[R] Using the mantel test in Ape Package
sarah.goslee at gmail.com
Thu Mar 15 00:32:47 CET 2012
On Wed, Mar 14, 2012 at 2:21 PM, Dorothea Hill
<dorothea.hill at zoo.ox.ac.uk> wrote:
> I am trying to use a mantel test on two distance matrices. The code I have entered for each is:
> Gen_dists <- read.csv(file.choose(),
> stringsAsFactors = FALSE,
> na.strings = c(" "),
> fill = T,
> header = FALSE,
> blank.lines.skip = FALSE)
> Gen_matrix <- as.matrix(Gen_dists)
> mantel.test(Geo_matrix, Gen_matrix, nperm = 999, graph = T, alternative = "great")
> I am getting a result but with lots of warning messages :
> "Warning: non-square matrix"
> However, my matrices are square!
Not according to R. Somewhere in the import or modification steps they
have become unsquare. Since you provide neither a reproducible example
nor any description of your matrices -- str() and dim() seem
particularly relevant -- we can't possibly tell you where.
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