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.
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@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)
--
Nevil Amos
Molecular Ecology Research Group
Australian Centre for Biodiversity
Monash University
CLAYTON VIC 3800
Australia
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