codyn (version 2.0.5)

confint.cyclic_shift: Confidence Intervals from a Cyclic Shift Permutation

Description

Calculates confidence intervals for the S3 object produced by cyclic_shift

Usage

# S3 method for cyclic_shift
confint(object, parm = "out", level = 0.95, ...)

Arguments

object

An object of class cyclic_shift

parm

which parameter is to be given a confidence interval. At present there is only one option: the mean of the null distribution. Defaults to "out", referring to the null distribution in objects of class cyclic_shift.

level

the confidence level required.

...

further arguments to quantile

Value

A dataframe with the following columns:

• lowerCI: A numeric column with the lowest confidence interval value.

• upperCI: A numeric column with the highest confidence interval value.

• nullMean: A numeric column with the average value of the specified test statistic when calculated on a null community.

References

Hallett, Lauren M., Joanna S. Hsu, Elsa E. Cleland, Scott L. Collins, Timothy L. Dickson, Emily C. Farrer, Laureano A. Gherardi, et al. "Biotic Mechanisms of Community Stability Shift along a Precipitation Gradient." Ecology 95, no. 6 (2014): 1693-1700.

Harms, Kyle E., Richard Condit, Stephen P. Hubbell, and Robin B. Foster. "Habitat Associations of Trees and Shrubs in a 50-Ha Neotropical Forest Plot." Journal of Ecology 89, no. 6 (2001): 947-59.

Examples

# NOT RUN {
# Calculate a covariance matrix on a null community
data(knz_001d)
a1_cyclic <- cyclic_shift(subset(knz_001d, subplot == "A_1"),
                   time.var = "year",
                   species.var = "species",
                   abundance.var = "abundance",
                   FUN = cov,
                   bootnumber = 10)

# Return CI on a1_cyclic
confint(a1_cyclic)
# }