distPres: (Inverse) distance to the nearest presence

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/distPres.R

Description

This function takes a matrix or data frame containing species presence (1) and absence (0) data and their spatial coordinates (optionally also a pre-calculated distance matrix between all localities), and calculates the (inverse) distance from each locality to the nearest presence locality for each species.

Usage

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distPres(data, sp.cols, coord.cols = NULL, id.col = NULL, 
dist.mat = NULL, method = "euclidian", suffix = "_D", p = 1, 
inv = TRUE)

Arguments

data

a matrix or data frame containing, at least, two columns with spatial coordinates, and one column per species containing their presence (1) and absence (0) data, with localities in rows.

sp.cols

names or index numbers of the columns containing the species presences and absences in data. It must contain only zeros (0) for absences and ones (1) for presences.

coord.cols

names or index numbers of the columns containing the spatial coordinates in data (in this order, x and y, or longitude and latitude).

id.col

optionally, the name or index number of a column (to be included in the output) containing locality identifiers in data.

dist.mat

optionally, if you do not want distances calculated with any of the methods available in dist, you may provide a distance matrix calculated elsewhere for the localities in data.

method

the method with which to calculate distances between localities. Available options are those of dist. The default is "euclidian".

suffix

character indicating the suffix to add to the distance columns in the resulting data frame. The default is "_D".

p

the power to which distance should be raised. The default is 1; use 2 or higher if you want more conservative distances.

inv

logical value indicating whether distance should be inverted, i.e. standardized to vary between 0 and 1 and then subtracted from 1, so that it varies between 0 and 1 and higher values mean closer to presence. The default is TRUE, which is adequate as a fuzzy version of presence-absence (for using e.g. with fuzSim and simMat). In this case, presences maintain the value 1, and inverse distance to presence is calculated only for absence localities.

Details

This function can be used to calculate a simple spatial interpolation model of a species' distribution (e.g. Barbosa 2015, Areias-Guerreiro et al. 2016).

Value

This function returns a matrix or data frame containing the identifier column (if provided in 'id.col') and one column per species containing the distance (inverse by default) from each locality to the nearest presence of that species.

Author(s)

A. Marcia Barbosa

References

Areias-Guerreiro J., Mira A. & Barbosa A.M. (2016) How well can models predict changes in species distributions? A 13-year-old otter model revisited. Hystrix - Italian Journal of Mammalogy, in press. DOI: http://dx.doi.org/10.4404/hystrix-27.1-11867

Barbosa A.M. (2015) fuzzySim: applying fuzzy logic to binary similarity indices in ecology. Methods in Ecology and Evolution, 6: 853-858

See Also

dist

Examples

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data(rotif.env)

head(rotif.env)

names(rotif.env)


# calculate plain distance to presence:

rotifers.dist <- distPres(rotif.env, sp.cols = 18:47, 
coord.cols = c("Longitude", "Latitude"), id.col = 1, p = 1, 
inv = FALSE, suffix = "_D")

head(rotifers.dist)


# calculate inverse squared distance to presence:

rotifers.invd2 <- distPres(rotif.env, sp.cols = 18:47, 
coord.cols = c("Longitude", "Latitude"), id.col = 1, p = 2, 
inv = TRUE, suffix = "_iDsq")

head(rotifers.invd2)

fuzzySim documentation built on Feb. 4, 2020, 5:06 p.m.