[adegenet-forum] Cross validation using xvalDapc

[Roman Lustrik]

Hi, 

can you make your example reproducible (simulate some data)? 

As for the n.pca.max argument. PCA is a dimension reduction technique. Which means it tries to present data of N variables (columns) as as few principal components as possible. If you think of a 3D cloud shaped like a sphere (3 variables describe this, call them x, y and z), PCA will try to show you the data in 2D (two principal components, call them PC1 and PC2). What you expect to see is a circle which explains most of the variation, since circle is quite good approximation of a sphere. If you add data from PC3, you get a sphere again (and all variation explained). 

Retaining all components is not practical so the function will retain only `n.pca.max` components. 

Cheers, 
Roman 

---- 
In god we trust, all others bring data. 

----- Original Message -----

From: "Kirsty Medcalf" <kirsty.m.medcalf at gmail.com> 
To: adegenet-forum at lists.r-forge.r-project.org 
Sent: Monday, September 28, 2015 4:44:06 AM 
Subject: [adegenet-forum] Cross validation using xvalDapc 

Hi 

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. If this is possible, I was wondering if anyone had a solution to this error message (below). I have looked online and through available tutorials and still cannot 
solve this issue. 

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

Also, I have confusion regarding the argument n.pca.max. My data frame has two grouping dependent factors, 12 predictor values and 80 observations. Would n.pca.max=80 be correct? 

If it is possible to help me, then thank you 

Best wishes, 
Kirsty 

CODE 

#Permute the data 
set.seed(999) 

#DAPC analysis 

windows(width=10, height=7) 
x<-LDA.scores[,2:13] 
grp1<-find.clusters(x, max.n.clust=12) 
dapc1<-dapc(x, grp1$grp) 
dapc1 

windows(width=10, height=7) 
x1 <- LDA.scores 
mat <- as.matrix(x1, method="mean") 
grp2 <- x1 
xval <- xvalDapc(mat, grp2, n.pca.max = 80, 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? 


Kirsty Medcalf 
kirsty.m.medcalf at gmail.com 
+447963374030 
skype contact: kirsty.medcalf 

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