Observed richness is counted directly; Chao1 and ACE are extrapolated
estimators of true richness based on the frequency of rare species. All
three are returned so downstream code can choose the appropriate measure.
Usage
get_alpha_S(df, feature_id = "feature_id", id_col = "SAMPLE")
Arguments
- df
A dataframe with features as rows and samples as columns
- feature_id
The name of the column with feature IDs
(default is "feature_id")
- id_col
The name of the column with sample IDs (default is "SAMPLE")
Value
A tibble with one row per sample and columns:
- sample_sum
Total read count (sequencing depth)
- S.obs
Observed species richness
- S.chao1
Chao1 richness estimator
- se.chao1
Standard error of Chao1
- S.ACE
ACE richness estimator
- se.ACE
Standard error of ACE