`clr.Rd`

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 )

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 |

clr-transformed matrix

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