growth {CTFS} | R Documentation |
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.
growth(census1, census2, rounddown = FALSE, method = "I", stdev = FALSE, mindbh = 10, err.limit = 4, maxgrow = 75, split1 = NULL, split2 = NULL)
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. |
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
.
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 |
$date1 |
mean date of second census |
If the vector(s) split1
and split2
are provided by the
user, then growth rates and associated statistics are computed for
each value of the vectors. The vectors are nested so that growth
rates is computed for each category of split2
within each
category of split1
Rick Condit and Pamela Hall
## Not run: 1. Default use of growth() growth.all.out <- growth(tst.bci90.full,tst.bci95.full) growth.all.out 2. Create a vector of species names for each tree to compute growth rates for each species. bci.spp.vct <- tst.bci90.full$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)