CTFS.mortality {CTFS} | R Documentation |
Provides an overview for the analysis of mortality rates for tree populations by a variety of categories. Overview includes the functions that are available, supporting functions and use of the options of the main functions.
FUNCTIONS TO COMPUTE MORTALITY RATES
mortality | Annual Mortality Rates by Categories (User defined groups) |
mortality.dbh | Annual Mortality Rates by DBH Classes |
mortality.eachspp | Annual Mortality Rate for Species by DBH Class |
mortality.calculation | A Single Annual Mortality Rate given N, S and Time |
FUNCTIONS FOR FORMATTING RESULTS
assemble.demography | Reformat the Output from Demographic Functions from List to Dataframe |
assemble.table.each | Reformat the Output from Demographic Functions from List to Dataframe |
FUNCTIONS CALLED BY MORTALITY FUNCTIONS
find.climits | Calculates confidences limits for mortality rates |
fill.dimension | Fills all the dimensions of a 2 dimensional array |
fill.1dimension | Fills all the dimensions of a 1 dimensional array |
COMPUTATION OF MORTALITY
The annual mortality rate is calculated as
m = (logN0 - logS) / mean(time1 - time0)
where N0
is the number of live individuals at the first census,
where S
is the number of surviving individuals of N0 at the second
census which is equal to N0 - D,
where time1
and time0
are expressed in years.
The confidence limits are computed using find.climits
which
returns the number of survivors, S
, out of N
individuals for
each confidence interval in turn. The beta distribution is used to
determine the number of S for the upper 95% and lower 5% (default
probability level). Confidence limits for mortality rate are computed as
from these CI for S
as:
rate.CI.upper = ( logN0 - log(S.lowerCI) ) / mean(time1 - time0)
rate.CI.lower = ( logN0 - log(S.upperCI) ) / mean(time1 - time0)
Note that S.lowerCI
is a lower value of S
which results in a higher
number of deaths and hence a higher mortality rate. And S.upperCI
is a
higher value of S
which results in a lower number of deaths and hence a
lower mortality rate.
Rick Condit and Pamela Hall