anova.cca question / missing data in constraining matrix

Dear Colleen,

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

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Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksanen at oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa

anova.cca question / missing data in constraining matrix

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