checkOcc: checkOcc: check if occurrences fall inside of an specific are

In thaisdoria/habitaR: Tools for mapping the species’ area of habitat (AOH) from geospatial data

Description

From 'SpatialPoints' of multiple species, gives the species and its occurrences that are inside of a polygon (ESRI shapefile format) representing a region of interest (e.g. study area, continent, country or other regions with specific boundaries).

Usage

checkOcc (occ, crs, poly, distOcc = NULL, SpOcc = FALSE)

Arguments

occ	Occurrences records of the species (coordinates in decimal degrees). 'It might correspond to path for a folder with the species occurrences files (.csv format) a list of 'data.frames' with the occurrences from multiple species (see data examples) 'spOcc' object corresponding to a list of 'SpatialPoints' from multiple species (see readOcc to obtain such object). NOTE: If path is provided, each .csv file should correspond to only one species and the file must be named with the corresponding species names. The files must have 3 columns identified as "species" (species names or other identification of taxa), "long" (longitude), "lat" (latitude). Longitude must be in a column before the latitude column.
crs	The Coordinate Reference System (CRS) specifing the projection and datum of dataset. Could be a CRS object or a character string.
distOcc	A value corresponding to the minimum distance to consider two coordinates as not duplicate. Values up to this distance will correspond to duplicates and removed. Units of this value must be in km. Default is zero (i.e. only exactly coincindent coordinates will be removed). For more details,see remove.duplicates. Optional and only used if 'occ' is a path for .csv files or a list of 'data.frame'. If 'occ' correspond to 'SpatialPoints', this argument ('distOcc') should be ignored (i.e. NULL).
poly	A polygon (ESRI shapefile from a 'SpatialPolygonsDataFrame' class) of the specific area to be checked.
SpOcc	(logical) Whether the output should also return the 'SpatialPoints' of species filtered based on the poly boundaries. Default is FALSE.

Details

The function filter the initial dataset of species (occ) based on a given region (poly). NOTE: if SpOcc is TRUE, the 'SpatialPoints' returned encompass all set of occurrences and not a subset that match with the specified region (poly). Therefore, the 'SpatialPoints' are NOT cleaned to remove the records falling outside the polygon checked and to restrict the 'SpatialPoints' only to occurrences recorded inside of polygon, but just filtered to reduce the species from initial dataset based in the area of poly.

Value

By default, checkOcc returns a data.frame of species and its respective occurrences matching with the provided polygon. If SpOcc is TRUE, checkdOcc returns a list with two elements:

• A data.frame with the species and total occurrences filtered by the polygon.

• A list of 'SpatialPoints' from each species that match with polygon, but without clean the records to remove those falling outside the polygon checked. See details.

Author(s)

Thaís Dória & Daniel Gonçalves-Souza

Examples

### List of 'data.frame' as Input ###

check1 <- checkOcc(occ_plants, crs = "+proj=longlat +datum=WGS84 +ellps=WGS84
 +towgs84=0,0,0", poly=poly, distOcc = NULL, SpOcc = TRUE)

### spOcc or list of 'SpatialPoints' as Input ###

check2 <- checkOcc(spOcc_plants, crs = "+proj=longlat +datum=WGS84 +ellps=WGS84
 +towgs84=0,0,0", poly=poly, distOcc = 0.1, SpOcc = TRUE)

thaisdoria/habitaR documentation built on Dec. 18, 2020, 8:09 p.m.