reorder vegdist objects

dist_b_reordered <- as.dist(as.matrix(dist_b)[attr(dist_a, "Labels"),

all.equal(dist_a, dist_b_reordered, check.attributes = FALSE)

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(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,
?kos Bede-Fazekas
Hungarian Academy of Sciences


2019.06.01. 1:53 keltez?ssel, Gian Maria Niccol? Benucci ?rta:

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,