In the CLR transform, each entry is divided by the geometric mean of its sample and then the logarithm is taken.

clr(
abundances,
minocc = 0,
pseudocount = 1,
scale.factor = 1,
omit.zeros = FALSE
)

## Arguments

abundances a matrix with taxa as rows and samples as columns prevalence filter; ignored if 0 or below zero replacement value; should be above 0 scaling factor; abundances will be multiplied with this factor if TRUE, ignore pseudocount and compute clr transform only on non-zero elements

## Value

clr-transformed matrix

## Details

When omit.zeros is set to true, the default behaviour of clr in the compositions package when applied column-wise is reproduced.