README.md

In Russel88/DOC: DOC analysis of microbial communities

DOC: Dissimilarity Overlap Curve analysis

This is an implementation of the DOC analysis proposed by Bashan et al. 2016 Universality of human microbial dynamics. Nature 534

This implementation is different from the original in one important aspect:

Instead of calculating the Fns value only once on the observed data, an Fns value is calculated for each bootstrap realization making it possible to asses the robustness of the measure. Besides this, I inteded to mimic the orignal Matlab code as much as possible, although note that the robust lo(w)ess algorithms in R and Matlab might give slightly different results.

Citation of this software:

The function runs in parallel, set the cores argument to enable this.

Installation

library(devtools)
install_github("Russel88/DOC")

# Plotting requires the ggplot2 package
install.packages("ggplot2")

Run the analysis

results <- DOC(otu)

The input is an OTU-table with taxa as rows

Plot the result

plot(results)

The vertical line is the median Overlap at which the fitted line has a negative slope.

DOC for null model

results.null <- DOC.null(otu)

Merge two or more DOC objects, and plot the whole thing

# The names (res1, res2, and res3) will appear in the plot
merged <- DOC.merge(list(res1 = results1, res2 = results2, res3 = results3))
plot(merged)

# If you merge a "real"" analysis with a "null" give them the same name:
merged <- DOC.merge(list(MyResults = results, MyResults = results.null))
plot(merged)

Russel88/DOC documentation built on Nov. 14, 2022, 3:50 p.m.