Re: [R-sig-phylo] Disagreement between "length" of data and "length" of phylogeny

[Eduardo Ascarrunz]

Hi,

It's not clear from your code how are you using `fixdata` in your
analysis. Is `SWSPeak` a vector you are extracting from the `fixdata`
table? Could it be that you still have the old (w/o species removed)
`SWSPeak` in memory from a previous session?

Best,

E.

On 5 January 2016 at 07:50, Michael Pauers  wrote:
> Dear List,
>
> I am having some difficulties calculating phylogenetic independent
> contrasts on a multiPhylo object using APE.  When I attempt to calculate a
> contrast, the following error message appears (preceded by the code I am
> using to calculate the PIC):
>
>> fixtree <- read.nexus("fixeddatatrees.nex")
>> fixdata <- read.table("newfix.txt")
>> PIC.SWSPeak <- mapply(pic, list(SWSPeak), fixtree)
> Error in (function (x, phy, scaled = TRUE, var.contrasts = FALSE,
> rescaled.tree = FALSE)  :
>   length of phenotypic and of phylogenetic data do not match
>
> I know that both the phylogenies ("fixeddatatrees.nex") and the phenotypic
> dataset ("newfix.txt") contain the same number of taxa (21).  However, when
> I ask APE for the length of the data, it tells me the following:
>
>> length(SWSPeak)
> [1] 39
>
> This is somewhat meaningful, as this particular analysis is restricted to a
> subset of my original group, which contained 39 species.  From my original
> phyloeny, then, I pruned the unnecessary 18 species, and also deleted them
> from the phenotypic dataset.  Could it be the case that there is some sort
> of artefact in either of these files that is left over from their "parent"
> files?  I should note that my analyses, also PICs, on the original tree and
> data went perfectly and without any error message.
>
> Thanks in advance for whatever help you can offer.
>
> Best,
>
> Mike Pauers
>
> [[alternative HTML version deleted]]
>
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[R-sig-phylo] Disagreement between "length" of data and "length" of phylogeny

[Michael Pauers]

Dear List,

I am having some difficulties calculating phylogenetic independent
contrasts on a multiPhylo object using APE.  When I attempt to calculate a
contrast, the following error message appears (preceded by the code I am
using to calculate the PIC):

> fixtree <- read.nexus("fixeddatatrees.nex")
> fixdata <- read.table("newfix.txt")
> PIC.SWSPeak <- mapply(pic, list(SWSPeak), fixtree)
Error in (function (x, phy, scaled = TRUE, var.contrasts = FALSE,
rescaled.tree = FALSE)  :
  length of phenotypic and of phylogenetic data do not match

I know that both the phylogenies ("fixeddatatrees.nex") and the phenotypic
dataset ("newfix.txt") contain the same number of taxa (21).  However, when
I ask APE for the length of the data, it tells me the following:

> length(SWSPeak)
[1] 39

This is somewhat meaningful, as this particular analysis is restricted to a
subset of my original group, which contained 39 species.  From my original
phyloeny, then, I pruned the unnecessary 18 species, and also deleted them
from the phenotypic dataset.  Could it be the case that there is some sort
of artefact in either of these files that is left over from their "parent"
files?  I should note that my analyses, also PICs, on the original tree and
data went perfectly and without any error message.

Thanks in advance for whatever help you can offer.

Best,

Mike Pauers

[[alternative HTML version deleted]]

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