Dear all, 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 about this?. Any assistance would be very welcome. Regards Patrick -- View this message in context: http://r.789695.n4.nabble.com/vegan-cca-syntax-tp3843617p3843617.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.