BCI.RdTree counts in 1-hectare plots in the Barro Colorado Island and associated site information.
data(BCI) data(BCI.env)
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.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.
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.
https://science.sciencemag.org/content/suppl/2002/01/24/295.5555.666.DC1 for community data and References for environmental data.
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.
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
#> 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## see changed species names oldnames <- attr(BCI, "original.names") taxa <- cbind("Old Names" = oldnames, "Current Names" = names(BCI)) noquote(taxa[taxa[,1] != taxa[,2], ])#> 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