vegan (version 2.6-6.1)

BCI: 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 tools:::Rd_expr_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 (DBH) in each one hectare quadrat in the 1982 BCI plot. Within each plot, all individuals were tallied and are recorded in this table. The full survey included smaller trees with DBH 1 cm or larger, but the BCI dataset is a subset of larger trees as compiled by Condit et al. (2002). The full data with thinner trees has densities above 4000 stems per hectare, or about ten times more stems than these data. The dataset BCI was provided (in 2003) to illustrate analysis methods in vegan. For scientific research on ecological issues we strongly recommend to access complete and more modern data (Condit et al. 2019) with updated taxonomy (Condit et al. 2020).

The data frame contains only the Barro Colorado Island subset of the full data table of Condit et al. (2002).

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.

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.

Condit R., Pérez, R., Aguilar, S., Lao, S., Foster, R. & Hubbell, S. (2019). Complete data from the Barro Colorado 50-ha plot: 423617 trees, 35 years [Dataset]. Dryad. tools:::Rd_expr_doi("https://doi.org/10.15146/5xcp-0d46")

Condit, R., Aguilar, S., Lao, S., Foster, R., Hubbell, S. (2020). BCI 50-ha Plot Taxonomy [Dataset]. Dryad. tools:::Rd_expr_doi("https://doi.org/10.15146/R3FH61")

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.

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. tools:::Rd_expr_doi("10.2307/3237007")

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. tools:::Rd_expr_doi("10.1038/nature12872") (published online Dec 22, 2013).

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], ])