\encoding{UTF-8}
\name{BCI}
\alias{BCI}
\alias{BCI.env}
\docType{data}
\title{Barro Colorado Island Tree Counts}
\description{
  Tree counts in 1-hectare plots in the Barro Colorado Island and
  associated site information.
}
\usage{
data(BCI)
data(BCI.env)
}
\format{
  
  A data frame with 50 plots (rows) of 1 hectare with counts of trees on
  each plot with total of 225 species (columns). Full Latin names are
  used for tree species. The names were updated against
  \url{http://www.theplantlist.org} and Kress et al. (2009) which allows
  matching 207 of species against \doi{10.5061/dryad.63q27} (Zanne et
  al., 2014). The original species names are available as attribute
  \code{original.names} of \code{BCI}. See Examples for changed names.

  For \code{BCI.env}, a data frame with 50 plots (rows) and nine site
  variables derived from Pyke et al. (2001) and Harms et al. (2001):

  \describe{
    \item{\code{UTM.EW}: }{UTM coordinates (zone 17N) East-West.}
    \item{\code{UTM.NS}: }{UTM coordinates (zone 17N) North-South.}
    \item{\code{Precipitation}: }{Precipitation in mm per year.}
    \item{\code{Elevation}: }{Elevation in m above sea level.}
    \item{\code{Age.cat}: }{Forest age category.}
    \item{\code{Geology}: }{The Underlying geological formation.}

    \item{\code{Habitat}: }{Dominant habitat type based on the map of
    habitat types in 25 grid cells in each plot (Harms et al. 2001,
    excluding streamside habitat). The habitat types are \code{Young}
    forests (\emph{ca.} 100 years), old forests on > 7 degree slopes
    (\code{OldSlope}), old forests under 152 m elevation
    (\code{OldLow}) and at higher elevation (\code{OldHigh}) and
    \code{Swamp} forests.}

    \item{\code{River}: }{\code{"Yes"} if there is streamside habitat
    in the plot.}
    \item{\code{EnvHet}: }{Environmental Heterogeneity assessed as the
    Simpson diversity of frequencies of \code{Habitat} types in 25
    grid cells in the plot.}

}

 }
\details{
  Data give the numbers of trees at least 10 cm in
  diameter at breast height (1.3 m above the ground) in each one hectare
  square of forest. Within each one hectare square, all individuals of
  all species were tallied and are recorded in this table.

  The data frame contains only the Barro Colorado Island subset of the
  original data.

  The quadrats are located in a regular grid. See \code{BCI.env} for the
  coordinates.

  A full description of the site information in \code{BCI.env} is
  given in Pyke et al. (2001) and Harms et al. (2001). \emph{N.B.}
  Pyke et al. (2001) and Harms et al. (2001) give conflicting
  information about forest age categories and elevation.

}
\source{
  \url{https://science.sciencemag.org/content/suppl/2002/01/24/295.5555.666.DC1}
  for community data and References for environmental data.
}

\seealso{

  Extra-CRAN package \pkg{natto}
  (\url{https://github.com/jarioksa/natto}) has data set
  \code{BCI.env2} with original grid data of Harms et al. (2001)
  habitat classification, and data set \code{BCI.taxon} of APG III
  classification of tree species.

}

\references{
  
  Condit, R, Pitman, N, Leigh, E.G., Chave, J., Terborgh, J., Foster,
  R.B., \enc{Nuñez}{Nunez}, P., Aguilar, S., Valencia, R., Villa, G.,
  Muller-Landau, H.C., Losos, E. & Hubbell, S.P. (2002).
  Beta-diversity in tropical forest trees. \emph{Science} 295,
  666--669.

  Harms K.E., Condit R., Hubbell S.P. & Foster R.B. (2001) Habitat
  associations of trees and shrubs in a 50-ha neotropical forest
  plot. \emph{J. Ecol.} 89, 947--959.

  Kress W.J., Erickson D.L, Jones F.A., Swenson N.G, Perez R., Sanjur
  O. & Bermingham E. (2009) Plant DNA barcodes and a community
  phylogeny of a tropical forest dynamics plot in Panama. \emph{PNAS}
  106, 18621--18626.

  Zanne A.E., Tank D.C., Cornwell, W.K., Eastman J.M., Smith, S.A.,
  FitzJohn, R.G., McGlinn, D.J., O’Meara, B.C., Moles, A.T., Reich,
  P.B., Royer, D.L., Soltis, D.E., Stevens, P.F., Westoby, M., Wright,
  I.J., Aarssen, L., Bertin, R.I., Calaminus, A., Govaerts, R.,
  Hemmings, F., Leishman, M.R., Oleksyn, J., Soltis, P.S., Swenson,
  N.G., Warman, L. & Beaulieu, J.M. (2014) Three keys to the radiation
  of angiosperms into freezing environments. \emph{Nature} 506,
  89--92.  \doi{10.1038/nature12872} (published online Dec 22, 2013).

  Pyke, C. R., Condit, R., Aguilar, S., & Lao, S. (2001). Floristic
  composition across a climatic gradient in a neotropical lowland
  forest. \emph{Journal of Vegetation Science} 12, 553--566.
  \doi{10.2307/3237007} 

}
\examples{
data(BCI, BCI.env)
head(BCI.env)
## see changed species names
oldnames <- attr(BCI, "original.names")
taxa <- cbind("Old Names" = oldnames, "Current Names" = names(BCI))
noquote(taxa[taxa[,1] != taxa[,2], ])
}
\keyword{datasets}
