[R-sig-eco] anova.cca question / missing data in constraining matrix

[ckellogg]

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   

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



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