Description Usage Arguments Details Value Author(s) References See Also Examples
This function permit to simulate, starting a ecological matrix, phylogenetic or functional composition of hypothetical samples based on uniform, normal and log.normal models.
1 | ecosimulator(x, r)
|
x |
a data frame with samples/sites as columns and species/functions as rows. |
r |
number of simulation |
For a given set of N feature vectors, each representing the phylogenetic (genus, phylum, etc) or the functional (gene, orthologous group, functional modules, etc) composition of a metagenomic sample, we simulated N hypothetical metagenomic samples containing the same number of features by sampling from a continuum as follows: template-uniform: each generated feature corresponds to a feature in the real dataset and its values across multiple samples is uniformly distributed between the minimum and maximum abundances of that feature in the real dataset template-Gaussian (normal): each generated feature corresponds to a feature in the real dataset and its values across multiple samples followed a Gaussian distribution with the same mean and standard deviation as observed in the corresponding real data template-log.normal: each generated feature corresponds to a feature in the real dataset and its values across multiple samples followed a log.normal distribution with the same mean and standard deviation as observed in the corresponding real data
Generated values are then normalized so that abundances within a sample sum to 1.
a list of class "ecosimulation"
uniform |
simulated |
normal |
simulated |
log.normal |
simulated |
.
Julien Tap
Arumugam et al. Enterotypes of of the human gut microbiome. Nature 2011. doi:10.1038/nature09944
1 2 3 4 | data(Titanium16S)
simul=ecosimulator(Titanium16S, 50)
simul
class(simul)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.