mortality: Mortality, forest-wide or based on one or two categories.

In forestgeo/ctfs: Tools for the Analysis of Forest Dynamics

Description

Calculate mortality for the entire forest, or based on one or two user-submitted factors.

Usage

mortality(census1, census2, alivecode = c("A", "AB", "AS"),
  split1 = NULL, split2 = NULL)

Arguments

census1	The R Analytical Table for a single census, either tree or stem.
census2	The matching R Analytical Table for a later census.
alivecode	character, codes of the variable status that indicate the tree is alive. The default 'A' is the standard CTFS designation for living trees or stems
split1	a vector of categories, one per individual
split2	another vector of categories, one per individual

Details

Mortality is the main function, and is constructed like growth and recruitment. It requires two complete datasets, one per census, with dbh, pom, and date for every individual of all species in at least 2 censuses (see Data Format).

Mortality is based on only on the column status: any tree without an alivecode in census 2 is considered dead. Individuals whose status is NA in either census are deleted from all counts, since it's impossible to count them either as survivors or dead.

Value

Output of the mortality function is a list with components:

• N, the number of individuals alive in the census 1 per category selected

• D, the number of individuals no longer alive in census 2

• rate, the mean annualized mortality rate constant per category selected, calculated as (log(N)-log(S))/time

• upper, upper confidence limit of mean rate

• lower, lower confidence limit of mean rate

• time, mean time interval in years

• date1, mean date included individuals were measured in census 1, as julian object (R displays as date, but treats as integer)

• date2, mean date in census 2

• dbhmean, mean dbh in census 1 of individuals included

Pass the list to assemble.demography() with type = "m" to convert the list a data.frame.

Examples

## Not run: 

CTFSplot("bci", 56)
mort.data = mortality(bciex::bci12t5mini, bciex::bci12t6mini)
mort.data$rate
mort.data = growth(
  bciex::bci12t5mini, bciex::bci12t6mini, 
  split1 = bciex::bci12t5mini$sp
)
mort.data$rate
assemble.demography(mort.data, type = 'm')

## End(Not run)

forestgeo/ctfs documentation built on May 3, 2019, 6:44 p.m.