Description Usage Arguments Details Value Author(s) Examples
This function calculates Shannon's, Simpson's, and/or Inverse Simpson's alpha diversity indices.
1 | alphaDiv_calc(omicsData, index = c("shannon", "simpson", "invsimpson"))
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omicsData |
an object of the class 'seqData' created by |
index |
a character vector stating which of the calculations to perform - "shannon" for Shannon's diversity index, "simpson" for Simpson's diversity index, and/or "invsimpson" for the inverse Simpson's diversity index. Default is to perform all 3 calculations. |
Alpha diversity is calculated for each sample in the data, using Shannon's diversity index (Shannon's H), Simpson's diversity index (Simpson's D), and/or inverse Simpson's diversity index.
Shannon or Shannon–Weaver (or Shannon–Wiener) index is defined as H = -sum(p_i*log(p_i)), where p_i is the proportional abundance of species i.
Both variants of Simpson's index are based on D = sum(p_i^2). Choice simpson returns 1-D and invsimpson returns 1/D.
An object of class alphaRes (also a data.frame) containing the diversity value(s) for every sample in the data object.
Allison Thompson
1 2 3 4 5 6 7 8 9 | ## Not run:
library(mintJansson)
data(rRNA_data)
rRNA_diversity <- alphaDiv_calc(omicsData = rRNA_data)
rRNA_diversity
summary(rRNA_diversity)
plot(rRNA_diversity)
## End(Not run)
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