R: Barro Colorado Island Tree Counts

BCI {vegan} | R Documentation

## 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 http://www.theplantlist.org and Kress et al. (2009) which allows matching 207 of species against http://datadryad.org/resource/doi:10.5061/dryad.63q27 (Zanne et al., 2014). The original species names are available as attribute `original.names` of `BCI`. See Examples for changed names.

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

`UTM.EW`:

  UTM coordinates (zone 17N) East-West.

`UTM.NS`:

  UTM coordinates (zone 17N) North-South.

`Precipitation`:

  Precipitation in mm per year.

`Elevation`:

  Elevation in m above sea level.

`Age.cat`:

  Forest age category.

`Geology`:

  The Underlying geological formation.

`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 `Young` forests (ca. 100 years), old forests on > 7 degree slopes (`OldSlope`), old forests under 152 m elevation (`OldLow`) and at higher elevation (`OldHigh`) and `Swamp` forests.

`River`:

  `"Yes"` if there is streamside habitat in the plot.

`EnvHet`:

  Environmental Heterogeneity assessed as the Simpson diversity of frequencies of `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 `BCI.env` for the coordinates.

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

### Source

http://www.sciencemag.org/cgi/content/full/295/5555/666/DC1 for community data and References for environmental data.

### References

Condit, R, Pitman, N, Leigh, E.G., Chave, J., Terborgh, J., Foster, R.B., Nuñez, P., Aguilar, S., Valencia, R., Villa, G., Muller-Landau, H.C., Losos, E. & Hubbell, S.P. (2002). Beta-diversity in tropical forest trees. 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. 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. 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. 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. Journal of Vegetation Science 12, 553–566. doi:10.2307/3237007

### See Also

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

### 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], ])

[Package vegan version 2.4-3 Index]