r - How to do a Mantel test (in VEGAN package) between geography and genetics WHILE leaving out specific observations? -


i wish carry out mantel test between matrix of geographical distances in kilometers (matrix 1) , corresponding matrix of bray-curtis distances in leave out values 0 geographical distance. (a distance of 0 km represent neighbouring samples not identical , should not pooled, not wholly independent of 1 either). therefore, wish keep them in analysis.

the simple mantel test easy: read in geographical matrix using basic 

    my_geodist_matrix <-read.table("my_geodist_matrix.txt",header=true,row.names=1)

the matrix looks this:

        1top    1bottom 2top    2bottom 3top    3bottom     1top    0   0   20.72   20.72   127.5   127.5     1bottom 0   0   20.72   20.72   127.5   127.5     2top    20.72   20.72   0   0   148.137 148.137     2bottom 20.72   20.72   0   0   148.137 148.137     3top    127.5   127.5   148.137 148.137 0   0     3bottom 127.5   127.5   148.137 148.137 0   0

then, calculate bc distances (using vegan package) thus:

    my_otu_table.dist<-vegdist(my_otu_table,method="bray")

(looks this):

        1top    1bottom 2top    2bottom 3top 1bottom 0.8341957   2top 0.9948253 0.9908943      2bottom 0.9919492    0.9853757   0.4667466     3top    0.9482715    0.6923454 0.9926684 0.9882600                                                                                                                                                                                                                                                                                                                                                 3bottom  0.9463127   0.6581957   0.9901074   0.9843602    0.1683397

and simple mantel test 

    mantel(my_geodist_matrix ,my_otu_table.dist)

so far, no trouble @ all. however, when try leave out pairs 0 in geographical matrix , corresponding bray-curtis values, goes wrong.

    my_geodist_matrix <- lapply(my_geodist_matrix, function(x){replace(x, x == 0, na)})

and

    my_ otu_table.dist[is.na(my_geodist_matrix)] <- na

when mantel test now, r gives following error messages:

    error in as.data.frame.default(x[[i]], optional = true) :        cannot coerce class ""dist"" data.frame

or 

    error in cor(as.vector(xdis), ydis, method = method, use = use) :        missing observations in cov/cor

how do desired comparison best way (and correctly!)?


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