[adegenet-forum] Find the slope (R square) value for Mantel test

[Roman Lustrik]

All information from the test is available by calling list elements. Which list elements? See the object structure with function str().

library(ade4)

data(yanomama)
gen <- quasieuclid(as.dist(yanomama$gen))
geo <- quasieuclid(as.dist(yanomama$geo))
r1 <- mantel.rtest(geo,gen)

str(r1)

List of 5
 $ sim   : num [1:99] -0.152 0.272 0.128 -0.198 -0.259 ...
 $ obs   : num 0.51
 $ rep   : int 99
 $ pvalue: num 0.01
 $ call  : language mantel.rtest(m1 = geo, m2 = gen)
 - attr(*, "class")= chr "rtest"


If you want pvalue, you would say r1$pvalue. Can you explain where R square/coefficient of determination come from in this test?

Cheers,
Roman

----
In god we trust, all others bring data.

----- Original Message -----
From: "Laura Benestan" <laura.benestan at icloud.com>
To: adegenet-forum at lists.r-forge.r-project.org
Sent: Friday, June 5, 2015 4:41:50 PM
Subject: [adegenet-forum] Find the slope (R square) value for Mantel test

Hi, 

I would like to extract the R square value (or determination coefficient) from the Mantel test.
How could I do it after obtaining results from this command:
ibd <- mantel.rtest(dist_geo, dist_fst, 10000)

Thanks,

Laura Benestan
PhD student
Institute of Integrative Biology and Systems (IBIS)
Laboratoire Louis Bernatchez 
Pavillon Charles- Eugène-Marchand
1030 Avenue of Medicine 
Université Laval
Quebec
G1V 0A6
Canada
418-265-7756
laura.benestan at icloud.com



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