Package: cloneRate 0.2.3.9000

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:Brian Johnson [cre, aut, cph], Yubo Shuai [aut, cph], Jason Schweinsberg [aut, cph], Kit Curtius [aut, cph]

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cloneRate/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/bdj34/clonerate/issues

On CRAN:

10 exports 4 stars 1.46 score 57 dependencies 8 scripts 203 downloads

Last updated 5 months agofrom:f56cde173d. Checks:OK: 1 NOTE: 8. Indexed: yes.

Exports:birthDeathMCMCcoal_to_treeinternalLengthsmaxLikelihoodsharedMutssimMutsimUltrasiteFrequencytruncate_treeultra2mut

Dependencies:abindapebackportsBHcallrcheckmateclicolorspacedescdigestdistributionalfansifarvergenericsggplot2gluegmpgridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangRmpfrrstanrstantoolsscalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr