[adegenet-forum] Cross validation using xvalDapc

Kirsty Medcalf kirsty.m.medcalf at gmail.com
Tue Sep 29 18:44:08 CEST 2015


I am attempting to cross validate my results from DAPC analysis with a 70 %
training set using the function xvalDapc (code below).  My data frame is
called LDA.scores. this is an updated version of a previous post after
taking into account the recommendationsbut I am still outputting the same
error message.  Do I have to change my data frame into a list? If so, what
would be the correct format to transform the data frame into this format.
If this is possible, I was wondering if anyone had a solution with how to
solve this error message (below).  I have looked online and through
available tutorials and still cannot solve this issue.  Words cannot
describe my gratitude if this is possible.

 #Permute the data



   grp1<-find.clusters(x, max.n.clust=12)
   dapc1<-dapc(x, grp1$grp)

#DAPC analysis

windows(width=10, height=7)
grp1<-find.clusters(x, max.n.clust=12)
dapc1<-dapc(x, grp1$grp)

#Loadings plot

contrib <- loadingplot(dapc1$var.contr, axis=2,
                       thres=.07, lab.jitter=1)

#Cross Validation
windows(width=10, height=7)
x1 <- LDA.scores
xval <- xvalDapc(x1, grp1, n.pca.max = 2, training.set = 0.7,
                 result = "groupMean", center = TRUE, scale = FALSE,
                 n.pca = NULL, n.rep = 30, xval.plot = TRUE)

Error in sort.list(y) : 'x' must be atomic for 'sort.list'
Have you called 'sort' on a list?

During the DAPC analysis,  I chose to retain 2 PCs and 2 LD's, and there
appears to be 3 clusters. Would n.pca.max=2 be correct?

My reproducible data, the logical steps that I took to chose the number of
PC's and LD's to retain,  and the number of chosen clusters is available on
stack overflow


If it is possible to help me, then thank you

Best wishes,
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