Centered log-ratio (CLR) transform

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
minocc

prevalence filter; ignored if 0 or below
pseudocount

zero replacement value; should be above 0
scale.factor

scaling factor; abundances will be multiplied with this factor
omit.zeros

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.