Package: scaleboot 1.0-1

scaleboot: Approximately Unbiased P-Values via Multiscale Bootstrap

Calculating approximately unbiased (AU) p-values from multiscale bootstrap probabilities. See Shimodaira (2004) <doi:10.1214/009053604000000823>, Shimodaira (2008) <doi:10.1016/j.jspi.2007.04.001>, Terada ans Shimodaira (2017) <arxiv:1711.00949>, and Shimodaira and Terada (2019) <doi.org/10.3389/fevo.2019.00174>.

Authors:Hidetoshi Shimodaira <[email protected]>

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scaleboot.pdf |scaleboot.html✨
scaleboot/json (API)

# Install 'scaleboot' in R:
install.packages('scaleboot', repos = c('https://shimosan.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • lung.pvclust - Clustering of 73 Lung Tumors
  • lung.sb - Clustering of 73 Lung Tumors
  • lung73.pvclust - Clustering of 73 Lung Tumors
  • lung73.sb - Clustering of 73 Lung Tumors
  • mam105.ass - Mammal Phylogenetic Analysis for 15 trees
  • mam105.aux - Mammal Phylogenetic Analysis for 15 trees
  • mam105.mt - Mammal Phylogenetic Analysis for 15 trees
  • mam105.relltest - Mammal Phylogenetic Analysis for 15 trees
  • mam15.ass - Mammal Phylogenetic Analysis for 15 trees
  • mam15.aux - Mammal Phylogenetic Analysis for 15 trees
  • mam15.mt - Mammal Phylogenetic Analysis for 15 trees
  • mam15.relltest - Mammal Phylogenetic Analysis for 15 trees
  • mam26.ass - Mammal Phylogenetic Analysis for 15 trees
  • mam26.aux - Mammal Phylogenetic Analysis for 15 trees
  • mam26.mt - Mammal Phylogenetic Analysis for 15 trees

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.86 score 24 scripts 174 downloads 3 mentions 25 exports 2 dependencies

Last updated 5 years agofrom:c0e40bf17c. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 16 2024
R-4.5-winNOTEOct 16 2024
R-4.5-linuxNOTEOct 16 2024
R-4.4-winNOTEOct 16 2024
R-4.4-macNOTEOct 16 2024
R-4.3-winNOTEOct 16 2024
R-4.3-macNOTEOct 16 2024

Exports:countw.assmaxcountw.shtestcountw.shtestassplot.scalebootplot.scalebootvread.assread.cntread.mtrelltestsbaicsbaic<-sbconfsbfitsblegendsbmodelnamessboptionssbphylosbplotbetasbpsi.genericsbpsi.polysbpsi.singsbpsi.sphesbpvalsbpvclustscaleboot

Dependencies:mvtnormpvclust

Multiscale Bootstrap using Scaleboot Package

Rendered fromusesb.Rnwusingutils::Sweaveon Oct 16 2024.

Last update: 2019-12-04
Started: 2017-09-18

Readme and manuals

Help Manual

Help pageTopics
Approximately Unbiased P-values via Multiscale Bootstrapscaleboot-package
Extract Model Coefficientscoef.scaleboot coef.scalebootv
Interface to External Packagesinterface.scaleboot read.ass read.cnt read.mt sbfit.pvclust sbpvclust
Clustering of 73 Lung Tumorslung.pvclust lung.sb lung73 lung73.pvclust lung73.sb
Mammal Phylogenetic Analysis for 15 treesmam105 mam105.ass mam105.aux mam105.mt mam105.relltest mam15 mam15.ass mam15.aux mam15.mt mam15.relltest mam26 mam26.ass mam26.aux mam26.mt
Plot Diagnostics for Multiscale Bootstraplines.scaleboot plot.scaleboot plot.scalebootv plot.summary.scaleboot plot.summary.scalebootv sblegend sbplotbeta
RELL Test for Phylogenetic Inferencerelltest summary.relltest
Akaike's Information Criterionsbaic sbaic.scaleboot sbaic.scalebootv sbaic<- sbaic<-.scaleboot sbaic<-.scalebootv
Bootstrap Confidence Intervalsplot.sbconf print.sbconf sbconf sbconf.default sbconf.sbconf
Fitting Models to Bootstrap Probabilitiesprint.scaleboot print.scalebootv sbfit sbfit.data.frame sbfit.default sbfit.matrix sbfit.scaleboot sbfit.scalebootv
Options for Multiscale Bootstrapsboptions
Tables for phylogenetic inferenceprint.sbphylo print.summary.sbphylo sbphylo summary.sbphylo
Model Specification Functionssbmodelnames sbpsi sbpsi.generic sbpsi.poly sbpsi.sing sbpsi.sphe
Extract P-valuessbpval sbpval.summary.scaleboot sbpval.summary.scalebootv
Multiscale Bootstrap Resamplingcountw.assmax countw.shtest countw.shtestass scaleboot
P-value Calculation for Multiscale Bootstrapprint.summary.scaleboot print.summary.scalebootv summary.scaleboot summary.scalebootv