R/data.R

In bramstone/qsip: Quantitative stable isotope probing for microbial ecology

#' Example qSIP dataset
#'
#' A data set demonstrating the general organization and data necessary
#'  for the calculation of fractional enrichment via qSIP
#'
#' \itemize{
#' \item asv_id. unique identifier for individual microbial taxa (here, amplicon sequence
#'  variants or ASVs) as identified by 16S amplicon sequencing
#' \item sampleID. unique identifier or code for experimental replicates
#' \item fraction. the fraction number of a replicate (1--22)
#' \item timepoint. the time of sampling for a replicate in days (0, 7)
#' \item isotope. factor of isotopes added to sample (values: NA, 16O, 18O)
#' \item iso_trt. factor specifying whether isotopes were added (light, label)
#' \item ecosystem. the site where soil samples originate from Northern Arizona (MC = mixed conifer, GL = grassland)
#' \item treatment. factor of nutrient amendments added (control, C for glcuose, CN for glucose and ammonium)
#' \item rep. numeric replicate from each plot (1--4 for unlabeled samples, 1--3 for labeled samples)
#' \item Density.g.ml. the density of individual fractions in grams per milliliter (1.6509988--1.736474)
#' \item avg_16S_g_soil. the concentration of bacterial 16S copies of individual fractions expressed per g dry soil (47--803,489)
#' \item seq_abund. the number of sequence reads per taxon (1--20,186)
#' \item Kingdom. the assigned kingdom of a taxon (Archaea, Bacteria, Unassigned, or Eukaryota)
#' \item Phylum. the assigned phylum of a taxon
#' \item Class. the assigned class of a taxon
#' \item Order. the assigned order of a taxon
#' \item Family. the assigned family of a taxon
#' \item Genus. the assigned genus of a taxon
#' }
#'
#' @docType data
#' @name example_qsip
#' @format A data.table with 14387 rows and 18 variables
#' @usage data(example_qsip)
#' @source <https://github.com/bramstone/density-dependence-qSIP/tree/main/data>
#' @references \url{https://doi.org/10.1007/s00442-023-05322-z}
"example_qsip"