ecospat.niche.overlap: From ecospat package 3.2 : ecospat.kd, ecospat.grid.clim.dyn...

In leca-dev/RFate: FATE with R

From ecospat package 3.2 : ecospat.kd, ecospat.grid.clim.dyn and ecospat.niche.overlap functions (and sp 1.4-5, adehabitatMA 0.3.14, adehabitatHR 0.4.19 packages

Description

From ecospat package 3.2 : ecospat.kd, ecospat.grid.clim.dyn and ecospat.niche.overlap functions (and sp 1.4-5, adehabitatMA 0.3.14, adehabitatHR 0.4.19 packages

Usage

ecospat.kd(x, ext, R = 100, th = 0, env.mask = c(), method = "adehabitat")
ecospat.grid.clim.dyn(glob, glob1, sp, R = 100, th.sp = 0, th.env = 0, 
geomask = NULL, kernel.method = "adehabitat", extend.extent = c(0, 0, 0, 0))
ecospat.niche.overlap(z1, z2, cor)

Arguments

x	two-column dataframe (or a vector)
ext	c(xmin, xmax)
R	The resolution of the grid.
th	quantile
env.mask	mask
method	kernel.method
glob	A two-column dataframe (or a vector) of the environmental values (in column) for background pixels of the whole study area (in row).
glob1	A two-column dataframe (or a vector) of the environmental values (in column) for the background pixels of the species (in row).
sp	A two-column dataframe (or a vector) of the environmental values (in column) for the occurrences of the species (in row).
th.sp	The quantile used to delimit a threshold to exclude low species density values.
th.env	The quantile used to delimit a threshold to exclude low environmental density values of the study area.
geomask	A geographical mask to delimit the background extent if the analysis takes place in the geographical space.It can be a SpatialPolygon or a raster object. Note that the CRS should be the same as the one used for the points.
kernel.method	Method used to estimate the the kernel density. Currently, there are two methods: by default, it is the methode from 'adehabitat'. Method from the library 'ks' is also available.
extend.extent	Vector with extention values of the window size (see details).
z1	Species 1 occurrence density grid created by ecospat.grid.clim.
z2	Species 2 occurrence density grid created by ecospat.grid.clim.
cor	Correct the occurrence densities of each species by the prevalence of the environments in their range (TRUE = yes, FALSE = no).

See Also

ecospat.grid.clim.dyn, ecospat.niche.overlap

leca-dev/RFate documentation built on Sept. 19, 2024, 6:09 a.m.