In the example for dplR::glk() is the mean calculated from complete matrix, including diagonal, which inflate the resulting mean glk - on diagonal are self-comparisons (always 1).
Corrected example:
library(utils)
data(ca533)
ca533.glklist <- glk(ca533)
mean(ca533.glklist$glk_mat[lower.tri(ca533.glklist$glk_mat)], na.rm = TRUE)
In the example for dplR::glk() is the mean calculated from complete matrix, including diagonal, which inflate the resulting mean glk - on diagonal are self-comparisons (always 1).
Corrected example:
library(utils)
data(ca533)
ca533.glklist <- glk(ca533)
mean(ca533.glklist$glk_mat[lower.tri(ca533.glklist$glk_mat)], na.rm = TRUE)