confint.cyclic_shift {codyn} | R Documentation |

## Confidence Intervals from a Cyclic Shift Permutation

### Description

Calculates confidence intervals for the S3 object produced by `cyclic_shift`

### Usage

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

### Arguments

`object` |
An object of class |

`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 |

`level` |
the confidence level required. |

`...` |
further arguments to |

### 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

```
# 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)
```

*codyn*version 2.0.5 Index]