richness {microbiome} | R Documentation |
Community richness index.
richness(x, index = c("observed", "chao1"), detection = 0)
x |
A species abundance vector, or matrix (taxa/features x samples)
with the absolute count data (no relative abundances), or
|
index |
"observed" or "chao1" |
detection |
Detection threshold. Used for the "observed" index. |
By default, returns the richness for multiple detection thresholds defined by the data quantiles. If the detection argument is provided, returns richness with that detection threshold. The "observed" richness corresponds to index="observed", detection=0.
A vector of richness indices
Contact: Leo Lahti microbiome-admin@googlegroups.com
alpha
data(dietswap) d <- richness(dietswap, detection=0)