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_PW(), MANOVA(), 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 
#> ... New best solution
#> ... Procrustes: rmse 3.936046e-06  max resid 1.87576e-05 
#> ... Similar to previous best
#> Run 2 stress 0.1536609 
#> Run 3 stress 0.1729702 
#> Run 4 stress 0.07227125 
#> ... Procrustes: rmse 5.981988e-06  max resid 2.874886e-05 
#> ... Similar to previous best
#> Run 5 stress 0.07227125 
#> ... Procrustes: rmse 2.19081e-06  max resid 8.275813e-06 
#> ... Similar to previous best
#> Run 6 stress 0.07227125 
#> ... Procrustes: rmse 7.02888e-06  max resid 2.808569e-05 
#> ... Similar to previous best
#> Run 7 stress 0.07227125 
#> ... Procrustes: rmse 9.669054e-06  max resid 3.852924e-05 
#> ... Similar to previous best
#> Run 8 stress 0.1476475 
#> Run 9 stress 0.07227125 
#> ... Procrustes: rmse 1.146136e-06  max resid 4.040052e-06 
#> ... Similar to previous best
#> Run 10 stress 0.07227125 
#> ... Procrustes: rmse 2.035528e-06  max resid 8.084339e-06 
#> ... Similar to previous best
#> Run 11 stress 0.07227126 
#> ... Procrustes: rmse 7.291375e-06  max resid 2.685535e-05 
#> ... Similar to previous best
#> Run 12 stress 0.1647891 
#> Run 13 stress 0.07227125 
#> ... Procrustes: rmse 6.998249e-06  max resid 2.725125e-05 
#> ... Similar to previous best
#> Run 14 stress 0.07227125 
#> ... Procrustes: rmse 5.714742e-06  max resid 2.216745e-05 
#> ... Similar to previous best
#> Run 15 stress 0.1606935 
#> Run 16 stress 0.07227125 
#> ... Procrustes: rmse 6.971938e-06  max resid 2.720148e-05 
#> ... Similar to previous best
#> Run 17 stress 0.07227125 
#> ... Procrustes: rmse 8.281581e-07  max resid 2.450366e-06 
#> ... Similar to previous best
#> Run 18 stress 0.1776127 
#> Run 19 stress 0.07227125 
#> ... Procrustes: rmse 4.920737e-06  max resid 1.945613e-05 
#> ... Similar to previous best
#> Run 20 stress 0.07227125 
#> ... Procrustes: rmse 1.953093e-06  max resid 6.877957e-06 
#> ... Similar to previous best
#> *** Best solution repeated 14 times

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