Thank you very much, I’ll try that!
> On Nov 5, 2019, at 2:20 PM, Liam Revell <liam.rev...@umb.edu> wrote:
>
> Hi Elizabeth.
>
> This does not do exactly what you want, but it is possible to use
> capture.output() to grab the printout of checkValidPhylo() and then
> grep() to see if it contains instances of "MODERATE" or "FATAL" errors.
>
> The following simple function does that. It returns 0 if neither
> MODERATE nor FATAL errors are detected in the "phylo" object, 1 if at
> least one MODERATE error (but no FATAL errors) is detected, and 2 if any
> FATAL errors are detected:
>
> chk.phylo<-function(x){
> object<-capture.output(checkValidPhylo(x))
> if(length(grep("FATAL",object))>0) return(2)
> else if(length(grep("MODERATE",object))>0) return(1)
> else return(0)
> }
>
> E.g.:
>
> library(ape)
>
> t1<-rtree(n=10)
>
> chk.phylo(t1) ## should return 0
>
> t2<-t1
> t2$Nnode<-9.5
>
> chk.phylo(t2) ## should return 1
>
> t3<-t1
> t3$edge<-t3$edge[-4,]
>
> chk.phylo(t3) ## should return 2
>
> All the best, Liam
>
> Liam J. Revell
> Associate Professor, University of Massachusetts Boston
> Profesor Asistente, Universidad Católica de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>
> Academic Director UMass Boston Chile Abroad (starting 2019):
> https://www.umb.edu/academics/caps/international/biology_chile
>
> On 11/5/2019 5:54 PM, Elizabeth Purdom wrote:
>> [EXTERNAL SENDER]
>>
>> Hello,
>>
>> I am working with the phylo object from the ape package in my own package in
>> which I am manipulating the trees. I would like to check that I have
>> successfully created a valid ape object, but the `checkValidPhylo` function
>> appears to be solely interactive — it prints out a display, and always
>> returns NULL.
>>
>> Is there a function in the ape package (or can there be?) that would do the
>> checks, but return the results in a way that I can then process in my
>> function? (e.g. return a vector of each of the checks as TRUE/FALSE) And I
>> don’t want anything printed out, since I don’t want that output to be
>> printed for users of my function).
>>
>> I see the package `paleotree` has ported some of those checks into a test,
>> so I’m guessing such a function doesn’t exist in ape — and I don’t really
>> want a dependency on another package just for these checks.
>>
>> Thanks,
>> Elizabeth Purdom
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