# msfit: Curve Fitting for Multiscale Bootstrap Resampling In pvclust: Hierarchical Clustering with P-Values via 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

 ``` 1 2 3 4 5 6 7 8 9 10``` ```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 documentation built on Nov. 19, 2019, 5:07 p.m.