[R] problem with vegan function rda()

Tue Nov 11 15:58:41 CET 2014

Hello R-list

Maybe someone knows what's going on here.

I'm trying to re-run a script I wrote earlier this year using the function
rda() in the vegan package. The script run fine back then, and I did not
change the dataset, so I was wandering whether there's some problem in a
updated version of the package (I re-installed R + all packages since then).

Thanks for any advice,
Lukas Kohl

--

So here's the output I get:

> rda(rel)
Call:
rda(X = rel)

Regularization parameters:
NULL

Prior probabilities of groups:
NULL

Misclassification rate:
       apparent:  %
Warning message:
In is.na(x$error.rate[1]) :
  is.na() applied to non-(list or vector) of type 'NULL'

There's no NA's in my dataset, which seems ok..

> sum(is.na(rel))
[1] 0
> nrow(rel)
[1] 59
> ncol(rel)
[1] 49
> head(rel)
      X14.0   i.15.0  ai.15.0    br.16.0      X15.1    n.15.0    i.16.0
br.17.0
1 0.8409636 2.758547 1.925111 0.00000000 0.03878272 0.8658653 1.2627433
0.00000000
2 0.8631263 2.999573 2.068838 0.00000000 0.04781487 0.9281469 1.2124018
0.01814870
3 1.1698988 4.017031 2.475490 0.00000000 0.06475970 0.8345328 1.8643781
0.04102243
4 1.1189279 3.543764 2.385878 0.00000000 0.04980440 0.7698666 1.7861071
0.03490974
5 1.2324211 2.017189 1.484382 0.02462469 0.03719938 0.8285019 1.1649025
0.00000000
6 1.1275200 1.984574 1.417046 0.00000000 0.02461027 0.7751023 0.7736307
0.01144489
     X16.0 X2.1.16.1a X10.Me.16.0 X2.3.16.1b     X2.4a X2.4.16.1w7
X2.5.i.17.0_
1 16.74626  0.4417955   1.0486484  0.3216925 0.4034028    4.357194
0.5073206
2 16.77015  0.4702506   1.1215379  0.3326751 0.3719471    4.753351
0.5005562
3 16.89350  0.7087030   2.5427811  0.3788973 0.4233197    4.578289
0.5389445
4 17.21581  0.6239133   2.5463528  0.3439109 0.4152840    4.537743
0.4928171
5 18.34007  0.2722663   0.8365801  0.1955707 0.4530307    3.462293
0.2493175
6 18.42559  0.2618034   0.8100510  0.1946894 0.4464420    3.396504
0.2508381
    X16.1c br.17.0.1    br17.1 X10.Me17.0   cy17.0    X18.0        X0
X18.1w9t._
1 1.342751  2.883930 0.5117392  0.3985677 2.214624 4.429970 0.1811544
0.1680561
2 1.456768  2.817626 0.7262325  0.3552404 2.370162 3.419123 0.4533272
0.1274811
3 1.819283  3.597939 0.7856195  0.6546772 2.029322 3.375979 0.3780399
0.1366054
4 1.748514  3.893054 0.7656742  0.5506949 2.114840 3.604125 0.3286007
0.2314595
5 1.041661  3.516501 0.3611086  0.2074937 1.722343 3.698022 0.1720278
0.1276793
6 1.008310  3.589629 0.3439892  0.2085050 1.788364 3.858083 0.0000000
0.1268165
   br19.0._ X18.1w9c   X18.1b    X18.1c    X18.2a X18.2w6.9 X18.3w6.9.12
cy.19.0
1 0.4214627 11.88366 7.042868 0.7785622 0.5296606  20.75001    0.3747013
0.1845085
2 0.3655930 12.00201 7.117161 0.7833297 0.2148572  21.92248    0.4152870
0.1879331
3 0.2086673 13.43202 6.233585 1.1172938 0.5660451  14.61465    0.4775747
0.2788579
4 0.2348959 13.74445 6.138005 1.0161645 0.2209565  15.53226    0.4344465
0.2116109
5 0.1659439 14.24557 5.240076 0.7881302 0.1541940  23.97948    0.5682993
0.1642502
6 0.1609455 14.29624 5.137798 0.7543159 0.2945796  24.54077    0.5711625
0.1318383
  cy.19.0.1      X0.1 X18.3w3.6.9     X20.0       X0.2     X18.2b
X21.0     X20.2
1  3.896800 0.1349484    3.392245 0.7221273 0.14947364 0.04188258 0.1495564
0.4198097
2  3.974945 0.1426084    3.216271 0.5750869 0.12714397 0.08999512 0.1339824
0.2883602
3  5.044190 0.3689036    2.116062 0.8468635 0.08036104 0.07226680 0.1390747
0.2504645
4  4.324061 0.3253495    2.270108 0.8674106 0.09904184 0.05582051 0.1436902
0.1901801
5  3.534329 0.1266162    3.941966 0.7320950 0.15424966 0.14193815 0.1310820
0.1926944
6  3.547334 0.1062227    4.118720 0.7581633 0.12410799 0.11998844 0.1402905
0.1977357
     X20.3a    X20.3b X20.4w6.9.12.15     X22.0 X20.5w3.6.9.12.15
X0.3    X23.0_
1 0.4094126 0.2474286       1.1500272 1.1227407         0.9296417 0.2243854
0.2339230
2 0.4186328 0.2084205       0.8633682 0.8924207         0.5396120 0.1732975
0.1987064
3 0.4683385 0.1670621       0.7293349 1.3617136         0.3184905 0.1806325
0.2426850
4 0.4419191 0.1784320       0.7967968 1.4136308         0.2825521 0.1660992
0.2709302
5 0.4628079 0.1882448       0.7705750 1.1223705         0.2243516 0.1713259
0.2452253
6 0.4212344 0.1971018       0.7522184 1.1690829         0.1822425 0.0000000
0.2481156
      X24.0      X25.0 X22.6w3.6.9.12.15.18
1 0.9094009 0.08456623           0.16707761
2 0.7546380 0.06352018           0.14586538
3 1.1081230 0.08133338           0.18639182
4 1.2978036 0.11136199           0.12997539
5 0.9084890 0.09101005           0.10949849
6 1.0261733 0.10038159           0.07969927

here are the package versions.

> version
               _
platform       x86_64-pc-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status

major          3
minor          0.2
year           2013
month          09
day            25
svn rev        63987
language       R
version.string R version 3.0.2 (2013-09-25)
nickname       Frisbee Sailing

> citation('vegan')

To cite package ‘vegan’ in publications use:

  Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter
  R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H.
  Stevens and Helene Wagner (2013). vegan: Community Ecology Package. R
  package version 2.0-10. http://CRAN.R-project.org/package=vegan

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