Setup | Data exploration | Full trees | Clone trees | Estimating growth rates | Understanding the function outputs | Downstream analysis | Metadata | Recreating figures | MPN vs. Normal (Fig. 5E) | Single vs. multi-driver (Fig. 5F) | Time from clone initiation to diagnosis (Fig. 5G) | Validation | References / Data sources:
This package is considered a duplicate. The official version of this package is found at:https://bdj34.r-universe.dev/cloneRate
Package: cloneRate 0.2.3
Brian Johnson
cloneRate: Estimate Growth Rates from Phylogenetic Trees
Quickly estimate the net growth rate of a population or clone whose growth can be approximated by a birth-death branching process. Input should be phylogenetic tree(s) of clone(s) with edge lengths corresponding to either time or mutations. Based on coalescent results in Johnson et al. (2023) <doi:10.1093/bioinformatics/btad561>. Simulation techniques as well as growth rate methods build on prior work from Lambert A. (2018) <doi:10.1016/j.tpb.2018.04.005> and Stadler T. (2009) <doi:10.1016/j.jtbi.2009.07.018>.
Authors:
cloneRate_0.2.3.tar.gz
cloneRate_0.2.3.zip(r-4.7-x86_64)cloneRate_0.2.3.zip(r-4.7-arm64)cloneRate_0.2.3.zip(r-4.6-x86_64)cloneRate_0.2.3.zip(r-4.6-arm64)
cloneRate_0.2.3.tar.gz(r-4.7-arm64)cloneRate_0.2.3.tar.gz(r-4.7-x86_64)cloneRate_0.2.3.tar.gz(r-4.6-arm64)cloneRate_0.2.3.tar.gz(r-4.6-x86_64)
cloneRate_0.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cloneRate/json (API)
| # Install 'cloneRate' in R: |
| install.packages('cloneRate', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bdj34/clonerate/issues
Pkgdown/docs site:https://bdj34.github.io
Datasets:
- exampleMutTrees - Example mutation tree data
- exampleUltraTrees - Example ultrametric tree data
- longitudinalData - Longitudinal validation data
- realCloneData - Real clone data from human blood
Last updated from:d5c4ff9c51. Checks:10 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 233 | ||
| linux-devel-x86_64 | OK | 274 | ||
| source / vignettes | OK | 304 | ||
| linux-release-arm64 | OK | 238 | ||
| linux-release-x86_64 | OK | 225 | ||
| windows-devel-arm64 | OK | 389 | ||
| windows-devel-x86_64 | OK | 361 | ||
| windows-release-arm64 | OK | 327 | ||
| windows-release-x86_64 | OK | 324 | ||
| wasm-release | OK | 194 |
Exports:birthDeathMCMCcoal_to_treeinternalLengthsmaxLikelihoodsharedMutssimMutsimUltrasiteFrequencyultra2mut
Dependencies:abindapebackportsBHcallrcheckmateclicpp11descdigestdistributionalfarvergenericsggplot2gluegmpgridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrmatrixStatsnlmenumDerivotelpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangRmpfrrstanrstantoolsS7scalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr
Analysis of human blood data
Last update: 2023-09-22
Started: 2023-09-22
Intro to validating growth rate estimates via simulation
Setup | Simulating trees | Ultrametric trees | Mutation trees | Quantitative comparisons | Max likelihood vs. internal lengths vs. shared mutations | Root Mean Square Error (RMSE) | Mean | Standard deviation | Coverage probability | Varying parameters | Varying n | Varying r (and/or cloneAge) | Varying r or cloneAge? | Performance across r values | References
Last update: 2023-09-22
Started: 2023-09-22
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The 'cloneRate' package. | cloneRate-package cloneRate |
| Growth rate estimate using MCMC | birthDeathMCMC |
| Generate tree from coalescence times | coal_to_tree |
| Example mutation tree data | exampleMutTrees |
| Example ultrametric tree data | exampleUltraTrees |
| Growth rate estimate using the sum of internal lengths | internalLengths |
| Longitudinal validation data | longitudinalData |
| Growth rate estimate using Maximum Likelihood | maxLikelihood |
| Real clone data from human blood | realCloneData |
| Growth rate estimate using the sum of shared mutations assuming a mutation tree | sharedMuts |
| Simulate mutation-based birth and death branching trees | simMut |
| Simulate ultrametric birth and death branching trees | simUltra |
| Get site frequency spectrum of a tree | siteFrequency |
| Add poissonian mutations to an ultrametric tree(s) | ultra2mut |