R help - Mar 2013 - Difficulty in caper: Error in phy$node.label[which(newNb > 0) - Ntip]

Hello,

I'm doing a comparative analysis of mammal brain and body size data.
I'm following Charlie Nunn and Natalie Cooper's instructions for
"Running PGLS in R using caper".

I run into the following error when I create my comparative dataset,
combining my phylogenetic tree (mammaltree) and taxon measures
(mammaldata):

"Error in phy$node.label[which(newNb > 0) - Ntip] : only 0's may be
mixed with negative subscripts"

My full script is provided at the bottom.

I have looked at the caper manual by David Orme to understand how
comparative.data() constructs the dataset, but still cannot interpret
the error. Many thanks to anyone who could provide me with insight.

Nicole Thompson
E3B Columbia University


> library(caper)
Loading required package: ape

Loading required package: MASS

Loading required package: mvtnorm
>
> mammaldata <-read.csv("R.Mammal_data.csv", header = TRUE)
> mammaltree <-read.nexus("BEphylotree.nex")
> mammal <- comparative.data(phy = mammaltree, data = mammaldata,
names.col = Taxon, vcv = TRUE, na.omit = FALSE, warn.dropped = TRUE) #names.col?
Error in phy$node.label[which(newNb > 0) - Ntip] : only 0's may be
mixed with negative subscripts





--
Nicole A Thompson
E3B Columbia University, NYCEP
nat2103 at columbia.edu
480.522.4212

On 2013-03-06 07:49, Nicole Thompson wrote:
> Hello,
>
> I'm doing a comparative analysis of mammal brain and body size data.
> I'm following Charlie Nunn and Natalie Cooper's instructions for
> "Running PGLS in R using caper".
>
> I run into the following error when I create my comparative dataset,
> combining my phylogenetic tree (mammaltree) and taxon measures
> (mammaldata):
>
> "Error in phy$node.label[which(newNb > 0) - Ntip] : only 0's
may be
> mixed with negative subscripts"
>
> My full script is provided at the bottom.
>
> I have looked at the caper manual by David Orme to understand how
> comparative.data() constructs the dataset, but still cannot interpret
> the error. Many thanks to anyone who could provide me with insight.
>
> Nicole Thompson
> E3B Columbia University
>
>
>
>> library(caper)
>
> Loading required package: ape
>
> Loading required package: MASS
>
> Loading required package: mvtnorm
>
>>
>
>> mammaldata <-read.csv("R.Mammal_data.csv", header = TRUE)
>
>> mammaltree <-read.nexus("BEphylotree.nex")
>
>> mammal <- comparative.data(phy = mammaltree, data = mammaldata,
names.col = Taxon, vcv = TRUE, na.omit = FALSE, warn.dropped = TRUE) #names.col?
>
> Error in phy$node.label[which(newNb > 0) - Ntip] : only 0's may be
> mixed with negative subscripts
Looks to me like 'which(newNb > 0) - Ntip' evaluates to a
vector that has both positive and negative elements.
Like this:

   x <- 1:5
   x[c(-2,-4)] ## ok
   x[c(-2, 0)] ## ok
   x[c(-2, 4)] ## generates your error

Peter Ehlers
>
>
>
>
>
> --
> Nicole A Thompson
> E3B Columbia University, NYCEP
> nat2103 at columbia.edu
> 480.522.4212
>