find.climits {CTFS} | R Documentation

## Computes 95% CI for a Survivorship

### Description

Computes the confidence intervals for the number of surviving trees. This can be used to compute confidence intervals for rates of mortality and recruitment. The intervals are based on the beta distribution.

### Usage

    find.climits(N, S, alpha = 0.05, kind = "upper")

### Arguments

`N` | number of individuals from a census
`S` | number of survivors
`alpha` | type I error
`kind` | type of confidence limit

### Details

This function is called from `mortality.calculation` and `recruitment.calculation`. On its own it computes the number of surviving trees for one confidence interval of a given `kind` for given values of `N`. For mortality, `N` should be N0 the number of individuals alive in the first census. For recruitment, `N` should be N1 the number of individuals alive in the second census. For both mortality and recruitment, `S` is the number of individuals that were alive in N0 AND in N1. Since the confidence intervals provided are limits are survivors, the lower confidence interval for survivorship provides the upper confidence interval for mortality rate (high survivorship = lower mortality) and upper confidence interval for recruitment rate (high survivorship = lower number of recruits). And the upper confidence interval for survivorship provides the lower confidence for mortality (low survivorship = higher mortality) and the lower confidence interval for recruitment rate (low survivorship = higher number of recruits).

The confidence limits for survivorship are computed using a beta distribution.

### Value

Returns the confidence limits in number of surviving trees:

`S` | numeric, the best estimate of the number of surviving trees for the given `kind` of limit.

### Author(s)

Rick Condit and Pamela Hall

### See Also

`CTFS.mortality`, `CTFS.recruitment`

### Examples

    ## Not run:
    # N0 = 100, Dead = 5, Recruits = 10, time = 5 yrs, therefore:
    # S = N0 - Dead = 100 - 5 = 95
    # N1 = N0 - Dead + Recruits = 100 - 5 + 10 = 105

    # find CI limits for mortality
    SM.upper <- find.climits(100,95,kind="upper")
    SM.lower <- find.climits(100,95,kind="lower")
    mort.rate.upper <- ( log(N0) - log(SM.lower) ) / 5
    mort.rate.lower <- ( log(N0) - log(SM.upper) ) / 5

    # find CI limits for recruitment
    SR.upper <- find.climits(105,95,kind="upper")
    SR.lower <- find.climits(105,95,kind="lower")
    rec.rate.upper <- ( log(N1) - log(SR.lower) ) / 5
    rec.rate.lower <- ( log(N1) - log(SR.upper) ) / 5

    ## End(Not run)

[Package CTFS version 1.00 Index]