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(...)oruscoresi(...)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 0.08660761
#> Run 2 stress 0.07844726
#> Run 3 stress 0.1350415
#> Run 4 stress 0.08660761
#> Run 5 stress 0.08660763
#> Run 6 stress 0.08639937
#> Run 7 stress 0.07788834
#> ... Procrustes: rmse 0.0118381 max resid 0.03749766
#> Run 8 stress 0.07788834
#> ... Procrustes: rmse 0.01183382 max resid 0.03750395
#> Run 9 stress 0.08660761
#> Run 10 stress 0.07844726
#> Run 11 stress 0.07788834
#> ... Procrustes: rmse 0.01183369 max resid 0.03750326
#> Run 12 stress 0.07851582
#> Run 13 stress 0.07844726
#> Run 14 stress 0.07851582
#> Run 15 stress 0.07851582
#> Run 16 stress 0.07851582
#> Run 17 stress 0.1275348
#> Run 18 stress 0.07793355
#> ... Procrustes: rmse 0.00756157 max resid 0.02870125
#> Run 19 stress 0.07844726
#> Run 20 stress 0.07844726
#> *** Best solution was not repeated -- monoMDS stopping criteria:
#> 8: stress ratio > sratmax
#> 12: scale factor of the gradient < sfgrmin
#> 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 0.1274958
#> Run 3 stress 0.07851582
#> Run 4 stress 0.08660761
#> Run 5 stress 0.07844726
#> Run 6 stress 0.07851582
#> Run 7 stress 0.08639937
#> Run 8 stress 0.07844726
#> Run 9 stress 0.08639938
#> Run 10 stress 0.07844726
#> Run 11 stress 0.07851582
#> Run 12 stress 0.08639938
#> Run 13 stress 0.07762542
#> ... New best solution
#> ... Procrustes: rmse 0.00928294 max resid 0.03814474
#> Run 14 stress 0.07851582
#> Run 15 stress 0.07844726
#> Run 16 stress 0.08660762
#> Run 17 stress 0.07762542
#> ... Procrustes: rmse 4.317837e-06 max resid 1.386284e-05
#> ... Similar to previous best
#> Run 18 stress 0.08660763
#> Run 19 stress 0.08639937
#> Run 20 stress 0.1294192
#> *** Best solution repeated 1 times
