provenance (version 4.4)

MDS: Multidimensional Scaling

Description

Performs classical or nonmetric Multidimensional Scaling analysis of provenance data

Usage

MDS(x, ...)
# S3 method for default
MDS(x, classical = FALSE, k = 2, ...)
# S3 method for compositional
MDS(x, classical = FALSE, k = 2, ...)
# S3 method for counts
MDS(x, classical = FALSE, k = 2, ...)
# S3 method for distributional
MDS(x, classical = FALSE, k = 2, nb = 0, ...)
# S3 method for varietal
MDS(x, classical = FALSE, k = 2, nb = 0, ...)

Value

an object of class MDS, i.e. a list containing the following items:

points: a two column vector of the fitted configuration

classical: a boolean flag indicating whether the MDS configuration was obtained by classical (TRUE) or nonmetric (FALSE) MDS.

diss: the dissimilarity matrix used for the MDS analysis

stress: (only if classical=TRUE) the final stress achieved (in percent)

Arguments

x

an object of class distributional, compositional, counts, varietal or diss

...

optional arguments

If x has class distributional, ... is passed on to diss.distributional.

If x has class compositional, ... is passed on to diss.compositional.

If x has class counts, ... is passed on to diss.counts.

If x has class varietal, ... is passed on to diss.varietal.

Otherwise, ... is passed on to cmdscale (if classical=TRUE), to isoMDS (if classical=FALSE).

classical

boolean flag indicating whether classical (TRUE) or nonmetric (FALSE) MDS should be used

k

the desired dimensionality of the solution

nb

number of bootstrap resamples. If nb>0, then plot.MDS(...) will visualise the sampling uncertainty as polygons (inspired by Nordsvan et al. 2020). The bigger nb, the slower the calculations. nb=10 seems a good compromise.

References

Nordsvan, A.R., Kirscher, U., Kirkland, C.L., Barham, M. and Brennan, D.T., 2020. Resampling (detrital) zircon age distributions for accurate multidimensional scaling solutions. Earth-Science Reviews, p.103149.

Vermeesch, P., 2013, Multi-sample comparison of detrital age distributions. Chemical Geology v.341, 140-146, doi:10.1016/j.chemgeo.2013.01.010

Examples

data(Namib)
plot(MDS(Namib$Major,classical=TRUE))