miMediation

miMediation is a R package for performing phylogeny-based mediation test (PhyloMed) for microbiome data.

See the following for comprehensive and up-to-date documentation:

• The miMediation R package manual.
• The tutorial walkthrough of the proposed PhyloMed.
• The article: Hong, Q., Chen, G., & Tang, Z. Z. (2023). PhyloMed: a phylogeny-based test of mediation effect in microbiome. Genome Biology, 24(1), 1-21.

Author

Qilin Hong @Tang lab

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison

Installation

You can install the package from github with:

devtools::install_github("KiRinHong/miMediation")

You can download the package source and install it manually with:

install.packages("miMediation_0.3.tar.gz", repos = NULL, type ="source", dependencies = c("Depends", "Imports")) 

You can force installation if you already have old version with:

devtools::install_github("KiRinHong/miMediation", force = TRUE)

Troubleshoot Dependencies

At this point, there may be complaints about missing dependencies. To install missing dependencies on either CRAN or Bioconductor, start a fresh R session and enter the following:

# For CRAN
install.packages("missing_package")
# For Biocondocutor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("missing_package") 
# ... and so on

Re-attempt miMediation Installation

Install again, after dependencies have been installed. You should now be done if the installation was successful.

Load Package, Explore Function Documentation and Vignette

library(miMediation)
help(package = "miMediation")
?data.cecal
?data.zeeviD
?phyloMed
?prepareTree

If you install the package manually from source, a vignette describing the use of the package is available from within R. Load the package and then use the vignette function.

vignette("miMediation", package = "miMediation")

Otherwise, it will not build vignette by default if you install the package from github because they are time consuming and may require additional packages (here, require prettydoc R package, install it before building vignette). You can force building (take ~7 mins) with:

devtools::install_github("KiRinHong/miMediation", build_vignettes = TRUE)

Then, the vignette would be available from within R.

Getting help

Please use the issue tracker to post any bugs, suggestions, or the installation problem.

News

• Version 0.1 (06/12/2023): Initial version released for publication.
• Version 0.2 (12/27/2023): Minor update.
  • Implemented simple permutation when no confounding variable is present.
  • Refactored the code for Smith's permutation.
• Version 0.3 (03/25/2024): Minor enhancements.
  • Address scenarios where the mediator matrix is rank-deficient in certain subcompositions.
  • Added an intermediate argument outcome_type to handle cases with only two unique values in the continuous outcome.

License

This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.

A copy of the GNU General Public License, version 3, is available at https://www.r-project.org/Licenses/GPL-3