Thank you Juan and Akos for all your help. It worked. Gian
On Mon, 3 Jun 2019 at 18:03, Juan Antonio Balbuena <j.a.balbu...@uv.es> wrote: > 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 <bfalevl...@gmail.com > > > <mailto:bfalevl...@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, > > > > > > > > > > _______________________________________________ > > > R-sig-ecology mailing list > > > R-sig-ecology@r-project.org <mailto:R-sig-ecology@r-project.org> > > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecolog > > > <https://stat.ethz.ch/mailman/listinfo/r-sig-ecology>y > > > > > > > > > > > > /----- Do not print this email unless you really need to. Save paper > > > and protect the environment! -----/ > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-ecology mailing list > > R-sig-ecology@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > > -- > -- > 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.balbu...@uv.es tel. +34 963 543 658 > +++++++++++++++++++++++++++++++++++++++++++++++++++ > NOTE! For shipments by EXPRESS COURIER use the > following street address: > C/ Catedrático José Beltrán 2, 46980 Paterna > (Valencia), Spain. > +++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- Gian Maria Niccolò Benucci, Ph.D. Michigan State University Department of Plant, Soil and Microbial Sciences 1066 Bogue Street 48825 East Lansing, MI Lab: +1 (517) 844-6966 Email: gian.benu...@gmail.com *----- Do not print this email unless you really need to. Save paper and protect the environment! -----* [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
