ciMANA3: Bootstrap confidence intervals 3

In fullfact: Full Factorial Breeding Analysis

Bootstrap confidence intervals 3

Description

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

Usage

ciMANA3(comp, level = 95, rnd_r = 3, rnd_p = 1, bias = NULL, accel = NULL,
remain = NULL, trait = NULL)

Arguments

comp	Data frame of bootstrap resampling results.
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.
bias	Optional vector of raw observed additive, non-additive, and maternal variance components for bias correction. Followed by any other components in the order of the vector remain, i.e. c(additive, non-additive, maternal, component1, component2, etc.).
accel	Optional data frame of jackknifed data model results for acceleration correction.
remain	Vector of column names for additional effects.
trait	Optional label for the phenotypic trait.

Details

Used for bootstrap resampling results produced using resampLmer3 for normal data or resampGlmer3 for non-normal data. Bootstrap-t confidence intervals, including bias and acceleration correction methods are described by Efron and Tibshirani (1993). Jackknife data model results for acceleration correction can be produced using JackLmer3, for normal data or JackGlmer3 for non-normal data. The 'bias fail' warning is if the bias calculation is Inf or -Inf, e.g. bias contains a zero value, so the uncorrected confidence interval is displayed.

Value

Prints a data frame containing the lower, median, and upper values of the bootstrap-t confidence interval for additive genetic, non-additive genetic, maternal, 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.

See Also

ciMANA, ciMANA2

Examples

#Import bootstrap resampled data model results
data(chinook_bootL) #Chinook salmon offspring length

#Extract un-corrected confidence interval
ciMANA3(comp=chinook_bootL,remain=c("tray","Residual"))

#Extract bias corrected confidence interval
ciMANA3(comp=chinook_bootL,remain=c("tray","Residual"),
bias=c(0,0.7192,0.2030,0.1077,0.5499))
#see details for 'bias' fail

#Extract bias and accelerated corrected confidence interval
#Import jackknife resampled data model results
data(chinook_jackL)
#
ciMANA3(comp=chinook_bootL,remain=c("tray","Residual"),
bias=c(0,0.7192,0.2030,0.1077,0.5499),accel=chinook_jackL)

fullfact documentation built on May 29, 2024, 1:21 a.m.