Hi Andrew, Yes, you cannot have NA values in your matrices. Instead, you could incorporate a model matrix.
See Legendre, P. & Fortin, M.J. Vegetatio (1989) 80: 107. https://doi.org/10.1007/BF00048036 for ideas. Sarah On Sun, Dec 31, 2017 at 12:55 PM, Andrew Marx <andrewjm...@gmail.com> wrote: > I'm trying to perform a mantel test that ignores specific pairs in my > distance matrices. The reasoning is that some geographic distances > below a certain threshold suffer from spatial autocorrelation, or > perhaps ecological relationships become less relevant that stochastic > processes above a certain threshold. > > The problem is that I can't find a way to do it. If I replace values > in either or both of the distance matrices with NA, mantel.rtest (ade4 > package) gives the following error: Error in if (any(distmat < tol)) > warning("Zero distance(s)") : missing value where TRUE/FALSE needed > > Here's a trivial example that tries to exclude elements of the first > matrix that equal 11: > > library(ade4) > a <- matrix(data = 1:36, nrow = 6) > b <- matrix(data = 1:36, nrow = 6) > a[a==11] <- NA > mantel.rtest(as.dist(a), as.dist(b)) > > Is there a way to do this, either with this package or another? > -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
