The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities
Fig 2
Relationships between dissimilarity measures for communities generated with the model.
The different dissimilarity measures (A: Jaccard similarity, B: Sørensen index, C: Whittaker index D: Bray-Curtis disimilarity, E: Horn similarty, F: Morisita-Horn similarity) are plotted against the Carrying capacity correlation ρK. Grey circles represent the 200 pairs of communities generated with the model. Each community has S = 104 OTUs. Each pair of communities have the same σ, extracted from an exponential distribution with mean 0.9. Values of K are extracted from a lognormal distribution with parameters μ = −19 and s = 5. 100 pairs have the same values of K, to mimic samples from the same community at different times. The remaining 100 pairs have correlated values of K, with ρk ranging between 0.5 and 1, obtained by exponentiating values extracted from a bivariate Gaussian distribution. For each community, abundances are extracted from a Gamma distribution with parameters K and σ. For the pairs with the same values of K, Gamma-distributed abundances have a correlation ranging from 0 to 0.5. Reads are obtained from the real abundances by simulating multinomial sampling with number of reads 3 * 104. Black lines are the binned average of the grey circles.