Compute the log center by the projection method, which allows for missing observations.

log_center_proj(mat, weights = rep(1, nrow(mat)))

References

van den Boogaart KG, Tolosana-Delgado R, Bren M. 2006. Concepts for handling of zeros and missing values in compositional data. Proc IAMG 6:1-4. http://www.stat.boogaart.de/Publications/iamg06_s07_01.pdf

Bren M, Tolosana-Delgado R, van den Boogaart KG. 2008. News from "compositions", the R package. https://core.ac.uk/download/pdf/132548286.pdf