jarioksa/vegan — Issue #3: simper with identical classes
Author: jarioksa
Created: 2012-02-20 14:22:19+00:00
State: open

In the following, we make a 'dummy' class that is a copy of 'ungrazed' class. The last 'ungrazed_dummy'
contrast compares two identical copies of the data:
```R
library(vegan)
data(varespec)
x <- varespec
x <- rbind(x, x[19:24,])
z <- c(rep("grazed",18), rep("ungrazed", 6), rep("dummy",6))
mod <- simper(x, z, permu=99)
summary(mod)
```
We do still get variable P-values.

In addition, although the rows are copies of each other and the means are identical, we still get simper
contributions to the differences (which in this case actually are to within-class variability):
```R
> mod
cumulative contributions of most influential species:
...
$ungrazed_dummy
Cla.ste Cla.ran Vac.vit Emp.nig Ple.sch
39.28130 53.28941 61.39104 68.85289 76.28894
```
This puts some shade over the whole method.