pvclust: msfit – R documentation

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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

`bp`	numeric vector of bootstrap probability values.
`r`	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.
`x`	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.

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.

Value

msfit returns an object of class msfit. It contains the following objects:

`p`	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.
`se`	numeric vector of estimated standard errors of p-values.
`coef`	numeric vector related to geometric aspects of hypotheses. `v` is signed distance and `c` is curvature of the boundary.
`df`	numeric value of the degree of freedom in curve fitting.
`rss`	residual sum of squares.
`pchi`	p-value of chi-square test based on asymptotic theory.

Author(s)

Ryota Suzuki suzuki@ef-prime.com

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.

pvclust

Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling

v2.2-0

GPL (>= 2)

Authors

Ryota Suzuki <suzuki@ef-prime.com>, Yoshikazu Terada <terada@sigmath.es.osaka-u.ac.jp>, Hidetoshi Shimodaira <shimo@i.kyoto-u.ac.jp>

Initial release

2019-11-19