[R-sig-eco] reorder vegdist objects

[Bede-Fazekas Ákos]

Dear Gian,
I'm not a statistician but software developer... hope that other members 
of the mailing list are expert of distance matrices and can answer your 
question.
Have a nice week,
Ákos

2019.06.03. 17:44 keltezéssel, Gian Maria Niccolò Benucci írta:
> Hi Akos,
>
> Thank you for the code. It worked. I reordered the dist objects as I 
> cannot access the dataset of one of the two distance matrix.
>
> > dist_b_reordered <- as.dist(as.matrix(dist_b)[attr(dist_a, 
> "Labels"), attr(dist_a, "Labels")])
> > all.equal(dist_a, dist_b_reordered, check.attributes = FALSE)
> [1] "Mean relative difference: 0.8977224"
>
> There is any statistical test that you suggest to compare the two 
> distances? I would like to see if the two matrices show a similar 
> pattern, e.g. mantel test?
>
> Thanks,
>
> Gian
>
>
>
>
>
>
> On Sat, 1 Jun 2019 at 00:55, Bede-Fazekas Ákos <bfalevlist using gmail.com 
> <mailto:bfalevlist using gmail.com>> wrote:
>
>     Dear Gian,
>     Let's do a small reproducible example:
>     library(vegan)
>     data(varespec)
>     set.seed(12345)
>     df_a <- t(varespec)
>     df_b <- t(varespec[, sample.int
>     <http://sample.int>(ncol(varespec))]) # shuffle the original
>     column order
>     dist_a <- vegdist(df_a); dist_b <- vegdist(df_b)
>     all.equal(dist_a, dist_b, check.attributes = FALSE)
>
>     Now, you have two options. If you have access to the original
>     data.frame/matrix from which the dist object was created, you can
>     reorder the rows of the second dataset to match that of the first
>     one.
>     Then do the distance matrix calculation again.
>     df_b_reordered <- df_b[rownames(df_a), ]
>     dist_b_reordered1 <- vegdist(df_b_reordered)
>     all.equal(dist_a, dist_b_reordered1, check.attributes = FALSE)
>
>     If you have no access to the original dataset and/or can not
>     recalculate
>     the distance matrix (e.g. due to computer capacity or time), you can
>     reorder the distance matrix (both the rows and columns).
>     dist_b_reordered2 <- as.dist(as.matrix(dist_b)[attr(dist_a,
>     "Labels"),
>     attr(dist_a, "Labels")])
>     all.equal(dist_a, dist_b_reordered2, check.attributes = FALSE)
>
>     HTH,
>     Ákos Bede-Fazekas
>     Hungarian Academy of Sciences
>
>
>     2019.06.01. 1:53 keltezéssel, Gian Maria Niccolò Benucci írta:
>     > Hello,
>     >
>     > I have two vegan::vegdist objects I want to use into a
>     vegan::mantel test.
>     > However, rows and columns of the two objects are not in the same
>     order. Is
>     > there a way to reorder them one another?
>     >
>     > For example,
>     >
>     >> dist_a
>     >          Lycovolu  Hupeaust  Lycofast  Lycodeut
>     > Hupeaust 0.9045557
>     >
>     > Lycofast 0.6835441 0.8569781
>     >
>     > Lycodeut 0.8036577 0.8294657 0.7958988   ...
>     > ...
>     >
>     >> dist_b
>     >           Lycodeut   Lycofast   Lycoscar   Lycovolu
>     > Lycofast 0.09340659
>     >
>     > Lycoscar 0.08974359 0.01831502
>     >
>     > Lycovolu 0.09073476 0.01099655 0.01008080   ...
>     > ...
>     >
>     > Thanks,
>     >
>
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