[R-sig-phylo] write.caic()

Chris Mcowen cm744 at st-andrews.ac.uk
Fri Feb 12 14:41:35 CET 2010


Hi,

I am looking to use the software macrocaic on my old mac. However to do this i need to transform my phylogeny (soon to be 1500spc) into a CAIC phylogeny. 

I have tried the write.caic() function in ape as i have been advises this has worked in the past.

The structure of my tree seems fine:

str(tree) 

List of 4
$ edge       : int [1:1052, 1:2] 528 529 530 531 532 532 531 533 533 530 ...
$ Nnode      : int 526
$ tip.label  : chr [1:527] "Acis_autumnalis" "Cyrtanthus_breviflorus" "Galanthus_nivalis" "Crinum_acaule" ...
$ edge.length: num [1:1052] 226 585 222 84 40 ...
- attr(*, "class")= chr "phylo"
Chris Mcowen

But using the write.caic function returns this - 

Error in caic.label(phy, action = "insert", charset) : 
 'phy' not of class 'phylo'

I have also tried the following

> write.caic(new2old.phylo(tree))
> Error in vector("character", length) : invalid 'length' argument

> and

> write.caic(old2new.phylo(tree))
> Error in paste(filebase, ".blen", sep = "") : 
>  argument "filebase" is missing, with no default

I was wondering if anybody else has had this problem or knows a work around?

Thanks



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