Non metric multidimensional scaling

A wrapper around vegan::metaMDS.

Usage

NMDS(x, distance = "bray", k = 2, try = 20, trymax = 20, ...)

Arguments

x

any Coe object

distance

a dissiminarity index to feed vegan::vegdist (default: bray)

k

numeric number of dimensions to feed vegan::metaMDS (default: 2)

try

numeric minimum number of random starts to feed vegan::metaMDS (default: 20)

trymax

numeric minimum number of random starts to feed vegan::metaMDS (default: 20)

...

additional parameters to feed vegan::metaMDS

Value

what is returned by vegan::metaMDS plus $fac. And prepend NMDS class to it.

Details

For Details, see vegan::metaMDS

See also

Other multivariate: CLUST(), KMEANS(), KMEDOIDS(), LDA(), MANOVA(), MANOVA_PW(), MDS(), MSHAPES(), PCA(), classification_metrics()

Examples

x <- bot %>% efourier %>% NMDS
#> 'norm=TRUE' is used and this may be troublesome. See ?efourier #Details
#> 'nb.h' set to 10 (99% harmonic power)
#> 'comm' has negative data: 'autotransform', 'noshare' and 'wascores' set to FALSE
#> Warning: results may be meaningless because data have negative entries
#>                  in method “bray”
#> Run 0 stress 0.07227125 
#> Run 1 stress 0.07227125 
#> ... Procrustes: rmse 8.334796e-06  max resid 3.047993e-05 
#> ... Similar to previous best
#> Run 2 stress 0.07227125 
#> ... New best solution
#> ... Procrustes: rmse 5.865887e-06  max resid 2.065795e-05 
#> ... Similar to previous best
#> Run 3 stress 0.07227125 
#> ... Procrustes: rmse 6.500411e-06  max resid 2.560239e-05 
#> ... Similar to previous best
#> Run 4 stress 0.07227126 
#> ... Procrustes: rmse 1.973897e-05  max resid 8.1637e-05 
#> ... Similar to previous best
#> Run 5 stress 0.07227125 
#> ... Procrustes: rmse 1.611046e-06  max resid 5.206746e-06 
#> ... Similar to previous best
#> Run 6 stress 0.07227125 
#> ... Procrustes: rmse 4.38684e-06  max resid 1.707128e-05 
#> ... Similar to previous best
#> Run 7 stress 0.07227125 
#> ... Procrustes: rmse 3.098236e-06  max resid 1.266529e-05 
#> ... Similar to previous best
#> Run 8 stress 0.07227125 
#> ... Procrustes: rmse 7.27379e-06  max resid 2.741795e-05 
#> ... Similar to previous best
#> Run 9 stress 0.07227125 
#> ... Procrustes: rmse 2.350358e-06  max resid 9.21327e-06 
#> ... Similar to previous best
#> Run 10 stress 0.07227125 
#> ... Procrustes: rmse 8.276153e-06  max resid 3.231576e-05 
#> ... Similar to previous best
#> Run 11 stress 0.1733868 
#> Run 12 stress 0.07227125 
#> ... Procrustes: rmse 5.645289e-06  max resid 2.294965e-05 
#> ... Similar to previous best
#> Run 13 stress 0.07227125 
#> ... New best solution
#> ... Procrustes: rmse 1.826633e-06  max resid 6.121634e-06 
#> ... Similar to previous best
#> Run 14 stress 0.1709375 
#> Run 15 stress 0.07227125 
#> ... Procrustes: rmse 6.363625e-06  max resid 2.436065e-05 
#> ... Similar to previous best
#> Run 16 stress 0.07227125 
#> ... Procrustes: rmse 2.991654e-06  max resid 1.240109e-05 
#> ... Similar to previous best
#> Run 17 stress 0.07227125 
#> ... Procrustes: rmse 6.666183e-06  max resid 2.63522e-05 
#> ... Similar to previous best
#> Run 18 stress 0.07227125 
#> ... Procrustes: rmse 8.082234e-06  max resid 3.110865e-05 
#> ... Similar to previous best
#> Run 19 stress 0.07227125 
#> ... Procrustes: rmse 5.577536e-06  max resid 2.153054e-05 
#> ... Similar to previous best
#> Run 20 stress 0.07227125 
#> ... Procrustes: rmse 2.058943e-06  max resid 7.515172e-06 
#> ... Similar to previous best
#> *** Best solution repeated 7 times

# Shepard diagram # before a Momocs wrapper
# vegan::stressplot(x)