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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