View source: R/phyloseq_transform.R
physeq_transform_anderson_log | R Documentation |
Log-transformation of OTU abundance table.
physeq_transform_anderson_log(physeq, ...)
physeq |
A phyloseq-class object |
... |
Additional arguments (e.g., "logbase" for the logarithm base) will be passed to |
Logarithmic transformation as suggested by Anderson et al. (2006) will be applied to the OTU table in phyloseq-object. First, non-integer data will be divided by smallest positive value. Second, log(x) + 1 for x > 0.
Default value of the logarithm base ("logbase" parameter) is 2.
This function is a wrapper to decostand
in vegan.
Phyloseq object with log-transformed counts in OTU table.
Anderson MJ, Ellingsen KE and McArdle BH. (2006) Multivariate dispersion as a measure of beta diversity. Ecology Letters 9, P. 683–693.
decostand
data(enterotype)
physeq_transform_anderson_log(enterotype)
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