[R-sig-eco] reorder vegdist objects

[Juan Antonio Balbuena]

Hi Gian,
A Mantel test looks right for your problem. Check also protest in vegan.
Best,

Juan A. Balbuena

> 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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> >
> >
> >
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Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary
Biology
University of Valencia
P.O. Box 22085
46071 Valencia, Spain
e-mail: j.a.balbuena using uv.es    tel. +34 963 543 658
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