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 <mjpau...@gmail.com> 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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