Description Usage Arguments Details Value Author(s) References See Also Examples
Calculates the community rarity index.
1 | rarity(x, index = "all", detection = 0.2/100, prevalence = 20/100)
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x |
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index |
If the index is given, it will override the other parameters. See the details below for description and references of the standard rarity indices. |
detection |
Detection threshold for absence/presence (strictly greater by default). |
prevalence |
Prevalence threshold (in [0, 1]). The required prevalence is strictly greater by default. To include the limit, set include.lowest to TRUE. |
The rarity index characterizes the concentration of species at low abundance.
The following rarity indices are provided:
log_modulo_skewness Quantifies the concentration of the least abundant species by the log-modulo skewness of the arithmetic abundance classes (see Magurran & McGill 2011). These are typically right-skewed; to avoid taking log of occasional negative skews, we follow Locey & Lennon (2016) and use the log-modulo transformation that adds a value of one to each measure of skewness to allow logarithmization. The values q=0.5 and n=50 are used here.
low_abundance Relative proportion of the least abundant species, below the detection level of 0.2%. The least abundant species are determined separately for each sample regardless of their prevalence.
rare_abundance Relative proportion of the non-core species, exceed the given detection level (default 20 at the given prevalence (default 20 This is complement of the core with the same thresholds.
A vector of rarity indices
Contact: Leo Lahti microbiome-admin@googlegroups.com
Kenneth J. Locey and Jay T. Lennon. Scaling laws predict global microbial diversity. PNAS 2016 113 (21) 5970-5975; doi:10.1073/pnas.1521291113.
Magurran AE, McGill BJ, eds (2011) Biological Diversity: Frontiers in Measurement and Assessment (Oxford Univ Press, Oxford), Vol 12
alpha, log_modulo_skewness, rare_abundance, low_abundance
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