mortality {CTFS}R Documentation

Annual Mortality Rates by Categories (User defined groups)

Description

Computes annual mortality rate for all trees or any user defined categorization of trees. Any two census datasets can be provided in order of date of census. The annual mortality rate and other statistics are computed for user defined categories.

Usage

mortality(census1, census2, alivecode = c("A", "AB", "AS"), 
        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
alivecode character, codes of the variable status that indicate the tree is alive. The most general valid categories are: "A" and "AB" and "AS".
split1 a vector of categorical values of the same length as census which groups trees into classes of interest for which mortality 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 mortality values are computed. This vector can be composed of characters or numbers.

Details

See CTFS.mortality for details on the computation of mortality 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.

Take care when creating a split vector based on dbh. Mortality is computed on the surviving trees which have valid dbhs in both censuses. However, dead trees only have a valid dbh for the first census of any interval. If the second census is used then no dead trees will be identified. So a dbh vector must be based on the first census of the interval. The inverse if true for recruitment. Therefore the same dbh split vector CANNOT be used for computations of recruitment and mortality. Use a dbh vector based on the census1 for mortality and on census2 for recruitment.

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

Value

mortality 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 living trees at the first census
$S the number of surviving trees from the first to second census
$D the number of trees that died between the first and second census
$rate the mortality in %/year
$lower the lower 95% confidence interval
$upper the upper 95% confidence interval
$dbhmean the mean dbh in mm for trees used to compute mortality
$meanyrs mean number of years between census for trees used in mortality rate computation.
$date1 mean date of first census
$date2 mean date of second census


If the vector(s) split1 and split2 are provided by the user, then mortality rates and associated statistics are computed for each value of the vectors. The vectors are nested so that mortality rates is computed for each category of split2 within each category of split1. Mortality values are returned for all levels of each vector and if no value can be computed then 0 or NA is returned as appropriate.

Author(s)

Rick Condit and Pamela Hall

See Also

CTFS.mortality

Examples

## Not run: 

1. Default use of mortality()
mort.out <- mortality(tst.bci90.full, tst.bci95.full)
mort.out

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

spp.vct <- tst.bci90.full$sp
mort.spp.out <- mortality(tst.bci90.full, tst.bci95.full, split1 = spp.vct)

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

habitat.vct <- sep.quadinfo(tst.bci90.full, bciquad.info, by.col = "hab")
spp.vct <- tst.bci90.full$sp

mort.spp.hab.out <- mortality(tst.bci90.full, tst.bci95.full, split1=spp.vct, split2=habitat.vct)
## End(Not run)

[Package CTFS version 1.00 Index]