biomeUtils: Utilities for microbiome analytics

#' @title FuentesIliGutData
#'
#' @description Fuentes S, et al. (2021) data in which the authors investigated
#'              associations between gut microbiota in respiratory infections and
#'              local and systemic immune markers in older adults during an influenza
#'              season.
#'
#' @details FuentesIliGutData consists of 905 taxa (ASV-level) in 589 samples from
#'          397 participants. The samples include follow-up (recovery) samples
#'          that were collected 7–9 weeks after the ILI event.
#'          Data on co-morbidities, medications, symptoms, pathogens are made
#'          available.
#'
#' @name FuentesIliGutData
#'
#' @docType data
#'
#' @author Sudarshan Shetty \email{sudarshanshetty9@gmail.com}
#'
#' @usage data(FuentesIliGutData)
#'
#' @return Loads the data set in R.
#'
#' @format Phyloseq object
#'
#' @keywords Data
#'
#' @references
#'
#' \itemize{
#' \item{}{Fuentes S, et al. (2021) Associations of faecal microbiota
#'        with influenza-like illness in participants aged 60 years or
#'        older: an observational study.
#'        \emph{The Lancet Healthy Longevity}, 2(1):e13-23.
#'        \url{https://doi.org/10.1016/S2666-7568(20)30034-9}
#' }
#' \item{}{Ferreira JA, Fuentes S. (2020). Some comments on certain
#'         statistical aspects of the study of the microbiome.
#'         \emph{Briefings in bioinformatics} 21(4), pp.1487-1494.
#'         \url{https://doi.org/10.1093/bib/bbz077}
#' }
#' }
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#' @title SprockettTHData
#'
#' @details The SprockettTHData dataset contains 16S rRNA gene based high-throughput
#'          profiling of 1966 Feces, 120 Saliva samples from 319 participants from
#'          Bolivia, Finland and Bangladesh. These include samples from adults,
#'          children, and infants. Several participants have longitudinal samples.
#'          The data consists of 2319 taxa from 2086 samples. The data
#'          set can be used to investigate assembly, structure, and dynamics as well
#'          as associations between several host related parameters with microbiota.
#'          The data is also made available in microbiomeDataSets pkg.
#'
#' @name SprockettTHData
#'
#' @docType data
#'
#' @author Sudarshan Shetty \email{sudarshanshetty9@gmail.com}
#'
#' @usage data(SprockettTHData)
#'
#' @return Loads the data set in R.
#'
#' @format Phyloseq object
#'
#' @keywords Data
#'
#' @references
#' Sprockett, D.D., Martin, M., Costello, E.K. et al. (2020) Microbiota assembly,
#' structure, and dynamics among Tsimane horticulturalists of the Bolivian
#' Amazon.
#' \emph{Nat Commun} 11, 3772 \url{https://doi.org/10.1038/s41467-020-17541-6}
#'
#' Subramanian, S., Huq, S., Yatsunenko, T., et al. (2014) Persistent gut microbiota
#' immaturity in malnourished Bangladeshi children.
#' \emph{Nature} 510, 417-421 \url{https://doi.org/10.1038/nature13421}
#'
#' Vatanen, T., Kostic A.D., d'Hennezel E., et al. (2016) Variation in microbiome LPS
#' immunogenicity contributes to autoimmunity in humans.
#' \emph{Cell} 165, 842-853 \url{https://doi.org/10.1016/j.cell.2016.04.007}
#'
#'
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