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]