Package: MicrobiomeSurv
Type: Package
Title: A Biomarker Validation Approach for Classification and
        Predicting Survival Using Microbiome Data
Version: 0.1.0
Authors@R: 
       c(person("Thi Huyen","Nguyen", email="thihuyen.nguyen@uhasselt.be", role=c("aut","cre")),
       person("Olajumoke Evangelina","Owokotomo", email="olajumoke.x.owokotomo@gsk.com", role="aut"),
       person("Ziv","Shkedy", email="ziv.shkedy@uhasselt.be", role="aut"))
Maintainer: Thi Huyen Nguyen <thihuyen.nguyen@uhasselt.be>
Description: An approach to identify microbiome biomarker for time to
        event data by discovering microbiome for predicting survival
        and classifying subjects into risk groups. Classifiers are
        constructed as a linear combination of important microbiome and
        treatment effects if necessary. Several methods were
        implemented to estimate the microbiome risk score such as
        majority voting technique, LASSO, Elastic net, supervised
        principle component analysis (SPCA), and supervised partial
        least squares analysis (SPLS). Sensitivity analysis on the
        quantile used for the classification can also be accessed to
        check the deviation of the classification group based on the
        quantile specified. Large scale cross validation can be
        performed in order to investigate the mostly selected
        microbiome and for internal validation. During the evaluation
        process, validation is accessed using the hazard ratios (HR)
        distribution of the test set and inference is mainly based on
        resampling and permutations technique.
URL: https://github.com/N-T-Huyen/MicrobiomeSurv
BugReports: https://github.com/N-T-Huyen/MicrobiomeSurv/issues/new
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Imports: graphics, stats, ggplot2, survival, survminer, glmnet,
        methods, superpc, lmtest, gplots, tidyr, dplyr, microbiome,
        pls, grDevices
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 2.10)
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libjpeg-dev
        libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://n-t-huyen.r-universe.dev
Date/Publication: 2023-10-04 10:34:30 UTC
RemoteUrl: https://github.com/n-t-huyen/microbiomesurv
RemoteRef: HEAD
RemoteSha: ae3e5454878c291fe2cb39e44e6e65a65d961e42
NeedsCompilation: no
Packaged: 2026-10-08 08:52:08 UTC; root
Author: Thi Huyen Nguyen [aut, cre],
  Olajumoke Evangelina Owokotomo [aut],
  Ziv Shkedy [aut]