CTFS.mortality {CTFS}R Documentation

Overview of Analysis of Mortality Rates in Tropical Tree Populations

Description

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.

Details

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.

Author(s)

Rick Condit and Pamela Hall

See Also

CTFS.groupcats


[Package CTFS version 1.00 Index]