biplot question: "Error in 1L:n : argument of length 0"
Use the `plot()` method provided by vegan. You won't get biplots from an NMDS as the method throws away the species data to when convert the data to dissimilarities before generating the k-d mapping. vegan allows species scores to be added (as the weighted averages of the site scores) if the raw data was given to metaMDS(), but these and the site scores don't form a traditional biplot if you mean that term specifically. G
On 29 July 2015 at 10:36, Michael Marsh <swamp at blarg.net> wrote:
I am trying to obtain biplots of NMDS results, ideally like the rpart.pca() result with mvpart. Can someone easily tell me why I get this error: Error in 1L:n : argument of length 0 from this script, and graphical output (below) lacking labels for either sites or species? x and y matrices are shown below script. modifying "y" by removing NaN rows did not change output. Thanks!, Mike Marsh swamp at blarg.net ---------------------- Q.wd<-as.data.frame(read.table(file.choose(),header=T))
#text dataset is Q.WD.foliar.revised.txt
library(vegan) Q09shrub.min<-vegtab(Q09shrub,min=2) Q09shrub.std<-decostand(Q09shrub.min, method="max") Q09shrub.dist<- dist(Q09shrub.std) Q09shrub.ward<-hclust(Q09shrub.dist,method="ward",members=NULL) NMDS.Q09shrub<-metaMDS(Q09shrub)
Wisconsin double standardization Run 0 stress 0.08176961 Run 1 stress 0.1011811 Run 2 stress 0.07507627 ... New best solution ... procrustes: rmse 0.04824229 max resid 0.1222105 Run 3 stress 0.1011877 Run 4 stress 0.07507602 ... New best solution ... procrustes: rmse 0.0001471213 max resid 0.0002974951 *** Solution reached
x<-plot(NMDS.Q09shrub, "sites") y<-plot(NMDS.Q09shrub, "species") biplot(x,y)
Error in 1L:n : argument of length 0
ordicluster(NMDS.Q09shrub, Q09shrub.ward) x
$sites
NMDS1 NMDS2
9Q05-ST -0.7781618 -0.05087985
9Q06-VS 0.6462465 -0.41377399
9Q12-ST -0.3126179 -0.80107514
9Q15ECS -0.8780461 0.20632944
9Q15WST -0.7672079 0.88777750
9Q16-VS 0.8652229 0.56684307
9Q19-ST 0.1374252 -0.41322443
9Q24-ST 0.3140148 -0.12115606
9Q26-ST -1.0044059 -0.15339828
9Q29-DS 0.9608797 0.35394121
9Q33-VS 0.8166505 -0.06138349
$species
NULL
attr(,"class")
[1] "ordiplot"
y
$sites
NULL
$species
NMDS1 NMDS2
ACMA3 NaN NaN
AMAL2 -0.05672919 -0.81171544
ARRI2 0.84801299 0.24651319
ARTR2 -0.93597835 0.02417604
ARTR4 -1.01337771 -0.05343535
GRSP NaN NaN
CHVI8 -0.74187745 -0.02949452
ERBL2 NaN NaN
ERNA10 -0.61157997 0.47464632
NEST5 0.87499085 -0.04070596
PREM -0.90401815 1.25730322
PRVI NaN NaN
PUTR2 0.16079095 -0.36676073
RICE -0.35775047 -0.46386377
ROWO NaN NaN
SYAL2 NaN NaN
SYOR2 -0.36836460 -1.13451214
attr(,"class")
[1] "ordiplot"
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