Re: [R] Vegan(ordistep) error: Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed

2012-01-12 Thread Jari Oksanen 
Nevil Amos  gmail.com> writes:

> 
> 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
> 
Nevil,

This still sounds like the same problem. I can't reproduce your problem, but
I could construct a case which gives similar error messages, and fixed that
problem. This is a bit like blind watchmaker's job, since I don't know what 
is your problem. However, go to http://vegan.r-forge.r-project.org/ and 
download and source() the latest version (rev2044) of ordistep.R and see
if that works. In either case, report the results to me (outside the list) 
so that I know whether I managed to fix the problem or I have to find new
blind ideas.

Cheers, Jari Oksanen

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Re: [R] Vegan(ordistep) error: Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed

2012-01-11 Thread Nevil Amos 
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. 
Constrained1.2635 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 
RDA9RDA10RDA11 
0.173325 0.126065 0.093396 0.086910 0.072219 0.063064 0.062034 0.058022 
0.050743 0.045038 0.043567 
   RDA12RDA13RDA14RDA15RDA16RDA17RDA18RDA19
RDA20RDA21RDA22 
0.039200 0.035363 0.033358 0.029372 0.028224 0.025715 0.024484 0.024007 
0.021999 0.020480 0.018853 
   RDA23RDA24RDA25RDA26RDA27RDA28RDA29 
0.017277 0.015510 0.015091 0.012845 0.011089 0.009377 0.006886 

Eigenvalues for unconstrained axes:
   PC1PC2PC3PC4PC5PC6PC7PC8 
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  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.
>> Conditional0.8681 0.4793   32
>> Constrained0. 0.0
>> 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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Re: [R] Vegan(ordistep) error: Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed

2012-01-11 Thread Jari Oksanen 
Nevil Amos  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.
> Conditional0.8681 0.4793   32
> Constrained0. 0.0
> 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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Vegan(ordistep) error: Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed

2012-01-10 Thread 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.


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.
Conditional0.8681 0.4793   32
Constrained0. 0.0
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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