micInt is an R package designed for analyzing microbial co-occurences. It takes in OTU tables was either pure dataFrames or as experiment-level phyloseq objects. Roughly, the package is composed of three major parts:
- CoNet-based analysis of pairwise co-occurences. Primary functions:
runAnalysis(high level) andccrepe(low level) - Lotka-Volterra modelling of time dynamics. Primary functions:
integralSystem,cv.LVandridge_fit - Utility functions, includes
refine_data,subset_by_environment,similarity_measuresandscale_by_column.
This package have the following dependencies which must be installed prior to installing this package:
From CRAN:
infotheomatrixStatsmagrittrdeSolveigraphdplyrrlangglueviridisRhpcBLASctlggplot2ggfortify
From Bioconductor:
phyloseq
If all dependencies are satisfied, the package can we installed from GitHub as follows:
install.packages("devtools")
library(devtools)
install_github("AlmaasLab/micInt")
For a quit start automatically installing all dependencies, consider:
install.packages("BiocManager","devtools")
devtools::install_github("AlmaasLab/micInt",repos=BiocManager::BiocManager::repositories())
Please read the article "Robust bacterial co-occurence community structures are independent of r- and K-selection history" (https://www.nature.com/articles/s41598-021-03018-z) where this package is used. The source code for the article is available on https://github.com/yaccos/Microbial-co-occurence.
Unfortunately, I have not yet taken the effort to write a proper vignette. However, if you are interested in using the package, don`t hasitate asking me for help, either as a github issue or directly ([email protected]).