The problem is that you haven't read the output from R! When you print 'RWA.all', one of the things it prints is:
> Some constraints were aliased because they were collinear (redundant) This means that some of the predictor variables in the data set are fully explained by one or more combinations of the the predictor variables. It is not possible to include them in the analysis hence only 9 RWA axes were fitted and hence why not all variables show up in the step output. HTH Gavin Sent from my HTC ----- Reply message ----- From: "carolina monmany" <[email protected]> Date: Sun, Feb 5, 2012 17:10 Subject: [R-sig-eco] vegan's ordistep function To: "[email protected]" <[email protected]> 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 >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> > > > > -- > --------------------------- > 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 [[alternative HTML version deleted]] [[alternative HTML version deleted]]
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