readOcc: readOcc: read species occurrences

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

Description

Read and clean the occurrences records files (.csv format) of multiples species from a specified folder and provide a list of 'SpatialPoints' of species through the removal of duplicates coordinates.

Usage

readOcc (occ = occ, crs = "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0",
distOcc = NULL, occSum = FALSE)

Arguments

occ	Path for a folder with the species occurrences records files (.csv format). Coordinates should be in decimal degrees. The names of .csv files should correspond to the species names and must have 3 columns identified as "species" (species names or other identification of taxa), "long" (longitude), "lat" (latitude). NOTE: 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 be consider as duplicates and removed. Units of this value must be in km. Optional. Default is zero (i.e. only exactly coincident coordinates will be removed). For more details, see remove.duplicates.
occSum	(logical) Whether the output should include also a data.frame with the number of occurrences records after the removal of duplicate coordinates. Default is FALSE.

Value

By default, readOcc returns a list with two elements:

• A 'spOcc' object corresponding to a species list with features of 'SpatialPoints' class.

• A data.frame with the number of occurrences records after the cleaning step to remove duplicate coordinates.

If occSum is FALSE, readOcc returns only the 'spOcc' object.

Author(s)

Thaís Dória & Daniel Gonçalves-Souza

See Also

remove.duplicates

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