I am using
mantel in R package Ecodist to perform a series of partial mantel tests. I am examining the correlation between a species composition (Bray-curtis dissimilarity) matrix and a series of environmental and spatial (UTM) variables (as separate euclidean distance matrices).
The structure of the mantel equation is:
mantel(spp.dist ~ x.dist + a.dist + b.dist + .... + geo.dist, nperm=10000, nboot=500)
spp.dist = the species dissimilarity matrix;
x.dist is an environmental variable of interest;
... are all other environmental variables; and
geo.dist = dissimilarity matrix of UTMN & UTME.
x.dist cycles between all other env variables to determine it's contribution to the pattern of correlation.
nboot set number of permutations and iterations for bootstrapping to use, respectively.
Here is an example of output (modified slightly from actual data):
plot Year position pH mantelr 0.03960184 0.000806223 -0.02970148 -0.009351586 pval1 0.0001 0.4534 0.9977 0.6981 pval2 1 0.5467 0.0024 0.302 pval3 0.0001 0.9407 0.0144 0.5925 llim.2.5% 0.03393448 -0.007369118 -0.03699412 -0.019564176 ulim.97.5% 0.04652775 0.008779442 -0.02203297 0.001134167
The R-help link included states:
mantelr = Mantel coefficient. pval1 = one-tailed p-value (null hypothesis: r <= 0). pval2 = one-tailed p-value (null hypothesis: r >= 0). pval3 = two-tailed p-value (null hypothesis: r = 0). llim = lower confidence limit. ulim = upper confidence limit.
So I understand that the mantel r is essentially the correlation between the
spp.dist matrix and each variable after having controlled for all other variables. But 2 questions I'm unsure about:
1. How do I interpret negative mantel r values?
2. Do I pay more attention to the one or two tail p-value? which should I report?