[R] Error message in vegan ordistep

[Nevil Amos]

I am getting the following erro rmessage in ordistep.  I have a number of similarly structured datasets using ordistep in a loop, and the message only occurs for some of the datasets.  

I cannot include a reproducible sample  - the specific datasets where this is occur ing are fairly large and there are several pcnm's in the rhs of the formula.

thanks for any pointers that may allow me to track down the cause of the error.

Nevil Amos

Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the first 50)
> traceback()
9: ordistep(myrda0, scope = formula(myrda1), direction = "both", 
       Pin = 0.05, Pout = 0.1) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
8: eval(expr, envir, enclos) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
7: eval(expr, pf) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
6: withVisible(eval(expr, pf)) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
5: evalVis(expr) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
4: capture.output(ordistep(myrda0, scope = formula(myrda1), direction = "both", 
       Pin = 0.05, Pout = 0.1)) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1: source("~/Documents/Dropbox/thesis/CH3/Analysis/RDAPARTIALSexandAgeConnectandGEOGraphy2.R")



> 
> print(myrda1)
Call: rda(formula = mygenind at tab ~ pcnmTRE_25_100_CS25 + pcnmTRE_25_10_CS25 + pcnmTRE_25_2_CS25 +
pcnmTRE_25_5_CS25 + mydata$TreeCov + mydata$Hab_Config + pcnmEYR_EO_100_CS25 +
pcnmEYR_EO_5000_CS25 + pcnmEYR_TH_10_CS25 + pcnmEYR_TH_2_CS25 + mydata$Site_No + mydata$Landscape
+ Condition(pcnmCS_NULL + mydata$LAT.x + mydata$LONG.x), na.action = "na.omit")

              Inertia Proportion Rank
Total          1.8110     1.0000     
Conditional    0.8681     0.4793   32
Constrained    0.0000     0.0000    0
Unconstrained  0.9429     0.5207   29
Inertia is variance 
Some constraints were aliased because they were collinear (redundant)

Eigenvalues for unconstrained axes:
    PC1     PC2     PC3     PC4     PC5     PC6     PC7     PC8 
0.16008 0.14733 0.12183 0.09054 0.07380 0.06971 0.05578 0.04215 
(Showed only 8 of all 29 unconstrained eigenvalues)