# ciJack3: Jackknife confidence intervals 3 In fullfact: Full Factorial Breeding Analysis

 ciJack3 R Documentation

## Jackknife confidence intervals 3

### Description

Extracts jackknife confidence intervals for additive genetic, non-additive genetic, and maternal variance components. Also extracts intervals for additional fixed and/or random effects.

### Usage

``````ciJack3(comp, full, remain = NULL, level = 95, rnd_r = 3, rnd_p = 1, trait = NULL)
``````

### Arguments

 `comp` Data frame of jackknife resampling results `full` A vector of raw observed additive, non-additive, maternal, and total variance component values for from the full observed data set, i.e. c(additive, non-additive, maternal, total). Followed by any other components in the order of the vector remain, i.e. c(additive, non-additive, maternal, total, component1, component2, etc.). `remain` Vector of column names for additional effects `level` Confidence level, as a percentage. Default is 95. `rnd_r` Number of decimal places to round the confidence interval of raw values. `rnd_p` Number of decimal places to round the confidence interval of percentage values. `trait` Optional label for the phenotypic trait.

### Details

Used for jackknife resampling results produced using JackLmer3 for normal data or JackGlmer3 for non-normal data. Jackknife confidence intervals, using pseudo-values are described by Efron and Tibshirani (1993). The standard errors are calculated from the pseudo-values and the Student's t distribution is used to provide the lower and upper confidence values. For delete-d jackknife resampling, M degrees of freedom are used for producing the confidence interval (Martin et al. 2004): M = N / d, where N is the total number of observations and d is the number of deleted observations. That is, M is the number of row in the jackknife resampling results. Large values of M, such as 1,000, can translate to the delete-d jackknife resampling method approaching bootstrap resampling expectations (Efron & Tibshirani 1993).

### Value

Prints a data frame containing the lower, median, and upper values of the jackknife confidence interval for additive genetic, non-additive genetic, maternal variance components, and any additional fixed effect and/or random effect variance components. Values are presented as raw and percentages of the total variance value within each row.

### References

Efron B, Tibshirani R. 1993. An introduction to the Bootstrap. Chapman and Hall, New York.

Martin, H., Westad, F. & Martens, H. (2004). Imporved Jackknife Variance Estimates of Bilinear Model Parameters. COMPSTAT 2004 – Proceedings in Computational Statistics 16th Symposium Held in Prague, Czech Republic, 2004 (ed J. Antoch), pp. 261-275. Physica-Verlag HD, Heidelberg.

`ciJack`, `ciJack2`
``````data(chinook_jackL) #Chinook salmon offspring length, delete-one jackknife