BCI: Barro Colorado Island Tree Counts

Description Usage Format Details Source References See Also Examples


Tree counts in 1-hectare plots in the Barro Colorado Island and associated site information.




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 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 coordinates (zone 17N) East-West.


UTM coordinates (zone 17N) North-South.


Precipitation in mm per year.


Elevation in m above sea level.


Forest age category.


The Underlying geological formation.


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.


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


Environmental Heterogeneity assessed as the Simpson diversity of frequencies of Habitat types in 25 grid cells in the plot.


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.


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


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.


data(BCI, 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], ])

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3
  UTM.EW  UTM.NS Precipitation Elevation Age.cat Geology  Habitat Stream EnvHet
1 625754 1011569          2530       120      c3      Tb OldSlope    Yes 0.6272
2 625754 1011669          2530       120      c3      Tb   OldLow    Yes 0.3936
3 625754 1011769          2530       120      c3      Tb   OldLow     No 0.0000
4 625754 1011869          2530       120      c3      Tb   OldLow     No 0.0000
5 625754 1011969          2530       120      c3      Tb OldSlope     No 0.4608
6 625854 1011569          2530       120      c3      Tb   OldLow     No 0.0768
      Old Names                     Current Names                 
 [1,] Abarema.macradenium           Abarema.macradenia            
 [2,] Acacia.melanoceras            Vachellia.melanoceras         
 [3,] Apeiba.aspera                 Apeiba.glabra                 
 [4,] Aspidosperma.cruenta          Aspidosperma.desmanthum       
 [5,] Cassipourea.elliptica         Cassipourea.guianensis        
 [6,] Cespedezia.macrophylla        Cespedesia.spathulata         
 [7,] Chlorophora.tinctoria         Maclura.tinctoria             
 [8,] Coccoloba.manzanillensis      Coccoloba.manzinellensis      
 [9,] Coussarea.curvigemmia         Coussarea.curvigemma          
[10,] Cupania.sylvatica             Cupania.seemannii             
[11,] Dipteryx.panamensis           Dipteryx.oleifera             
[12,] Eugenia.coloradensis          Eugenia.florida               
[13,] Eugenia.oerstedeana           Eugenia.oerstediana           
[14,] Guapira.standleyana           Guapira.myrtiflora            
[15,] Hyeronima.alchorneoides       Hieronyma.alchorneoides       
[16,] Inga.marginata                Inga.semialata                
[17,] Lonchocarpus.latifolius       Lonchocarpus.heptaphyllus     
[18,] Maquira.costaricana           Maquira.guianensis.costaricana
[19,] Phoebe.cinnamomifolia         Cinnamomum.triplinerve        
[20,] Swartzia.simplex.var.ochnacea Swartzia.simplex.continentalis
[21,] Tabebuia.guayacan             Handroanthus.guayacan         

vegan documentation built on April 14, 2018, 5:04 p.m.