test-2

.gitignore

@@ -6,11 +6,10 @@
 *~
 inst/extras/*.rds
 inst/extras/*.R
-
+inst/exdata/*.R
 
 # Never put this in version control
 OAtoken
-*.R
 *.rds
 data-raw/old/ili_data.rda
 data-raw/ILI pseq

NAMESPACE

@@ -36,6 +36,7 @@ importFrom(microbiome,abundances)
 importFrom(microbiome,core_members)
 importFrom(microbiome,meta)
 importFrom(phyloseq,sample_data)
+importFrom(readr,write_tsv)
 importFrom(reshape2,melt)
 importFrom(rstatix,add_significance)
 importFrom(rstatix,adjust_pvalue)

R/data.R

@@ -0,0 +1,43 @@
+#' @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{[email protected]}
+#'
+#' @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}
+#' }
+#' }
+NULL