adiv_table | R Documentation |
Calculate the alpha diversity of each sample.
adiv_table(
biom,
adiv = "Shannon",
md = ".all",
transform = "none",
cpus = NULL
)
biom |
An rbiom object, such as from |
adiv |
Alpha diversity metric(s) to use. Options are: |
md |
Dataset field(s) to include in the output data frame, or |
transform |
Transformation to apply. Options are:
|
cpus |
The number of CPUs to use. Set to |
A data frame of alpha diversity values.
Each combination of sample/depth/adiv
has its own row.
Column names are .sample, .depth, .adiv,
and .diversity, followed by any metadata fields requested by
md
.
Other alpha_diversity:
adiv_boxplot()
,
adiv_corrplot()
,
adiv_stats()
library(rbiom)
# Subset to 10 samples.
biom <- slice(hmp50, 1:10)
adiv_table(biom)
biom <- rarefy(biom)
adiv_table(biom, md = NULL)
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