Plot U-score Nonmetric Multidimensional Scaling of censored data

Plots an NMDS of uscores output from the uscores or uscoresi functions.

uMDS(uscor, group = NULL, title = NULL, legend.pos = "bottomleft")

Arguments

uscor	A data frame of uscores or ranks of uscores produced by either the uscores(...) or uscoresi(...) functions
group	Optional grouping variable. Sites will be represented by different colored symbols for each group.
title	Optional title for the NMDS graph.
legend.pos	For when group is specified, the location of the legend on the graph showing the colors representing each group’s data. Default is “bottomleft”. Alternatives are “topright” and “centerleft”, etc.

Value

Prints an NMDS plot of censored data groupings based on U-scores #' @references Helsel, D.R., 2011. Statistics for Censored Environmental Data using Minitab and R, 2nd ed. John Wiley & Sons, USA, N.J.

Examples

data(PbHeron)

PbHeron.u <- uscores(PbHeron[,4:15])
uMDS(PbHeron.u)
#> Run 0 stress 0.07773434 
#> Run 1 stress 0.07793355 
#> ... Procrustes: rmse 0.007559895  max resid 0.02871233 
#> Run 2 stress 0.07793355 
#> ... Procrustes: rmse 0.007554071  max resid 0.02867208 
#> Run 3 stress 0.07762542 
#> ... New best solution
#> ... Procrustes: rmse 0.00928285  max resid 0.03814576 
#> Run 4 stress 0.07844726 
#> Run 5 stress 0.07851582 
#> Run 6 stress 0.1271665 
#> Run 7 stress 0.07851582 
#> Run 8 stress 0.07762542 
#> ... New best solution
#> ... Procrustes: rmse 2.614786e-06  max resid 1.107653e-05 
#> ... Similar to previous best
#> Run 9 stress 0.07793355 
#> ... Procrustes: rmse 0.01225709  max resid 0.03832487 
#> Run 10 stress 0.1294192 
#> Run 11 stress 0.07851582 
#> Run 12 stress 0.07762542 
#> ... New best solution
#> ... Procrustes: rmse 1.192086e-06  max resid 3.066164e-06 
#> ... Similar to previous best
#> Run 13 stress 0.07851582 
#> Run 14 stress 0.08639937 
#> Run 15 stress 0.07762542 
#> ... Procrustes: rmse 5.301069e-06  max resid 2.08152e-05 
#> ... Similar to previous best
#> Run 16 stress 0.07851582 
#> Run 17 stress 0.1302845 
#> Run 18 stress 0.1271667 
#> Run 19 stress 0.07851582 
#> Run 20 stress 0.08660761 
#> *** Solution reached
#> species scores not available

# With group specific
uMDS(PbHeron.u,group=PbHeron$DosageGroup)
#> Run 0 stress 0.07773434 
#> Run 1 stress 0.07851582 
#> Run 2 stress 0.07851582 
#> Run 3 stress 0.07844726 
#> Run 4 stress 0.07851582 
#> Run 5 stress 0.1274958 
#> Run 6 stress 0.07844726 
#> Run 7 stress 0.07773434 
#> ... Procrustes: rmse 4.04054e-06  max resid 1.285038e-05 
#> ... Similar to previous best
#> Run 8 stress 0.1394876 
#> Run 9 stress 0.07851582 
#> Run 10 stress 0.1384417 
#> Run 11 stress 0.07851582 
#> Run 12 stress 0.07793355 
#> ... Procrustes: rmse 0.007556411  max resid 0.02868253 
#> Run 13 stress 0.1275349 
#> Run 14 stress 0.07851582 
#> Run 15 stress 0.07793355 
#> ... Procrustes: rmse 0.007557406  max resid 0.02869248 
#> Run 16 stress 0.07844726 
#> Run 17 stress 0.07773434 
#> ... Procrustes: rmse 3.356474e-06  max resid 1.14275e-05 
#> ... Similar to previous best
#> Run 18 stress 0.07851582 
#> Run 19 stress 0.07788834 
#> ... Procrustes: rmse 0.01183696  max resid 0.03750011 
#> Run 20 stress 0.07851582 
#> *** Solution reached