faramea: Faramea occidentalis abundance in Panama

Description Usage Format Details References Examples


This dataset describes the abundance (number of trees with diameter at breast height equal or larger than 10 cm) of the tree species Faramea occidentalis as observed in a 1-ha quadrat survey from the Barro Colorada Island of Panama. For each quadrat, some environmental characteristics are also provided.




A data frame with 45 observations on the following 8 variables.


a numeric vector


a numeric vector


a numeric vector


a numeric vector


a numeric vector


a factor with levels c1 c2 c3


a factor with levels pT Tb Tbo Tc Tcm Tgo Tl


a numeric vector


Although the original survey documented tree species composition of all 1-ha subplots of larger (over 1 ha) sample plot, only the first (and sometimes the last) quadrats of the larger plots were included. This selection was made to avoid that larger sample plots dominated the analysis. This selection of sites is therefore different from the selection of the 50 1-ha quadrats of the largest sample plot of the same survey (BCI and BCI.env)

This dataset is the main dataset used for the examples provided in chapters 6 and 7 of the Tree Diversity Analysis manual (Kindt & Coe, 2005).


Pyke CR, Condit R, Aguilar S and Lao S. (2001). Floristic composition across a climatic gradient in a neotropical lowland forest. Journal of Vegetation Science 12: 553-566.

Condit, R, Pitman, N, Leigh, E.G., Chave, J., Terborgh, J., Foster, R.B., Nunez, 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.

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.




Example output

Loading required package: tcltk
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: vegan3d
Loading required package: rgl
Registered S3 methods overwritten by 'lme4':
  method                          from
  cooks.distance.influence.merMod car 
  influence.merMod                car 
  dfbeta.influence.merMod         car 
  dfbetas.influence.merMod        car 
BiodiversityR 2.12-2: Use command BiodiversityRGUI() to launch the Graphical User Interface; 
to see changes use BiodiversityRGUI(changeLog=TRUE, backward.compatibility.messages=TRUE)

Warning messages:
1: no DISPLAY variable so Tk is not available 
2: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
3: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 

BiodiversityR documentation built on April 20, 2021, 5:07 p.m.