msfit: Curve Fitting for Multiscale Bootstrap Resampling

Description

msfit performs curve fitting for multiscale bootstrap resampling. It generates an object of class msfit. Several generic methods are available.

Usage

msfit(bp, r, nboot)

## S3 method for class 'msfit':
plot(x, curve=TRUE, main=NULL, sub=NULL, xlab=NULL, ylab=NULL, ...)

## S3 method for class 'msfit':
lines(x, col=2, lty=1, ...)

## S3 method for class 'msfit':
summary(object, digits=3, ...)

Arguments

numeric vector of bootstrap probability values.

numeric vector of relative sample size of bootstrap samples defined as $r=n'/n$ for original sample size $n$ and bootstrap sample size $n'$.

nboot

numeric value (vector) of the number of bootstrap replications.

object of class msfit.

curve

logical. If TRUE, the fitted curve is drawn.

main, sub, xlab, ylab, col, lty

generic graphic parameters.

object

object of class msfit.

digits

integer indicating the precision to be used in rounding.

...

other parameters to be used in the functions.

Value

msfit returns an object of class msfit. It contains the following objects:
pnumeric vector of $p$-values. au is AU (Approximately Unbiased) $p$-value computed by multiscale bootstrap resampling, which is more accurate than BP value (explained below) as unbiased $p$-value. bp is BP (Bootstrap Probability) value, which is simple but tends to be unbiased when the absolute value of c (a value in coef vector, explained below) is large.
senumeric vector of estimated standard errors of $p$-values.
coefnumeric vector related to geometric aspects of hypotheses. v is signed distance and c is curvature of the boundary.
dfnumeric value of the degree of freedom in curve fitting.
rssresidual sum of squares.
pchi$p$-value of chi-square test based on asymptotic theory.

Details

function msfit performs the curve fitting for multiscale bootstrap resampling. In package pvclust this function is only called from the function pvclust (or parPvclust), and may never be called from users. However one can access a list of msfit objects by x$msfit, where x is an object of class pvclust.

References

Shimodaira, H. (2004) "Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling", Annals of Statistics, 32, 2616-2641. Shimodaira, H. (2002) "An approximately unbiased test of phylogenetic tree selection", Systematic Biology, 51, 492-508.