SigDiff: Identify Regions of Significant Differences

In SDMTools: Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises

Description

SigDiff computes the significance of the pairwise differences relative to the mean and variance of all differences between the two input datasets. This is useful for identifying regions of significant difference between two datasets (e.g., different DEMs (Januchowski et al. 2010) or different species distribution model predictions (Bateman et al 2010)).

ImageDiff is a wrapper to the image.asc command in adehabitat package that uses the result from SigDiff to create an image mapping the regions of significant differences (positive and negative).

NOTE: it is assumed the input data are of the same extent and cellsize.

Usage

SigDiff(x, y, pattern = TRUE)

ImageDiff(tasc, sig.levels = c(0.025, 0.975), tcol = terrain.colors(3), ...)

Arguments

x	a vector or matrix of data; the matrix can be of can be a raster of class 'asc' (adehabitat package), 'RasterLayer' (raster package) or 'SpatialGridDataFrame' (sp package)
y	a vector or matrix of data with the same dimensions and class of 'x'
pattern	logical value defining if differences are respective to relative patterning (TRUE) or absolute values (FALSE)
tasc	a matrix of probability values (0 to 1) likely created by SigDiff; The matrix can be a raster of class 'asc' (adehabitat package), 'RasterLayer' (raster package) or 'SpatialGridDataFrame' (sp package)
sig.levels	the significance levels to define significantly above and below. Default settings represent significance at the 0.05 level
tcol	a set of 3 colors for use in the image to represent significantly lower or greater, and not significant
...	other graphical parameters defined by image() or plot()

Value

SigDiff returns a vector or matrix of the same dimensions and class of the input representing the significance of the pairwise difference relative to the mean and variance of all differences between the two inputs.

ImageDiff returns nothing but creates an image of the areas of significant differences

Author(s)

Stephanie Januchowski [e-mail]

References

Januchowski, S., Pressey, B., Vanderwal, J. & Edwards, A. (2010) Characterizing errors in topographic models and estimating the financial costs of accuracy. International Journal of Geographical Information Science, In Press.

Bateman, B.L., VanDerWal, J., Williams, S.E. & Johnson, C.N. (2010) Inclusion of biotic interactions in species distribution models improves predictions under climate change: the northern bettong Bettongia tropica, its food resources and a competitor. Journal of Biogeography, In Review.

Examples

#create some simple objects of class 'asc'
tasc = as.asc(matrix(1:50,nr=50,nc=50)); print(tasc)
#modify the asc objects so that they are slightly different
tasc1 = tasc + runif(n = 2500, min = -1, max = 1)
tasc2 = tasc + rnorm(n = 2500, mean = 1, sd = 1)

#create graphical representation
par(mfrow=c(2,2),mar=c(1,1,4,1))
image(tasc1,main='first grid',axes=FALSE)
image(tasc2,main='second grid',axes=FALSE)

#get significant difference by spatial patterning
out = SigDiff(tasc1,tasc2)
ImageDiff(out,main="Pattern Differences",axes=FALSE)

#get significant difference
out = SigDiff(tasc1,tasc2,pattern=FALSE)
ImageDiff(out,main="Absolute Differences",axes=FALSE)
legend('topleft',legend=c('-ve','ns','+ve'),title='significance',
  fill=terrain.colors(3),bg='white')

Example output

Raster map of class "asc":
Cell size:  1 
Number of rows:  50 
Number of columns:  50 
Type:  numeric 

SDMTools documentation built on Jan. 11, 2020, 9:23 a.m.