Whilst the constrained proportion was 0 in the example below I am getting the
error in cases where this is not so. See new output pasted below
[1] "ORDISTEP RDA1 BOTH WAYS"
[1]
"________________________________________________________________________________________________"
[1] "SFW ALL Adult"
[1] mds3dSFW_EO_100_CS25 mds3dSFW_EO_5000_CS25 mds3dSFW_TH_10_CS25
mds3dSFW_TH_2_CS25
Call: rda(formula = mygenind@tab ~ mds3dTRE_25_100_CS25 + mds3dTRE_25_10_CS25 +
mds3dTRE_25_2_CS25 + mds3dTRE_25_5_CS25 + mydata$TreeCov + mydata$Hab_Config +
mydata$Site_No + mydata$Landscape + mds3dCS_NULL + mydata$LAT.x +
mydata$LONG.x, na.action
= "na.omit")
Inertia Proportion Rank
Total 4.5099 1.0000
Constrained 1.2635 0.2802 29
Unconstrained 3.2464 0.7198 142
Inertia is variance
Some constraints were aliased because they were collinear (redundant)
Eigenvalues for constrained axes:
RDA1 RDA2 RDA3 RDA4 RDA5 RDA6 RDA7 RDA8
RDA9 RDA10 RDA11
0.173325 0.126065 0.093396 0.086910 0.072219 0.063064 0.062034 0.058022
0.050743 0.045038 0.043567
RDA12 RDA13 RDA14 RDA15 RDA16 RDA17 RDA18 RDA19
RDA20 RDA21 RDA22
0.039200 0.035363 0.033358 0.029372 0.028224 0.025715 0.024484 0.024007
0.021999 0.020480 0.018853
RDA23 RDA24 RDA25 RDA26 RDA27 RDA28 RDA29
0.017277 0.015510 0.015091 0.012845 0.011089 0.009377 0.006886
Eigenvalues for unconstrained axes:
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8
0.2037 0.1710 0.1670 0.1450 0.1343 0.1155 0.1120 0.1015
(Showed only 8 of all 142 unconstrained eigenvalues)
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()
6: ordistep(myrda0, scope = formula(myrda1), direction = "both",
Pin = 0.05, Pout = 0.1) at #55
5: eval(expr, envir, enclos) at #55
4: eval(expr, pf) at #55
3: withVisible(eval(expr, pf)) at #55
2: evalVis(expr) at #55
1: capture.output(ordistep(myrda0, scope = formula(myrda1), direction = "both",
Pin = 0.05, Pout = 0.1)) at #55
Cheers
Nevil Amos
>
> Nevil Amos <nevil.amos <at> monash.edu> writes:
>
>>
>> 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.
>>
>> Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed
>>
> Nevil,
>
> It seems to me that the source of the problem appears in this table:
>
>> 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)
>>
>
> The key point is that "Constrained" component is completely alaised (Inertia
> 0,
> Rank 0) and therefore it cannot be analysed in permutation tests. You get the
> same error message with this model:
>
> mod <- rda(dune ~ Moisture + Condition(Moisture), dune.env)
>
> and for the same reason. In your case, PCNM's seem to explain everything and
> there is nothing left for other variables, and therefore you cannot analyse
> them.
>
> Cheers, Jari Oksanen
>
> I can see how to fix this in vegan. All I can do is to handle these cases
> smoothly and with comprehensible error messages, though. They cannot be
> handled
> with permutation tests since there is nothing to do if "Constrained" component
> is zeroed.
>
> Cheers, Jari Oksanen
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