msfit performs curve fitting for multiscale
bootstrap resampling. It generates an object of class
msfit. Several generic methods are available.
msfit(bp, r, nboot)# S3 method for msfit
plot(x, curve=TRUE, main=NULL, sub=NULL, xlab=NULL, ylab=NULL, ...)
# S3 method for msfit
lines(x, col=2, lty=1, ...)
# S3 method for msfit
summary(object, digits=3, ...)
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 \(n'\).
numeric value (vector) of the number of bootstrap replications.
object of class msfit.
logical. If TRUE, the fitted curve is drawn.
generic graphic parameters.
object of class msfit.
integer indicating the precision to be used in rounding.
other parameters to be used in the functions.
msfit returns an object of class msfit. It contains
the following objects:
numeric 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.
numeric vector of estimated standard errors of \(p\)-values.
numeric vector related to geometric aspects of
hypotheses. v is signed distance and c is curvature of
the boundary.
numeric value of the degree of freedom in curve fitting.
residual sum of squares.
\(p\)-value of chi-square test based on asymptotic theory.
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.
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.