CoDaLoMic-package: CoDaLoMic

In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

CoDaLoMic

Description

This package contain functions to model compositional and longitudinal microbiome datasets. This package contains the functions needed to execute the models published in the articles:

• Creus-Martí, I., Moya, A., Santonja, F. J. (2018), A Statistical Model with a Lotka-Volterra Structure for Microbiota Data, Lucas Jodar, Juan Carlos Cortes and Luis Acedo, Modelling for engineering and human behavior 2018, Instituto Universitario de Matematica Multidisciplinar, ISBN: 978-84-09-07541-6.

• Creus-Martí, I., Moya, A., Santonja, F. J. (2021). A Dirichlet autoregressive model for the analysis of microbiota time-series data. Complexity, 2021, 1-16.

• Creus-Martí, I., Moya, A., Santonja, F. J. (2022). Bayesian hierarchical compositional models for analysing longitudinal abundance data from microbiome studies. Complexity, 2022.

In addition, the package contains one real dataset extracted from:

• Marín-Miret, J., Pérez-Cobas, A. E., Domínguez-Santos, R., Pérez-Rocher, B., Latorre, A., & Moya, A. (2024). Adaptability of the gut microbiota of the German cockroach Blattella germanica to a periodic antibiotic treatment. Microbiological Research, 287, 127863.

Details

We refer to the model described in Creus-Martí (2018) as Dirich-gLV, we refer to the model described in Creus-Martí (2021) as FBM and we refer to the model described in Creus-Martí (2022) as BPBM.

Access to Additional Files

This package includes files in the directory 'inst/extdata'. Users can access these files using 'system.file()'. The following files are available:

• README.pdf, README.Rmd, README.R: Basic instructions for using the package.

• 1-s2.0-S0944501324002647-mmc6.xlsx: Original cockroach dataset extracted from Marín-Miret et al (2024).

• Simulated.R: Code use to obtain the Simulated dataset.

• cockroach.R: Code use to obtain the cockroach dataset.

To access these files, use: base::system.file("extdata", "filename", package = "CoDaLoMic")

For instance: base::system.file("extdata", "README.pdf", package = "CoDaLoMic")

On Windows, the PDF can be opened as follows: base::shell.exec(system.file("extdata", "README.pdf", package = "CoDaLoMic"))

Author(s)

Maintainer: Irene Creus Martí [e-mail] (ORCID)

CoDaLoMic documentation built on April 12, 2025, 2:18 a.m.