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]