Hi all,
Another question on ordistep() in vegan. I am running a RDA, have 16
explanatory variables and five of them were not even listed in the Biplot
scores for constraining variables. When I analyzed the VIF, it also appeard
a NA in their place. This happened also when data were first standardized.
Now I want to choose the best model using ordistep().
Here, the five explanatory variables that I mentioned before are included
(the last five in the formula).
>RDA.all <- rda(main ~ ., data=second)
> RDA.all
> Call: rda(formula = main ~ MeanAsp + SDAsp + MenaSlo + SDSlo + Urban +
> Treelines + TreeGroups +
> SolTress + IntermGrass + TallGrass + Highways + Canals + DistDCA +
> MeanTrackDens + SDTrackDens +
> MeanMagnetism, data = second)
>
> Inertia Proportion Rank
> Total 0.005999 1.000000
> Constrained 0.005999 1.000000 9
> Unconstrained 0.000000 0.000000 0
> 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
> 4.421e-03 1.406e-03 8.930e-05 5.354e-05 1.413e-05 8.836e-06 4.612e-06
> 1.324e-06 3.500e-07
# Here's the problem
> step.forward <- ordistep(rda(main ~ 1, data=second), RDA.all,
direction="forward", pstep=1000)
Start: main ~ 1
>
The process stops in less than a second and it just does not give any
output. So I asked for:
> step.forward$anova
NULL
# Why null?
# And then,
>summary(step.forward)
Call:
rda(formula = main ~ 1, data = second)
Partitioning of variance:
Inertia Proportion
Total 0.005999 1
Unconstrained 0.005999 1
Eigenvalues, and their contribution to the variance
Importance of components:
PC1 PC2 PC3 PC4 PC5
PC6 PC7 PC8 PC9
Eigenvalue 0.004421 0.001406 0.0000893 5.354e-05 1.413e-05
8.836e-06 4.612e-06 1.324e-06 3.5e-07
Proportion Explained 0.736960 0.234350 0.0148800 8.920e-03 2.360e-03
1.470e-03 7.700e-04 2.200e-04 6.0e-05
Cumulative Proportion 0.736960 0.971320 0.9862000 9.951e-01 9.975e-01
9.990e-01 9.997e-01 9.999e-01 1.0e+00
Scaling 2 for species and site scores
* Species are scaled proportional to eigenvalues
* Sites are unscaled: weighted dispersion equal on all dimensions
* General scaling constant of scores: 0.5068435
Species scores
PC1 PC2 PC3 PC4 PC5 PC6
T30 0.020230 0.0260141 1.640e-03 0.0009593 0.0016298 1.494e-03
T60 0.029968 -0.0416358 5.082e-02 -0.0033992 -0.0033624 7.331e-03
T90 0.040460 0.0520283 3.280e-03 0.0019185 0.0032597 2.988e-03
T120 0.138776 0.1828691 1.381e-02 -0.0063556 0.0100248 6.255e-06
T150 0.083839 0.0991670 -1.549e-03 0.0246916 -0.0144196 -4.801e-03
T180 0.017788 -0.0189122 4.420e-03 -0.0192773 0.0054548 -1.322e-02
T210 0.032552 0.0531892 -1.255e-02 -0.0353441 -0.0138663 3.979e-03
T240 -0.002133 0.0006171 -2.533e-06 -0.0001967 0.0002564 -3.974e-04
X.1dia 0.398124 -0.0909282 -8.897e-03 0.0008550 0.0005249 6.968e-04
X.2dias 0.014241 -0.0188583 2.790e-02 -0.0021515 -0.0070527 -9.956e-03
Site scores (weighted sums of species scores)
PC1 PC2 PC3 PC4 PC5 PC6
D1N -0.02813 0.012849 -0.0937696 -0.32021 0.04749 -0.19677
D1S 0.29325 -0.300213 0.1317071 -0.08004 0.05188 -0.07038
D1E 0.29622 0.380916 0.0240131 0.01405 0.02387 0.02188
D1W -0.08521 0.011027 0.3446805 0.05417 -0.18557 -0.09601
D2N 0.06379 -0.071989 -0.2057112 0.28033 -0.24678 -0.12687
D2S -0.02582 -0.053152 0.1201434 0.04442 0.05756 0.35846
D2E -0.13478 0.039000 -0.0001601 -0.01243 0.01620 -0.02512
D2W -0.05436 -0.004211 -0.1337934 -0.22111 -0.28460 0.19936
D4N 0.04743 -0.095968 -0.1891478 0.08302 0.18306 0.09654
D4S -0.10152 0.011007 -0.0243409 0.05661 0.12162 -0.03389
D4E -0.13543 0.035367 0.0131894 0.05059 0.10763 -0.06359
D4W -0.13543 0.035367 0.0131894 0.05059 0.10763 -0.06359
I would appreciate any help in understanding why I am not given an output.
I also tried turning OFF the "Buffered output" option in Menu/Misc in
Windows.
Thanks!
Carolina
2012/2/5 carolina monmany <[email protected]>
> That was the mistake. Now it worked. Thanks a lot, Roman and Olmo and
> thanks for the recommendation on the code editor!
>
> Carolina
>
>
> 2012/2/5 Olmo <[email protected]>
>
>> Hi Carolina, it could be a syntaxis ommition indeed, I see a space
>> that I think it must not be there, between < and the minus - ,
>> (probably = is simpler but I use <- too):
>>
>> > step.forward < - ordistep(rda(main ~ 1, data=second),
>> scope=formula(RDA.all), direction="forward", pstep=1000)
>>
>> > step.forward <- ordistep(rda(main ~ 1, data=second),
>> scope=formula(RDA.all), direction="forward", pstep=1000)
>>
>> Check that, just in case.
>>
>> Hope this helps,
>> Olmo.
>>
>>
>> El Sat, 4 Feb 2012 15:03:08 -0400
>> carolina monmany <[email protected]> escribió:
>> > Dear all,
>> >
>> > I am running a redundancy analysis in vegan and I am using ordistep to
>> > perform a forward selection of variables in my model. I'm following
>> > Borcard et al. (2011) for this. I got stuck in one of the steps and
>> > couldn't find out why.
>> >
>> > > RDA.all <- rda(main ~ ., data=second)
>> > > RDA.all
>> > Call: rda(formula = main ~ MeanAsp + SDAsp + MenaSlo + SDSlo + Urban +
>> > Treelines + TreeGroups +
>> > SolTress + IntermGrass + TallGrass + Highways + Canals + DistDCA +
>> > MeanTrackDens + SDTrackDens +
>> > MeanMagnetism, data = second)
>> >
>> > Inertia Proportion Rank
>> > Total 0.005999 1.000000
>> > Constrained 0.005999 1.000000 9
>> > Unconstrained 0.000000 0.000000 0
>> > 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
>> > 4.421e-03 1.406e-03 8.930e-05 5.354e-05 1.413e-05 8.836e-06 4.612e-06
>> > 1.324e-06 3.500e-07
>> >
>> > # And here's the problem,
>> >
>> > > step.forward < - ordistep(rda(main ~ 1, data=second),
>> > scope=formula(RDA.all), direction="forward", pstep=1000)
>> > Error: object 'step.forward' not found
>> >
>> > I hope it's a syntaxis ommition or error. Any clue?
>> >
>> > Thanks a lot,
>> >
>> > Carolina
>> >
>>
>>
>> _______________________________________________
>> R-sig-ecology mailing list
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>>
>
>
>
> --
> ---------------------------
> A. CAROLINA MONMANY
> Universidad de Puerto Rico
> Departamento de Biologia - CN 235
> POBOX 23360
> San Juan, Puerto Rico 00931-3360
> Tel: +1 787 764 0000 x2847
> Fax: +1 787 764 2610
>
--
---------------------------
A. CAROLINA MONMANY
Universidad de Puerto Rico
Departamento de Biologia - CN 235
POBOX 23360
San Juan, Puerto Rico 00931-3360
Tel: +1 787 764 0000 x2847
Fax: +1 787 764 2610
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