenceAbsence Class

In letsR: Data Handling and Analysis in Macroecology

PresenceAbsence Class

Description

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.

Details

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)

letsR documentation built on Nov. 23, 2023, 9:07 a.m.