generate_community: Generate a simulated microbial community.
In wilkox/rdrsimulate: Simulate Microbial Communities and their rRNA:rDNA Ratios

Description Usage Arguments Details Value References See Also Examples

Following the approach of Steven et al. 2017, generate_community generates a simulated microbial community, including both cell and ribosomal RNA abundances.

1	generate_community(n = 5000)

`n`	Number of OTUs in the simulated community (i.e. richness)

rDNA abundances (i.e. cell counts) for each OTU are drawn from a log-normal distribution with parameters μ = 0, σ = 1.

The community is randomly divided into metabolic states of dead, dormant, stationary or growing, with the proportion of each state drawn at random from a uniform distribution. The metabolic state of each OTU is independent of the OTU's rDNA abundance.

Each OTU is assigned a ribosomal amplification value, representing the number of ribosomes per cell. This value is determined by the cell's metabolic state:

Dead cells always have 1 ribosome per cell
Dormant cells always have a 100 ribosomes per cell
Maintenance cells have a ribosomal amplification drawn at random from the uniform distribution U(200, 1000)
Growing cells have a ribosomal amplification drawn at random from the uniform distribution U(500, 10000)

The rRNA:rDNA ratio is calculated for each OTU.

Note that there are some key differences to the approach described in Steven et al. 2017:

Only integer rDNA abundance are permitted (Steven et al. allowed fractional abundances)
The ribosome amplification value for each metabolic state is drawn from a uniform distribution (Steven et al. selected at random one of three discrete values representing low, medium and high amplification)

A tibble containing the simulated community.

Steven, B., Hesse, C., Soghigian, J., Gallegos-Graves, L. V. & Dunbar, J. Simulated rRNA/DNA Ratios Show Potential To Misclassify Active Populations as Dormant. Appl Env Microbiol 83, e00696-17-11 (2017).

sample_community