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Mantel test

Source: R/mantel_test.R
mantel_test.Rd

[Stable]

Performs a Mantel test between two correlation/distance matrices. The function calculates the correlation between two matrices, the Z-score that is is the sum of the products of the corresponding elements of the matrices and a two-tailed p-value (null hypothesis: r = 0).

Usage

mantel_test(mat1, mat2, nboot = 1000, plot = FALSE)

Arguments

mat1, mat2

A correlation matrix or an object of class dist.

nboot

The number of permutations to be used. Defaults to 1000.

plot

if plot = TRUE, plots the density estimate of the permutation distribution along with the observed Z-score as a vertical line.

Value

  • mantel_r The correlation between the two matrices.

  • z_score The Z-score.

  • p-value The quantile of the observed Z-score. in the permutation distribution.

See also

pairs_mantel()

Author

Tiago Olivoto tiagoolivoto@gmail.com

Examples

# \donttest{
library(metan)
# Test if the correlation of traits (data_ge2 dataset)
# changes between A1 and A2 levels of factor ENV
A1 <- corr_coef(data_ge2 %>% subset(ENV == "A1"))[["cor"]]
A2 <- corr_coef(data_ge2 %>% subset(ENV == "A2"))[["cor"]]
mantel_test(A1, A2, plot = TRUE)

#> $mantel_r
#> [1] 0.7154291
#> 
#> $z_score
#> [1] 12.07974
#> 
#> $p_value
#> [1] 0.000999001
#> 

# }