BCI.env2: Habitat Types of Barro Colorado Island Forest Plots

In jarioksa/natto: An Extreme 'vegan' Package of Experimental Code

Habitat Types of Barro Colorado Island Forest Plots

Description

Habitat types of Barro Colorado Island Forest Dynamics Plots classified in 25 grid cells in each 1-ha plot (Harms et al. 2001).

Usage

data("BCI.env2")

Format

A data frame with 50 observations on the area (in ha) of following habitat types:

Young

Young forests of ca. 100 years.

Stream

Streamside vegetation.

Swamp

Swamp.

OldHigh

Old forests on flat surface above 152 m altitude.

OldLow

Old forests on flat surface at or below 152 m altitude.

OldSlope

Old forests on steep slopes (> 7 degrees).

Mixed

Mixed habitat.

Details

The data set provides habitat type classification for the Barro Colorado Island data BCI in the vegan package. The vegan package provides alternative environmental data BCI.env which has variables derived from this data set: Dominant habitat type excluding Stream, presence of Stream grid cells in the plot, and habitat type diversity of each plot (see Examples).

The data were extracted from Harms et al. (2001: Fig. 1) who give a map of 50 forest plots divided into 25 grid cells, and the areas are expressed in ha (at 0.04 ha resolution).

Source

Harms et al. (2001), Fig. 1.

References

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.

Examples

## Derive variables in BCI.env data in vegan
data(BCI.env2)
## 1. The dominant habitat type in each plot
k <- apply(BCI.env2[,-2], 1, which.max)
Habitat <- (names(BCI.env2)[-2])[k]
## 2. Presence of streamside habitats in the plot
Stream <- with(BCI.env2, ifelse(Stream > 0, "Yes", "No"))
## 3. Habitat type diversity (needs vegan)
if (require(vegan)) {
EnvHet <- diversity(BCI.env2, "simpson")
}

## The combined variables in BCI.env and the original area variables in
##  BCI.env2 give nearly equal constraints.
if (require(vegan)) {
data(BCI)
## habitat areas per 1-ha plot
ord <- cca(BCI ~ ., BCI.env2)
## dominant habitat type of each 1-ha plot
ord0 <- cca(BCI ~ Habitat)
plot(procrustes(ord, ord0))
}

jarioksa/natto documentation built on March 28, 2024, 12:45 a.m.