Package: CoDaLoMic 0.1.0

Irene Creus Martí

CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Implementation of models to analyse compositional microbiome time series taking into account the interaction between groups of bacteria. The models implemented are described in Creus-Martí et al (2018, ISBN:978-84-09-07541-6), Creus-Martí et al (2021) <doi:10.1155/2021/9951817> and Creus-Martí et al (2022) <doi:10.1155/2022/4907527>.

Authors:Irene Creus Martí [aut, cre]

CoDaLoMic_0.1.0.tar.gz
CoDaLoMic_0.1.0.tar.gz(r-4.5-noble)CoDaLoMic_0.1.0.tar.gz(r-4.4-noble)
CoDaLoMic_0.1.0.tgz(r-4.4-emscripten)CoDaLoMic_0.1.0.tgz(r-4.3-emscripten)
CoDaLoMic.pdf |CoDaLoMic.html✨
CoDaLoMic/json (API)

# Install 'CoDaLoMic' in R:

install.packages('CoDaLoMic', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

Datasets:

Simulated - Gut microbiome simulated dataset
cockroach - Cockroach dataset

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

jags cpp

1.00 score 44 exports 59 dependencies

Last updated 6 hours agofrom:0f9dc71314. Checks:2 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 20 2025
R-4.5-linux	OK	Jan 20 2025

Exports:B1MODImatrizP B1MODImodel Balance BPBM_Matrix Estimate_Param_EstParmFunc Estimate_Param_FBM Estimating_BPBM EstParmFunc EstParmFunc_FBM ExpectedValue_EstParmFunc ExpectedValues_EstParmFunc_FBM ExpectedValuess_BPBM FromVectorToMatrix_BPBM FVectorPBmodeloPredi Graphics GraphicsPrediction GraphicsPredictionBPBM GraphicsSPBal LogVeroFuncBUENA MaxBacteria MaxBacteriaPred ObtainigValuePB ObtainigValueSPBal ObtainingDIC PBalance PBalancePredi PBmodel PCAbiplot Percen_Variance PlotDendogram PredictionBPBM PredictionEstParmFunc PredictionFBM PreparingTheData QualityControl ridgeregression rxnrate StudyingParam Table_alr_Dirich_glv TableBPBM TableFBM TauAndParameters_EstParmFunc_FBM vecttor ZeroData

Dependencies:abind backports bayesm boot broom cli coda colorspace compositions cpp11 DEoptimR dplyr fansi farver generics ggbiplot ggplot2 glue gtable isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell NADA nlme pillar pkgconfig plyr purrr R2jags R2WinBUGS R6 RColorBrewer Rcpp RcppArmadillo reshape2 rjags rlang robustbase scales stringi stringr survival tensorA tibble tidyr tidyselect truncnorm utf8 vctrs viridisLite withr xtable zCompositions

Citation

Readme and manuals

Help Manual

Help page	Topics
CoDaLoMic	CoDaLoMic-package CoDaLoMic
Ridge regression matrix	B1MODImatrizP
Obtaining the regression value of the FBM	B1MODImodel
Calculating the balance of the FBM model	Balance
Obtains the matrix of covariates of the BPBM	BPBM_Matrix
cockroach dataset	cockroach
Estimating Parameters of EstParmFunc	Estimate_Param_EstParmFunc
Estimating Parameters of EstParmFunc_FBM	Estimate_Param_FBM
Estimating BPBM	Estimating_BPBM
Writting the loglikelihood of the dirichlet	EstParmFunc
Writting the loglikelihood of the dirichlet	EstParmFunc_FBM
Obtaining the value of the Dirichlet parameters, the expected value and the variance.	ExpectedValue_EstParmFunc
Obtainig the value of the dirichlet parameters, the expected value and the variance.	ExpectedValues_EstParmFunc_FBM
Obtainig the value of the dirichlet parameters, the expected value and the variance.	ExpectedValuess_BPBM
Writting the parameters in the matrix form required in BPBM model	FromVectorToMatrix_BPBM
Obtaining a vector with the covariates of the prediction	FVectorPBmodeloPredi
Plots the time series	Graphics
Plots the time series	GraphicsPrediction
Plots the time series	GraphicsPredictionBPBM
Obtaining the graphic of the SPBal at all time points	GraphicsSPBal
Writting the loglikelihood of the dirichlet	LogVeroFuncBUENA
Putting the reference bacteria at the last row	MaxBacteria
Putting the reference bacteria at the last row	MaxBacteriaPred
Obtaining the principal balances values	ObtainigValuePB
Obtaining the selected principal balances values	ObtainigValueSPBal
Writting the loglikelihood of the dirichlet	ObtainingDIC
Calculating balances	PBalance
Calculating balances for a composition	PBalancePredi
Obtaining the regression value of the BPBM	PBmodel
PCA of the estimated parameters	PCAbiplot
Percentage of variance	Percen_Variance
Plotting a dendogram	PlotDendogram
Predicting using BPBM	PredictionBPBM
Predicting using dirichl-gLV	PredictionEstParmFunc
Predicting using FBM	PredictionFBM
Preparing dataset	PreparingTheData
Analysing the quality of the estimation	QualityControl
Ridge regression	ridgeregression
Solving the right side of the gLV equations	rxnrate
Gut microbiome simulated dataset	Simulated
Controlling quality of the convergence in BPBM	StudyingParam
Obtainig a table with the interpretable parameters	Table_alr_Dirich_glv
Obtaining a table with the SPBal information of the BPBM	TableBPBM
Obtainig a table with the interpretable parameters	TableFBM
Obtaining the value of tau and the estimate value of the rest of the parameters	TauAndParameters_EstParmFunc_FBM
Alr of a bacteria	vecttor
Zero replacement	ZeroData

Package: CoDaLoMic 0.1.0

CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)