tibber: Test-Inversion Bootstrap

In distillery: Method Functions for Confidence Intervals and to Distill Information from an Object

Description

Calculate (1 - alpha) * 100 percent confidence intervals for an estimated parameter using the test-inversion bootstrap method.

Usage

tibber(x, statistic, B, rmodel, test.pars, rsize, block.length = 1, v.terms,
    shuffle = NULL, replace = TRUE, alpha = 0.05, verbose = FALSE, ...)

tibberRM(x, statistic, B, rmodel, startval, rsize, block.length = 1, 
    v.terms, shuffle = NULL, replace = TRUE, alpha = 0.05, step.size, 
    tol = 1e-04, max.iter = 1000, keep.iters = TRUE, verbose = FALSE, 
    ...)

Arguments

x	numeric vector or data frame giving the original data series.
statistic	function giving the estimated parameter value. Must minimally contain arguments data and ....
B	number of replicated bootstrap samples to use.
rmodel	function that simulates data based on the nuisance parameter provided by test.pars. Must minimally take arguments: data, par, n, and .... The first, data, is the data series (it need not be used by the function, but it must have this argument, and the original data are passed to it via this argument), par is the nuisance parameter, n is the sample size, and ... are any additional arguments that might be needed.
test.pars	single number or vector giving the nuisance parameter value. If a vector of length greater than one, then the interpolation method will be applied to estimate the confidence bounds.
startval	one or two numbers giving the starting value for the nuisance parameter in the Robbins-Monro algorithm. If two numbers are given, the first is used as the starting value for the lower bound, and the second for the upper.
rsize	(optional) numeric less than the length of the series given by x, used if an m-out-of-n bootstrap sampling procedure should be used.
block.length	(optional) length of blocks to use if the circular block bootstrap resampling scheme is to be used (default is iid sampling).
v.terms	(optional) gives the positions of the variance estimate in the output from statistic. If supplied, then Studentized intervals are returned instead of (tibberRM) of in addition to (tibber) the regular intervals. Generally, such intervals are not ideal for the test-inversion method.
shuffle	n (or rsize) by B matrix giving the indices for the resampling procedure (obviates arguments block.length and B).
replace	logical stating whether or not to sample with replacement.
alpha	significance level for the test.
step.size	Step size for the Robbins-Monro algorithm.
tol	tolerance giving the value for how close the estimated p-value needs to be to alpha before stopping the Robbins-Monro algorithm.
max.iter	Maximum number of iterations to perform before stopping the Robbins-Monro algorithm.
keep.iters	logical, should information from each iteration of the Robbins-Monro algorithm be saved?
verbose	logical should progress information be printed to the screen.
...	Optional arguments to booter, statistic and rmodel.

Details

The test-inversion bootstrap (Carpenter 1999; Carpenter and Bithell 2000; Kabaila 1993) is a parametric bootstrap procedure that attempts to take advantage of the duality between confidence intervals and hypothesis tests in order to create bootstrap confidence intervals. Let X = X_1,...,X_n be a series of random variables, T, is a parameter of interest, and R(X) is an estimator for T. Further, let x = x_1,...,x_n be an observed realization of X, and r(x) an estimate for R(X), and let x* be a bootstrap resample of x, etc. Suppose that X is distributed according to a distribution, F, with parameter T and nuisance parameter V.

The procedure is carried out by estimating the p-value, say p*, from r*_1, ..., r*_B estimated from a simulated sample from rmodel assuming a specific value of V by way of finding the sum of r*_i < r(x) (with an additional correction for the ties r*_i = r(x)). The procedure is repeated for each of k values of V to form a sample of p-values, p*_1, ..., p*_k. Finally, some form of root-finding algorithm must be employed to find the values r*_L and r*_U that estimate the lower and upper values, resp., for R(X) associated with (1 - alpha) * 100 percent confidence limits. For tibber, the routine can be executed one time if test.pars is of length one, which will enable a user to employ their own root-finding algorithm. If test.pars is a vector, then an interpolation estimate is found for the confidence end points. tibberRM makes successive calls to tibber and uses the Robbins-Monro algorithm (Robbins and Monro 1951) to try to find the appropriate bounds, as suggested by Garthwaite and Buckland (1992).

Value

For tibber, if test.pars is of length one, then a 3 by 1 matrix is returned (or, if v.terms is supplied, then a 4 by 1 matrix) where the first two rows give estimates for R(X) based on the original simulated series and the median from the bootstrap samples, respectively. the last row gives the estimated p-value. If v.terms is supplied, then the fourth row gives the p-value associated with the Studentized p-value.

If test.pars is a vector with length k > 1, then a list object of class “tibbed” is returned, which has components:

results	3 by k matrix (or 4 by k, if v.terms is not missing) giving two estimates for R(X) (one from the simulated series and one of the median of the bootstrap resamples, resp.) and the third row giving the estimated p-value for each value of V.
TIB.interpolated, STIB.interpolated	numeric vector of length 3 giving the lower bound estimate, the estimate from the original data (i.e., r(x)), and the estimated upper bound as obtained from interpolating over the vector of possible values for V given by test.pars. The Studentized TIB interval, STIB.interpolated, is only returned if v.terms is provided.
Plow, Pup, PstudLow, PstudUp	Estimated p-values used for interpolation of p-value.
call	the original function call.
data	the original data passed by the x argument.
statistic, B, rmodel, test.pars, rsize, block.length, alpha, replace	arguments passed into the orignal function call.
n	original sample size.
total.time	Total time it took for the function to run.

For tibberRM, a list of class “tibRMed” is returned with components:

call	the original function call.
x, statistic, B, rmodel, rsize, block.length, alpha, replace	arguments passed into the orignal function call.
result	vector of length 3 giving the estimated confidence interval with the original parameter estimate in the second component.
lower.p.value, upper.p.value	Estimated achieved p-values for the lower and upper bounds.
lower.nuisance.par, upper.nuisance.par	nuisance parameter values associated with the lower and upper bounds.
lower.iterations, upper.iterations	number of iterations of the Robbins-Monro algorithm it took to find the lower and upper bounds.
total.time	Total time it took for the function to run.

Author(s)

Eric Gilleland

References

Carpenter, James (1999) Test inversion bootstrap confidence intervals. J. R. Statist. Soc. B, 61 (1), 159–172.

Carpenter, James and Bithell, John (2000) Bootstrap confidence intervals: when, which, what? A practical guide for medical statisticians. Statist. Med., 19, 1141–1164.

Garthwaite, P. H. and Buckland, S. T. (1992) Generating Monte Carlo confidence intervals by the Robbins-Monro process. Appl. Statist., 41, 159–171.

Kabaila, Paul (1993) Some properties of profile bootstrap confidence intervals. Austral. J. Statist., 35 (2), 205–214.

Robbins, Herbert and Monro, Sutton (1951) A stochastic approximation method. Ann. Math Statist., 22 (3), 400–407.

See Also

booter, pbooter

Examples

# The following example follows the example provided at:
#
# http://influentialpoints.com/Training/bootstrap_confidence_intervals.htm
#
# which is provided with a creative commons license:
#
# https://creativecommons.org/licenses/by/3.0/ 
#
y <- c( 7, 7, 6, 9, 8, 7, 8, 7, 7, 7, 6, 6, 6, 8, 7, 7, 7, 7, 6, 7,
        8, 7, 7, 6, 8, 7, 8, 7, 8, 7, 7, 7, 5, 7, 7, 7, 6, 7, 8, 7, 7,
        8, 6, 9, 7, 14, 12, 10, 13, 15 )

trm <- function( data, ... ) {

    res <- try( mean( data, trim = 0.1, ... ) )
    if( class( res ) == "try-error" ) return( NA )
    else return( res )

} # end of 'trm' function.

genf <- function( data, par, n, ... ) {

    y <- data * par
    h <- 1.06 * sd( y ) / ( n^( 1 / 5 ) )
    y <- y + rnorm( rnorm( n, 0, h ) )
    y <- round( y * ( y > 0 ) )

    return( y )

} # end of 'genf' function.

look <- tibber( x = y, statistic = trm, B = 500, rmodel = genf,
    test.pars = seq( 0.85, 1.15, length.out = 100 ) )

look

plot( look )
# outer vertical blue lines should cross horizontal blue lines
# near where an estimated p-value is located.

tibber( x = y, statistic = trm, B = 500, rmodel = genf, test.pars = 1 )


## Not run: 
look2 <- tibberRM(x = y, statistic = trm, B = 500, rmodel = genf, startval = 1,
    step.size = 0.03, verbose = TRUE )

look2
# lower achieved est. p-value should be close to 0.025
# upper should be close to 0.975.

plot( look2 )

trm2 <- function( data, par, n, ... ) {

    a <- list( ... )
    res <- try( mean( data, trim = a$trim ) )
    if( class( res ) == "try-error" ) return( NA )
    else return( res )

} # end of 'trm2' function.

tibber( x = y, statistic = trm2, B = 500, rmodel = genf,
    test.pars = seq( 0.85, 1.15, length.out = 100 ), trim = 0.1 )

# Try getting the STIB interval.  v.terms = 2 below because mfun
# returns the variance of the estimated parameter in the 2nd position.
#
# Note: the STIB interval can be a bit unstable.

mfun <- function( data, ... ) return( c( mean( data ), var( data ) ) )

gennorm <- function( data, par, n, ... ) {

    return( rnorm( n = n, mean = mean( data ), sd = sqrt( par ) ) )

} # end of 'gennorm' function.

set.seed( 1544 )
z <- rnorm( 50 )
mean( z )
var( z )

# Trial-and-error is necessary to get a good result with interpolation method.
res <- tibber( x = z, statistic = mfun, B = 500, rmodel = gennorm,
    test.pars = seq( 0.95, 1.10, length.out = 100 ), v.terms = 2 )

res

plot( res )

# Much trial-and-error is necessary to get a good result with RM method.
# If it fails to converge, try increasing the tolerance.
res2 <- tibberRM( x = z, statistic = mfun, B = 500, rmodel = gennorm,
    startval = c( 0.95, 1.1 ), step.size = 0.003, tol = 0.001, v.terms = 2,
    verbose = TRUE )
# Note that it only gives the STIB interval.

res2

plot( res2 )


## End(Not run)

distillery documentation built on May 19, 2021, 9:08 a.m.