virtual_list: Virtual floristic list (VFL)

In interacquas/ignobioR: Managing biodiversity occurrence data considering uncertainty

Description

A list of species potentially occurring within a study site, in which a probability of occurrence is computed for every taxon

Usage

virtual_list(
  data_flor,
  site,
  year_study = NULL,
  excl_areas = NULL,
  CRS.new = 3035,
  tau,
  upperlimit = 20,
  verbose = TRUE
)

Arguments

data_flor	dataframe having 5 columns, namely ‘Taxon’ (species identity), ‘Long’ (longitude coordinates), ‘Lat’ (latitude coordinates), ‘uncertainty’ (radius of uncertainty, in metres), and ‘year’ (year of the record)
site	a layer object of class ‘SpatialPolygonsDataFrame’ representing the study area, having CRS: +init=epsg:4326
year_study	the present-year in which you perform the analysis
excl_areas	a layer object of class ‘SpatialPolygonsDataFrame’ to delimit certainly unsuitable areas adjacent or within the study area, having CRS: +init=epsg:4326
CRS.new	the new Coordinate Reference System. Note: must be in a projected CRS. Default = 3035
tau	percentual value of taxa loss in 100 years time-span (see below for further details)
upperlimit	maximum number of floristic records for a given taxon managed by the algorithm to compute the VFL. You can increase this number; a number between 20 and 30 is suggested. Then, the algorithm considers only the n most relevant, in terms of probability, occurrence records
verbose	an optional logical value. If TRUE information on the evolution of the algorithm is printed. Default is TRUE (suggested for large dataset)

Value

an object of class list with 2 slots:

• "The virtual floristic list"A dataframe with five columns

• "Statistics"A set of summarising statistics of the VFL drafting process

Examples

## Not run: 

data(floratus)
data(park)
data(unsuitablezone)

# Short example
set.seed(123)
vfl <- virtual_list(data_flor= floratus[sample(nrow(floratus), 2000), ], site = park, excl_areas = unsuitablezone, tau = 30, upperlimit = 25)

# Extended example 
vfl <- virtual_list(data_flor = floratus, site = park, excl_areas = unsuitablezone, tau = 30, upperlimit = 25)


## End(Not run)

interacquas/ignobioR documentation built on July 2, 2021, 3:13 a.m.