I am a beginner with R and have managed to use vegan to run a CCA on
my data. I am evaluating the habitat relationships of select species
in riparian areas around creeks before and after logging across three
sampling intervals (pre-logging, two-years post-logging,. and 10
years post-logging). I sampled from 18 sites of 3 treatments (n = 6
sites for each treatment). When I plot my pre-treatment data, I am
plotting data from all 18 sites and have selected 12 species and
boiled my habitat variables down to 10. The plot shows all 18 sites,
all 12 species, and all 10 habitat variable - this is good. However,
when I do the CCA on a sub-set of my data, (e.g., Control sites only
[n = 6]) the plot displays all 6 sites, all 12 species, but only 5 of
the 10 habitat variables. Any ideas why the tri-plot of the sub-set
of my data will not show all of the habitat variables? Am I
encountering a minimum sample size problem? How can I plot all
environmental variables?
Thanks in advance,
Virgil Hawkes
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