occs_userOccs {wallace} | R Documentation |
occs_userOccs Loads user provided occurrence records
Description
Load user database with species occurrence records. Returns a list of lists, one per species provided in database in each species list with a set of appropriate fields
Usage
occs_userOccs(txtPath, txtName, txtSep = ",", txtDec = ".", logger = NULL)
Arguments
txtPath |
path to database including database name and extension |
txtName |
name of database without the extension. Database must have at least three columns named 'scientific_name', 'longitude', 'latitude' |
txtSep |
field separator used in database (as in read.delim) |
txtDec |
decimal separator used for coordinates in database |
logger |
Stores all notification messages to be displayed in the Log Window of Wallace GUI. Insert the logger reactive list here for running in shiny, otherwise leave the default NULL |
Details
This function is called by the module occs_queryDb to load a user provided database for species occurrence records, subset to only those records with coordinates, remove records with duplicate coordinates, and select some columns with fields appropriate to studies in biogeography.
Value
List of lists. One list per species with occurrence records. Each individual species list with appropriate fields for analysis
Author(s)
Jamie Kass <jamie.m.kass@gmail.com>
Gonzalo E. Pinilla-Buitrago <gepinillab@gmail.com>
Examples
txtPath <- system.file("extdata/Bassaricyon_alleni.csv", package = "wallace")
txtName <- 'Bassaricyon_alleni'
user.occs <- occs_userOccs(txtPath, txtName)