fullfact (version 1.0)

ciMANA2: Bootstrap confidence intervals 2

Description

Extracts bootstrap-t confidence intervals for additive genetic, non-additive genetic, and maternal variance components. Also extracts intervals for optional position and block variance components.

Usage

ciMANA2(comp, level = 95, rnd_r = 3, rnd_p = 1, position = NULL, block = NULL,
bias = NULL, accel = 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.

position

Optional column name containing position factor information.

block

Optional column name containing block factor information.

bias

Optional vector of raw observed additive, non-additive, maternal, position and/or block variance component values for bias correction, i.e. c(additive, non-additive, maternal, position/block). If there is a position and a block c(..., maternal, position, block).

accel

Optional data frame of jackknifed data model results for acceleration correction.

trait

Optional label for the phenotypic trait.

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 optional position and/or block variance components. Values are presented as raw and percentages of the total variance value within each row.

Details

Used for bootstrap resampling results produced using resampLmer2 for normal data or resampGlmer2 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 JackLmer2, for normal data or JackGlmer2 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.

References

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

See Also

ciMANA, ciMANA3

Examples

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

#Extract un-corrected confidence interval
ciMANA2(comp=chinook_bootL,position="tray")

#Extract bias corrected confidence interval
ciMANA2(comp=chinook_bootL,bias=c(0.0000000,0.7192253,0.2029684,0.1077423),position="tray")
#see details for 'bias' fail

#Extract bias and accelerated corrected confidence interval
#Import jackknife resampled data model results
data(chinook_jackL)
#
ciMANA2(comp=chinook_bootL,bias=c(0.0000000,0.7192253,0.2029684,0.1077423),
accel=chinook_jackL,position="tray")
#see details for 'bias' fail