View source: R/lets_presab_points.R

lets.presab.points | R Documentation |

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

```
lets.presab.points(
xy,
species,
xmn = NULL,
xmx = NULL,
ymn = NULL,
ymx = NULL,
resol = NULL,
remove.cells = TRUE,
remove.sp = TRUE,
show.matrix = FALSE,
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). If NULL, limits will be calculated based on the limits of the shapes object. |

`xmx` |
Maximun longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object. |

`ymn` |
Minimun latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object. |

`ymx` |
Maximun latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object. |

`resol` |
Numeric vector of length 1 or 2 to set the grid resolution. If NULL, resolution will be equivalent to 1 degree of latitude and longitude. |

`remove.cells` |
Logical, if |

`remove.sp` |
Logical, if |

`show.matrix` |
Logical, if |

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

`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 a list 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

`plot.PresenceAbsence`

`lets.presab.birds`

`lets.presab`

`lets.shFilter`

```
## 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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