ecole: ecole: School of Ecology Package

#' @name braun
#' @title Emma Lucy Braun forest plots in eastern North America
#' @aliases braun
#' @docType data
#' @description
#' Relative abundances of tree species for the forest plots described
#'     in E. Lucy Brauns (1950) book, \emph{Deciduous Forests of
#'     Eastern North America}, as communicated by Ricklefs (2018).
#'
#' @format A list of 2 data.frames:\cr
#'     - \code{spe} 347 observations of 122 woody plant species,\cr
#'     - \code{env} 347 observations of 33 environmental variables.
#'
#' @details Species matrix values are relative abundances of tree
#'     species in 347 plots (removing one of Ricklefs which had no
#'     species abundance information).  Species names follow Ricklefs
#'     Table 3; those beginning with \code{X_} indicate that no
#'     species name was provided.\cr
#'
#'     Environmental matrix values include plot names, bibliographic
#'     information, location information and WorldClim climate values
#'     per Ricklefs (2018).\cr
#'
#' @source Ricklefs (2018).
#'
#' @references
#' Braun, E. L. 1950. Deciduous Forests of Eastern North America.
#'     Hafner, New York.
#'
#' Ricklefs, R. E. 2018. Emma Lucy Brauns forest plots in eastern
#'     North America. Ecology 99(2):504.
#'
#' @seealso https://en.wikipedia.org/wiki/Emma_Lucy_Braun
#'
#' @examples
#' # split into two data.frames
#' data(braun)
#' spe <- braun$spe
#' env <- braun$env
#'
#' # describe the species abundance matrix
#' mx_diversity(spe) # high beta-diversity
#'
#' # remove rare species and depauperate plots
#' rare <- (colSums((spe>0)*1) < 5)
#' poor <- (rowSums((spe>0)*1) < 3)
#' spe <- spe[!poor, !rare]
#' env <- env[!poor, ]
#' mx_diversity(spe)
#' mx_valid(spe)
#'
#' # visualize the species abundance matrix
#' plot_heatmap(spe, logbase=10, labcex=0.5, yexp=1.3)
#'
#' # gradient analysis (ordination)
#' m <- vegan::metaMDS(spe, 'bray') # tune for real usage!
#' s <- vegan::scores(m)
#' set_par(4, pch=16)
#' plot(s, col=colvec(env$bio3), main='Isothermality')
#' plot(s, col=colvec(env$bio1), main='Mean Ann Temp')
#' plot(env$lon, env$lat, col='#00000030', main='Plots')
#' plot(env$lon, env$lat, col=colvec(s[,1]), main='NMS1 scores')
#'
#' @keywords datasets
"braun"