fuzzySim (version 4.33)

distPres: (Inverse) distance to the nearest presence

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

distPres(data, sp.cols, coord.cols = NULL, id.col = NULL,
dist.mat = NULL, CRS = NULL, method = "auto", suffix = "_D",
p = 1, inv = TRUE, verbosity = 2)

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.

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

optional pre-computed pairwise distance matrix for the localities in 'data'. If provided, arguments 'CRS' and 'method' are not used.

CRS

coordinate reference system of the 'coord.cols' in 'data', in one of the following formats: WKT/WKT2, <authority>:<code>, or PROJ-string notation (see terra::crs()). Ignored if 'dist.mat' is not NULL. Otherwise, if 'CRS' is provided and the 'terra' package is installed, distances are computed with terra::distance(), thus accounting for the curvature of the Earth.

method

(if 'dist.mat' is NULL) argument to pass to dist or to terra::distance() specifying the method for computing the distance matrix. Results are more accurate if a terra::distance() method is used and the 'CRS' argument is provided. The default is "auto". With this, the method is "euclidean" if the 'terra' package isn't available; else "haversine" if there are distances < 1 m or 0.00001 degrees, or "cosine" (faster but inaccurate for small distances) otherwise. You can instead choose method="geo" for the most accurate, yet slowest distance method (see ?terra::distance). For 'terra' versions before 1.8.7, only "geo" is available and will be used.

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.

verbosity

integer specifying the amount of messages to display along the process. The default is 2, for the maximum amount of messages available.

Author

A. Marcia Barbosa

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).

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

data(rotif.env)

head(rotif.env)

names(rotif.env)


# calculate plain distance to presence:

rotifers.dist0 <- distPres(rotif.env, sp.cols = 18:47,
coord.cols = c("Longitude", "Latitude"), id.col = 1, p = 1,
inv = FALSE, suffix = "_D")  # in degrees (inconsistent across latitudes)

rotifers.dist <- distPres(rotif.env, sp.cols = 18:47,
coord.cols = c("Longitude", "Latitude"), id.col = 1, p = 1,
inv = FALSE, suffix = "_D", CRS = "EPSG:4326")  # in meters

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", CRS = "EPSG:4326")

head(rotifers.invd2)