R/datasets_OTU.R

# This file contains documentation for datasets composed of OTUs (T-RFs) as
# exported by the online analysis tool T-REX.

#' OTU (TRF) matrices for a suite of replicate MTRFLP samples
#'
#' Object "replicates_OTUs" is a list of OTU abundance matrices (based
#' on T-RF peak area) as output by the TREX web platform and processed in the
#' file "create_package.R" (not included in built packages).
#'
#' The analysis parameters varied are: noise filtering (1 vs. 1.5 standard
#' deviations); T-RF bin width (0.5 vs 1 bp either side of max/min peaks); and
#' permitting multiple peaks within a sample per T-RF (yes vs no). This
#' generates 8x combinations of settings. Sample codes corresponding to
#' combinations of parameter settings are given in
#' vignette("optimal_TREX_diversity"). In addition, there are data for 4x taxa
#' (Archaea, Bacteria, Fungi, Eukarya), within each perumutation of settings,
#' generating a total of 32x data matrices.
#'
#' @format A list containing 32 numerical matrices, each with different numbers
#'   of columns but with 27 rows.
#'   \describe{
#'   \item{TREX settings}{Each matrix is named with a prefix A - H to denote the combination of TREX data processing
#'   settings used.}
#'   \item{Taxon}{Each matrix contains OTU data for Archaea, Bacteria, Fungi or Eukarya, and is named with a corresponding suffix.}
#'   }
#' @source Personal lab work.
"replicates_OTUs"

#' OTU (TRF) matrices for aquifer communities at Wellington, New South Wales
#'
#' Object "wellington_OTUs" is a list containing OTU abundance matrices (based
#' on T-RF peak area) as output by the TREX web platform and processed in the
#' file "create_package.R" (not included in built packages).
#'
#' @format A list containing 32 numerical matrices, each with different numbers
#'   of columns but with 27 rows.
#'   \describe{
#'   \item{Taxon}{Each matrix contains OTU data for one of Archaea, Bacteria,
#'   Fungi or Eukarya, and is named accordingly.}
#'   }
#' @source Personal lab work.
mixtrak/wellington.aquifer.ecol documentation built on Nov. 30, 2017, 4:25 a.m.