scalogram: Function to compute a scalogram

In adespatial: Multivariate Multiscale Spatial Analysis

Description

The function decompose the variance of a variable x on a basis of orthogonal vectors. The significance of the associated R-squared values is tested by a randomization procedure. A smoothed scalogram is obtained by summing the R-squared values into nblocks.

Usage

scalogram(x, orthobasisSp, nblocks = ncol(orthobasisSp), nrepet = 999,
  p.adjust.method = "none")

## S3 method for class 'scalogram'
plot(x, pos = -1, plot = TRUE, ...)

Arguments

x	a numeric vector (for scalogram) or an object of class scalogram (for plot.scalogram)
orthobasisSp	an object of class orthobasisSp
nblocks	an integer indicating the number of blocks
nrepet	an integer indicating the number of permutations used in the randomization procedure
p.adjust.method	a string indicating a method for multiple adjustment, see p.adjust.methods for possible choices.
pos	an integer indicating the position of the environment where the data are stored, relative to the environment where the function is called. Useful only if <e2><80><98>storeData<e2><80><99> is <e2><80><98>FALSE<e2><80><99>
plot	a logical indicating if the graphics is displayed
...	additional graphical parameters (see <e2><80><98>adegpar<e2><80><99> and <e2><80><98>trellis.par.get<e2><80><99>)

Details

On the plot, oberved R-squared values are represent by bars. A black line indicate the 0.95 quantile of the values obtained by permutations. Significant values are indicated by a '*'

Value

The function scalogram returns an object of class scalogram, subclass krandtest. The plot function returns an object of class ADEgS, generated by the functions of the adegraphics package

Author(s)

St<c3><a9>phane Dray [e-mail]

References

Dray S., P<c3><a9>lissier R., Couteron P., Fortin M.J., Legendre P., Peres-Neto P.R., Bellier E., Bivand R., Blanchet F.G., De Caceres M., Dufour A.B., Heegaard E., Jombart T., Munoz F., Oksanen J., Thioulouse J., Wagner H.H. (2012). Community ecology in the age of multivariate multiscale spatial analysis. Ecological Monographs 82, 257–275.

See Also

mem orthobasis

Examples

if(require("ade4", quietly = TRUE) & require("spdep", quietly = TRUE)){
data(mafragh)
me <- mem(nb2listw(mafragh$nb))

if(require("adegraphics", quietly = TRUE)){
sc1 <- scalogram(mafragh$mil$Conduc, me, nblocks = 10)
plot(sc1)
}
}

Example output

Attaching package: 'ade4'

The following object is masked from 'package:adespatial':

    multispati

Warning message:
version 0.2.9.4 of 'spData' masked by 0.2.5.0 in /usr/local/lib/R/site-library 

adespatial documentation built on May 2, 2019, 4:43 p.m.