Please also reply to the list, not just to me.
Unfortunately, I still don't get it. Can you show what you want the *final*
matrix to look like for this specific example?
Best,
Wolfgang
>-Original Message-
>From: Jarrett Phillips [mailto:phillipsjarre...@gmail.com]
>Sent: Sunday, 05 February, 2023 18:30
>To: Viechtbauer, Wolfgang (NP)
>Subject: Re: [R-sig-phylo] Generating a matrix of interspecfic genetic
>distances
>
>Thanks Wolfgang,
>
>‘dists’ contains both intraspecific and interspecific comparisons. The ‘inter’
>variable extracts interspecific values from ‘dists’, but returns a vector
>instead
>of a matrix.
>
>I’m wondering how (if it is possible) I can return ‘inter’ as a matrix. The
>result likely will not be a square matrix, which is okay.
>
>As mentioned in my previous email, as.matrix(inter) simply returns a matrix
>with
>a single column, so destroys the block structure of matrices, and also drops
>relevant row and column names found in ‘dists’.
>
>‘res’ is used to return all elements of ‘dists’ except the main diagonal.
>
>If things are still unclear, please let me know.
>
>Cheers,
>
>Jarrett
>
>On Sun, Feb 5, 2023 at 6:10 AM Viechtbauer, Wolfgang (NP)
> wrote:
>Dear Jarrett,
>
>I am not sure what it is that you are trying to accomplish with the last two
>lines. Isn't 'dists' already what you want? If you just want to set the
>diagonal
>of 'dists' to NA, then 'diag(dists) <- NA' would do that. But maybe I am
>missing
>the point here entirely.
>
>Best,
>Wolfgang
>
>>-Original Message-
>>From: R-sig-phylo [mailto:r-sig-phylo-boun...@r-project.org] On Behalf Of
>Jarrett
>>Phillips
>>Sent: Sunday, 05 February, 2023 8:31
>>To: r-sig-phylo@r-project.org
>>Subject: [R-sig-phylo] Generating a matrix of interspecfic genetic distances
>>
>>Hi All,
>>
>>I am using the ape R package to extract interspecific distances from a
>>pairwise distance matrix.
>>
>>Consider the woodmouse example.
>>
>> library(ape)
>>
>> data(woodmouse)
>>
>> dists <- dist.dna(woodmouse, model = "raw", as.matrix = TRUE)
>> isSymmetric(dists) # TRUE
>> dists[upper.tri(dists, diag = FALSE)] <- NA # replace upper triangle
>>with NA and then subset to get lower triangular matrix
>> isSymmetric(dists) # FALSE
>> dists # this is a matrix
>>
>> labs <- labels(woodmouse) # get species names
>>
>> res <- outer(labs, labs, "==") # get cases where matrix elements are
>>equal
>> inter <- na.omit(dists[!res]) # get interspecific distances by taking
>>elements that are not equal
>>
>>The problem I am facing is that I need 'inter' to be a matrix instead of a
>>vector, so that I can tell which distances belong to which pairs of
>>specimens. The 'inter' matrix should have the same row and column names as
>>the 'dists' variable. Simply doing
>>
>> as.matrix(inter)
>>
>>will not suffice in this case since row names and column names are not
>>preserved.
>>
>>Once I have a matrix of only interspecific distances, I can then find
>>nearest neighbours for all species in my dataset and continue from there.
>>
>>I feel it is an easy solution, but something is just not clicking.
>>
>>Any ideas?
>>
>>Please let me know if anything is unclear.
>>
>>Thanks.
>>
>>Cheers,
>>
>>Jarrett
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