R: Curve Fitting for Multiscale Bootstrap Resampling

msfit {pvclust} | R Documentation

## 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.

[Package pvclust version 2.0-0 Index]