This is my first question here so please excuse any mistakes I (may or may not) make.
The premise:
I got a vegetational dataset containing paired data on different plots for old and new observations. I used the 'openxlsx'-package to load my data, and 'vegan'-package to execute an NMDS as follows:
mydata <- read.xlsx(mydata)
mydataMDS <- metaMDS(mydata, k=2, trymax=500)
The result is then used for a model via the "envfit()"-function, including environmental variables:
myenvdata <- read.xlsx(myenvdata)
mydataMDS_fit <- envfit(mydataMDS, myenvdata, perm=10000, na.rm=TRUE)
plot(mydataMDS, display="sites")
plot(mydataMDS_fit, p.max=0.01, axis=TRUE)
Now I have a plot with my statistical "mydataMDS"-analyses, including vectors produced by the "mydataMDS_fit" R calculated.
The problem:
I want to colour and connect certain points within this plot. As "mydata" consists of observations within the same plot at different times, I intend to colour all points of old observations in one colour, and all the new ones in a different one. I've read about adding columns in order to group old and new observations, but as I'm working with a model there are no columns. How can I edit my datasets ("mydata", "mydataMDS", "myenvdata", "mydataMDS_fit") in order to show old and new plots in 2 different colours (one colour for old, one colour for new), and connect the paired observations with lines? Or: Is there a possibility to directly re-colour the points within my graphical output via checking for old/new observations?
(Sorry, I feel like my explanation is quite complicated, but I still hope someone may be able to help)