[R] vegan cca: syntax
fgraz at unam.na
Mon Sep 26 14:36:16 CEST 2011
I am a new member to the list - and to the analysis that I am attempting.
I have the following case
A group of us have been monitoring (over a period of a few years) a number
of paired plots that were flooded and / or burnt.
The plots are located in two topographical settings, some were burnt, some
were flooded, some were burnt & flooded and some were not affected at all.
At each location one plot was fenced to exclude grazing while another was
left unfenced to include the effect of grazing. Effectively, I guess, we
have a split plot design in a longitudinal study.
The plots were established opportunistically, so there were some practical
aspects that might not be ideal... but then when is this ever the case...
I now want to determine importance of various effects of these … effects...
and used vegan's cca in the following context:
1. I read in the count data
2. transformed the counts using a 4th root transformation into count.dbf2 –
based on a suggestion from a colleague and following up in “Quinn, G. P.,
and M. J. Keough. 2002. Experimental design and data analysis for
biologists, 1st edition”.
3. I then used the following two commands to generate an ANOVA table:
> out.cca2 = cca(count.df2 ~ Flood*(Fence+Fire+age)+topo, predictor.df)
> anova(out.cca2, by="term", step=2000)
4. Since the order in which the factors are entered seems to matter, I tried
a number of iterations obtaining similar results to:
Model: cca(formula = response.df2 ~ Flood * (Fence + Fire + age) + topo,
data = predictor.df)
Df Chisq F N.Perm Pr(>F)
Flood 1 0.4643 13.3495 1999 5e-04 ***
Fence 1 0.1507 4.3342 1999 5e-04 ***
Fire 1 0.1049 3.0152 1999 5e-04 ***
age 1 0.1756 5.0492 1999 5e-04 ***
topo 1 0.1520 4.3710 1999 5e-04 ***
Flood:Fence 1 0.0868 2.4949 1999 5e-04 ***
Flood:Fire 1 0.0952 2.7378 1999 5e-04 ***
Flood:age 1 0.1235 3.5510 1999 5e-04 ***
Residual 171 5.9470
I am somewhat isolated here and have no-one to cross check the syntax. I
could not include the 'split plot' aspect in the equation. Should I worry
Any assistance would be very welcome.
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