Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/lets_presab_points.R

Convert species' occurrences into a presence-absence matrix based on a user-defined grid.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
lets.presab.points(
xy,
species,
xmn = -180,
xmx = 180,
ymn = -90,
ymx = 90,
resol = 1,
remove.cells = TRUE,
remove.sp = TRUE,
show.matrix = FALSE,
crs = CRS("+proj=longlat +datum=WGS84"),
count = FALSE
)
``` |

`xy` |
A matrix with geographic coordinates of species occurrences, first column is the longitude (or x), and the second latitude (or y). |

`species` |
Character vector with species names, in the same order as the coordinates. |

`xmn` |
Minimun longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest) |

`xmx` |
Maximun longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest) |

`ymn` |
Minimun latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest) |

`ymx` |
Maximun latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest) |

`resol` |
Numeric vector of length 1 or 2 to set the grid resolution. |

`remove.cells` |
Logical, if |

`remove.sp` |
Logical, if |

`show.matrix` |
Logical, if |

`crs` |
Character representign the PROJ.4 type description of a Coordinate Reference System (map projection) of the points. |

`count` |
Logical, if |

The function creates the presence-absence matrix based on a raster file. Depending on the cell size, extension used and number of species it may require a lot of memory,
and may take some time to process it. Thus, during the process, if `count`

argument is set `TRUE`

, a counting window will open so you can see the progress (i.e. in what polygon the function is working). Note that the number of
polygons is not the same as the number of species that you have (i.e. a species may have more than one polygon/shapefiles).

The result is an object of class `PresenceAbsence`

with the following objects:

**Presence-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 data;

**Species name**: A character vector with species' names contained in the matrix.

*But see the optional argument `show.matrix`

.

Bruno Vilela & Fabricio Villalobos

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
## Not run:
species <- c(rep("sp1", 100), rep("sp2", 100),
rep("sp3", 100), rep("sp4", 100))
x <- runif(400, min = -69, max = -51)
y <- runif(400, min = -23, max = -4)
xy <- cbind(x, y)
PAM <- lets.presab.points(xy, species, xmn = -93, xmx = -29,
ymn = -57, ymx = 15)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
main = "Species richness map (simulated)")
# Map of the specific species
plot(PAM, name = "sp1")
## End(Not run)
``` |

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