Dear Colleen, On 03/06/2013, at 22:32 PM, ckellogg wrote: > Hello Jari, > Thank you for your help with this. The solution you suggested in your > second post worked quite well. However, i think another subset of my data > is too 'holey', because when I run CCA on this set of environmental > variables (or the a CCA with the previous environmental variables and the > additional ones), I get an error: > >> toolik250.cca2 >> <-cca(toolikotus250.ra~logtemp+conductivity+pH+logBacProd+DIC+logDCO2+sqrtDCH4+logDOC+sqrtPhosphate+sqrtNitrate+sqrtTDN+sqrtTDP+logPC+logPN+Ca+Mg+logNa+logK+SO4+logChloride+Silica,toolikenv.s, >> na.action=na.exclude) > Error in predict.cca(x, newdata = excluded, type = "wa", model = "CA") : > model “CA” has rank 0 > > The CCA runs if I use na.action=na.omit, but then when I run the anovas, > there is apparently no residual component. For example, > No residual component > > Model: cca(formula = toolikotus250.ra ~ logtemp + conductivity + pH + > logBacProd + DIC + logDCO2 + sqrtDCH4 + logDOC + sqrtPhosphate + sqrtNitrate > + sqrtTDN + sqrtTDP + logPC + logPN + Ca + Mg + logNa + logK + SO4 + > logChloride + Silica, data = toolikenv.s, na.action = na.omit, subset = > -toolik250.cca2$na.action) > Df Chisq F N.Perm Pr(>F) > Model 12 5.3003 0 > Residual 0 0.0000 > Yes, probably too many holes. You have no residual variation which indicates that the number of predictor variables (constraints) is higher than the number of remaining observations.
Cheers, Jari Oksanen > So, I am thinking that examining the relationship between the microbial > community and this subset of environmental variables might not be possible > without my first manually curating which samples and variables should be > included, correct? > > Thank you, > Colleen > > > > -- > View this message in context: > http://r-sig-ecology.471788.n2.nabble.com/anova-cca-question-missing-data-in-constraining-matrix-tp7578175p7578179.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 -- Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland jari.oksa...@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology