Package: MSCsimtester 1.2
MSCsimtester: Tests of Multispecies Coalescent Gene Tree Simulator Output
Statistical tests for validating multispecies coalescent gene tree simulators, using pairwise distances and rooted triple counts. See Allman ES, Baños HD, Rhodes JA 2023. Testing multispecies coalescent simulators using summary statistics, IEEE/ACM Trans Comput Biol Bioinformat, 20(2):1613–1618. <doi:10.1109/TCBB.2022.3177956>.
Authors:
MSCsimtester_1.2.tar.gz
MSCsimtester_1.2.zip(r-4.7-any)MSCsimtester_1.2.zip(r-4.6-any)MSCsimtester_1.2.zip(r-4.5-any)
MSCsimtester_1.2.tgz(r-4.6-any)MSCsimtester_1.2.tgz(r-4.5-any)
MSCsimtester_1.2.tar.gz(r-4.7-any)MSCsimtester_1.2.tar.gz(r-4.6-any)
MSCsimtester_1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MSCsimtester/json (API)
| # Install 'MSCsimtester' in R: |
| install.packages('MSCsimtester', repos = c('https://eallman.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:b859fc4046. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 115 | ||
| source / vignettes | OK | 157 | ||
| linux-release | OK | 113 | ||
| macos-release | OK | 165 | ||
| macos-oldrel | OK | 199 | ||
| windows-devel | OK | 58 | ||
| windows-release | OK | 65 | ||
| windows-oldrel | OK | 65 | ||
| wasm-release | OK | 98 |
Exports:ADtestpairwiseDistplotEdgeOrderplotPopsrootedTriple
Dependencies:apedigestkSampleslatticenlmerbibutilsRcppRdpackSuppDists
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Validity tests of simulators of the multspecies coalescent model in phylogenomics. | MSCsimtester-package MSCsimtester |
| Anderson-Darling test comparing sample and theoretical pairwise distance distributions. | ADtest |
| Simulated gene tree dataset. | genetreeSample |
| Compute and plot sample and theoretical pairwise distance densities. | pairwiseDist |
| Plot species tree, with edge numbers on edges. | plotEdgeOrder |
| Plot species tree, with population sizes on edges. | plotPops |
| Print function for objects of class 'ADtestOutput'. | print.ADtestOutput |
| Print function for objects of class 'rootedTripleOutput'. | print.rootedTripleOutput |
| Compare expected and sample frequencies of topological rooted triples. | rootedTriple |