sgf.area {CTFS}R Documentation

Number of Species, Genera and Families for a single defined Area

Description

Counts the number of species, genera and families of the individuals found in a given single defined area of a plot. There area is defined by x, y coordinates and can be of any size. This function is used by other species area functions.

Usage

sgf.area(census1, spp.info, corners = c(0, 1000, 0, 500), 
        alivecode = c("A"), mindbh = NULL, unidennames = c("**", "UNID", "uniden", "UNIDEN"))

Arguments

census1 name of the datafame of a single census
spp.info name of dataframe that contains each species and information about it, eg. bcispp.info
corners x, y coordinates, in pairs of the corners of the area of the plot to be included
alivecode character, codes of the variable status that indicate the tree is alive. The most general valid categories are: "A" and "AB" and "AS". The default for this function is "A"
mindbh Minimum DBH for inclusion in computation
unidennames vector of codes for unidentified species, codes vary among sites and datasets

Details

This is the base function for all of the other sgf.* functions. Given any coordinates, it subsets the dataset for trees within those coordinates and calculates the number of individuals, species, genera and families. alivecode, mindbh and unidennames control which trees are included.

Pay attention to the default values of alivecode and mindbh. Any tree with alivecode not equal to “A” has a dbh = NA and so will not contribute to the results of this computation. Setting mindbh to some value other than NULL will affect the trees that are included in the calculation. Use mindbh to select trees larger than 10 mm dbh. Use alivecode to select trees to be counted as being alive but have no dbh measurement.

All areas are squares. For other shapes use spp.randarea.range

Value

Returns a vector of the following information for the defined area.

n.ind number of individuals
n.spp number of species
n.gen number of genera
n.fam number of families
r.sppgen ratio of number of species to number of genera
r.sppfam ratio of number of species to number of families
r.genfam ratio of number of genera to number of families

Author(s)

Rick Condit, Suzanne Lao and Pamela Hall

See Also

CTFS.diversity

Examples

## Not run: 
1. default use gives the total number of species, genera, families for
a given census
sgf.area(bci90.full,bcispp.info)
 
2. for the first hectare
sgf.area(bci90.full,bcispp.info,corners=c=(0,100,0,100))

3. note the differences among values for alivecode and mindbh, keep
track of the default settings for each

sgf.area(bci90.full,bcispp.info,alivecode=c("A","AB","AS"))
sgf.area(bci90.full,bcispp.info,mindbh=NULL)
sgf.area(bci90.full,bcispp.info,alivecode=c("A","AB","AS"),mindbh=NULL)
## End(Not run)

[Package CTFS version 1.00 Index]