R/brook_trout.R

In brouwern/compbio4all: Datasets and helpful functions for learning bioinformatics and computational biology

#' Brook trout impacts on Chinook salmon survival - original data
#'
#' Levin et al. 2002 studied the impacts of brook trout introduced for sport fishing
#' on native Chinook salmon.  Whitlock & Shulter used a subset
#' of these data as an example in their textbook Analysis of Biological Data.
#'
#'
#' @format A data frame, including:
#' \describe{
#'   \item{site}{Name of study site or stream}
#'   \item{trout.PRES.ABS}{Are brook trout present in the stream or absent from it?}
#'   \item{yr}{Year}
#'   \item{release}{Number of Chinook salmon released}
#'   \item{recap}{Number of juvenile chinook salmon "recaptured" by detecting their PIT tag; this was not reported in original paper but was estimated using published survival rate.  The survival rate estiamted using mark-recapture methods to account for detection probabilities.}
#'   \item{surv}{survival rate}
#' }
#'
#'
#' @source \url{http://rspb.royalsocietypublishing.org/content/269/1501/1663.short}

#' @references Levin et al.  2002.  Non-indigenous brook trout and the demise of Pacific salmon:
#' a forgotten threat?  PRSB 269.  DOI: 10.1098/rspb.2002.2063
#'
#' Whitlock & Schulter.  2nd ed.  Analysis of Biological Data.
#'
#' @examples
#'
#' ## t-test on survival rate (ignores years)
#' t.test(surv ~ trout.PRES.ABS, data = brook_trout)
#'
"brook_trout"