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

Roman Lustrik roman.lustrik at biolitika.si
Mon Jun 8 12:25:29 CEST 2015

```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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