select.window: Select cells inside a defined window of a gridded dataset

In CommEcol: Community Ecology Analyses

Description

Selection of cells (or sites) around a focal cell. Cells must have have xy coordinates. Users should define a 'radius' from the focal cell that will define the window

Usage

select.window(xf, yf, radius = 1, xydata)

Arguments

xf	The x-coordinate of the focal cell.
yf	The y-coordinate of the focal cell.
radius	The radius that define the window to select neighbor cells.
xydata	A matrix-like object. The first and second columns of data must have x and y coordinates, respectively. The remaining columns must contain species or other atributes to be selected.

Details

The function is intended to be used in gridded data, but should work on sites irregularly scattered in the xy-space.

Value

A matrix-like object in which the first and second columns are the x and y coordinates. The remaining columns includes species (or attributes) observed in the selected cells.

Author(s)

Adriano Sanches Melo

Examples

x<-rep(1:5,each=5)
y<-rep(1:5,5)
spp<-matrix(1:100,25,4)
colnames(spp)<-c("sp1","sp2","sp3","sp4")
xyspp<-cbind(x,y,spp)
resu<-select.window(xf=3, yf=3, radius=1.1, xydata=xyspp)
resu

plot(x,y) # maintain the plot window open.
points(resu[,1:2],col=2,cex=2 ) # cells of the selected window in red.

#A reduced number of cells will be selected for focal cells located in margins.
resu<-select.window(xf=5, yf=5, radius=1.1, xydata=xyspp)
plot(x,y) # maintain the plot window open.
points(resu[,1:2],col=2,cex=2 ) # cells of the selected window in red.

# Unrecorded species in the selected window are removed from resulting dataframe (or matrix):
spp<-matrix(rep(0:1,each=50),25,4)
colnames(spp)<-c("sp1","sp2","sp3","sp4")
xyspp<-cbind(x,y,spp)
select.window(xf=3, yf=3, radius=1.1, xydata=xyspp)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ape
Loading required package: picante
Loading required package: nlme
      x y sp1 sp2 sp3 sp4
 [1,] 3 3  13  38  63  88
 [2,] 2 2   7  32  57  82
 [3,] 2 3   8  33  58  83
 [4,] 2 4   9  34  59  84
 [5,] 3 2  12  37  62  87
 [6,] 3 4  14  39  64  89
 [7,] 4 2  17  42  67  92
 [8,] 4 3  18  43  68  93
 [9,] 4 4  19  44  69  94
      x y sp3 sp4
 [1,] 3 3   1   1
 [2,] 2 2   1   1
 [3,] 2 3   1   1
 [4,] 2 4   1   1
 [5,] 3 2   1   1
 [6,] 3 4   1   1
 [7,] 4 2   1   1
 [8,] 4 3   1   1
 [9,] 4 4   1   1

CommEcol documentation built on March 16, 2021, 9:07 a.m.