Hello, I am using the cca function in Vegan to examine the relationship between microbial community structure and a (large) suite of environmental variables. My constraining/environmental data matrix as a lot of holes in it so I have been exploring using the na.action argument. This is the command I am currently using: toolik250.cca<-cca(toolikotus250.ra~julianday+logwindspd_max_1dayprior+lograin_3dayprior+sqrtwindspd_1dayprior+windspd_3dayprior+days_since_thaw+days_since_iceout+days_btw_iceoutandthaw+toolikepitemp_24h+logtemp+conductivity+pH, toolikenv.s, na.action=na.omit)
The CCA seems to run just fine, but when I attempt to do the posthoc tests such as anova.cca (anova(toolik250.cca,by='terms',perm=999), I get an error message: "Error in anova.ccabyterm(object, step = step, ...) : number of rows has changed: remove missing values?" What exactly is occurring here to cause this error - I suspect it must be related to the fact that the environmental data matrix has a lot of missing data. I don't quite understand why it states that the number of rows has changed...changed from what? Is there any way to get around having missing data when running the anovas as you can when running the CCA itself? One other question I have is when I try and run the CCA on all the data in my environmental data matrix (toolikenv.s), not just a subset of variables as I do above, using this command: toolik250.cca <-cca(toolikotus250.ra~., toolikenv.s, na.action=na.omit) I get the following error message. "Error in svd(Xbar, nu = 0, nv = 0) : a dimension is zero" What might be causing this error message to be thrown? Thank you so much for your help. Maybe I will just have to filter out the samples with missing environmental data (or filter out some of the variables themselves if they have too much missing data), but I was just hoping to avoid having to do this. Colleen -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/anova-cca-question-missing-data-in-constraining-matrix-tp7578175.html Sent from the r-sig-ecology mailing list archive at Nabble.com. _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology