Hi,

I'd like to find out how to do temporal trajectory plots by site as part of
an NMDS in vegan. I can run an NMDS on my data when the data is structured
by combined site/time codes:

JInv <- read.csv("JInv.csv", header=T, row.names = NULL)

library(vegan)

JInv.NMDS <- metaMDS(JInv, distance="bray")
JInv.NMDS
JInv.NMDS$stress
par(mfrow=c(1,1))
plot(JInv.NMDS, type="t", main=paste("NMDS/Bray - Stress =",
round(JInv.NMDS$stress,3)))

and think this is how to specify 2 variables as factors
date <- factor(JInv$date)
site <- factor(JInv$site)

but am not sure what to do next. How do I add trajectories for each of the
nine sites over time?

I found an example about how to do a trajectory plot (for PCA) across all
data points (below), but am not sure how to adapt this to my case. Can
anyone help?

# for the trajectory lines the coordinates of the unscaled PC1/2 scores
have to be obtained

 scores.unsc <- scores(PCA, scaling = 0)

# connect the sites in an ascending order of the year

lines(x = scores.unsc$sites[, 1][order(Data.transf <#_msocom_2>$Year)], y =
scores.unsc$sites[, 2][order(Data.transf$Year)], lty = 1, col = "blue")
Thanks in advance,
Lien

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