growth {CTFS}R Documentation

Annual Growth Rates by Categories (User defined groups)

Description

Computes annual growth rate for all trees or any user defined categorization of trees. Two growth rates can be computed: simple change in dbh over time and relative growth rate. Unrealistically high and low values are removed from the summary values. Growth rate in mm dbh per year, relative growth rate in % change in dbh per year, standard deviation or 95% confidence limits, and sample size are provided. Two datasets must be used, one for each census.

Usage

growth(census1, census2, 
        rounddown = FALSE, method = "I", stdev = FALSE, 
        mindbh = 10, err.limit = 4, maxgrow = 75, 
        split1 = NULL, split2 = NULL)

Arguments

census1 name of census datafile for first census, must be a dataframe, must be of same length as census2
census2 name of census datafile for second census, must be a dataframe, must be of same length as census1
rounddown logical value in caps. When TRUE, if either of census is < 55, then the floor of the dbh value / 5 is provided. When FALSE, no change in the dbh is made.
method character indicating the type of growth rate to be calculated. When "I" the annual change in dbh is provided. When "E" the relative growth rate is provided. see CTFS.growth for more details on method.
stdev logical value in caps. When TRUE, the standard deviation of growth is provided. When FALSE, a 95% condfidence interval is provided. The confidence limits are not computed.
mindbh minimum DBH in census1 for inclusion in computation.
err.limit number of standard deviations: used for determining if an individual tree growth rate is too high or low for inclusion.
maxgrow maximum absolute growth rate, mm per year: used for determining if an individual tree growth rate is too high for inclusion.
split1 a vector of categorical values of the same length as census which groups trees into classes of interest for which growth values are computed. This vector can be composed of characters or numbers.
split2 a second vector of categorical values of the same length as census which groups trees into classes of interest for which growth values are computed. This vector can be composed of characters or numbers.

Details

See CTFS.growth for details on the computation of growth rates and associated functions.

Any two censuses on a datafile must be used. They do not have to be sequential, only that census1 has to be before census2.

The vectors split1 and split2 must be of the same length as census1 and census2 but can contain NA.

The results of growth can be organized into dataframes with the use of assemble.demography.

Value

growth returns a list of arrays with the values of split1 as the first dimension and the values of split2 as the second dimension of the array. The array contains the following named components:

$N0 the number of trees used to compute growth rate
$rate the annual mean growth rate in mm per year or % per year, type determined by the argument method
$clim the 95% confidence limit based on a normal distribution
$dbhmean the mean dbh in mm for trees used to compute growth rate
$meanyrs mean number of years between census for trees used in growth rate computation.
$date0 mean date of first census
$date1 mean date of second census


If the vector(s) split1 and split2 are provided by the user, then growth rates and associated statistics are computed for each value of the vectors. The vectors are nested so that growth rates is computed for each category of split2 within each category of split1

Author(s)

Rick Condit and Pamela Hall

See Also

CTFS.growth

Examples

## Not run: 
1. Default use of growth()

growth.all.out <- growth(tst.bci90.full,tst.bci95.full)
growth.all.out

2. Create a vector of species names for each tree to compute growth 
rates for each species.

bci.spp.vct <- tst.bci90.full$sp
names(growth.spp.out)
growth.spp.out$rate

3.  Create 2 vectors: the first of habitats based on the quad location 
of each tree and the second of tree species names.

bci.hab.vct <- sep.quadinfo(tst.bci90.full,bciquad.info,by.col="hab")
growth.spp.hab.out <- growth(tst.bci90.full,tst.bci95.full,split1=bci.spp.vct,split2=bci.hab.vct)
growth.spp.hab.out$rate

## End(Not run)

[Package CTFS version 1.00 Index]