Package: CongreveLamsdell2016 1.0.3

CongreveLamsdell2016: Distance Metrics for Trees Generated by Congreve and Lamsdell

Includes the 100 datasets simulated by Congreve and Lamsdell (2016) <doi:10.1111/pala.12236>, and analyses of the partition and quartet distance of reconstructed trees from the generative tree, as analysed by Smith (2019) <doi:10.1098/rsbl.2018.0632>.

Authors:Martin R. Smith [aut, cre, cph], Curtis R. Congreve [cph, dtc], James C. Lamsdell [cph, dtc]

CongreveLamsdell2016_1.0.3.tar.gz
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CongreveLamsdell2016_1.0.3.tgz(r-4.5-any)CongreveLamsdell2016_1.0.3.tgz(r-4.4-any)CongreveLamsdell2016_1.0.3.tgz(r-4.3-any)
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CongreveLamsdell2016.pdf |CongreveLamsdell2016.html✨
CongreveLamsdell2016/json (API)
NEWS

# Install 'CongreveLamsdell2016' in R:
install.packages('CongreveLamsdell2016', repos = c('https://ms609.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ms609/congrevelamsdell2016/issues

Datasets:

On CRAN:

Conda:

4.48 score 1 scripts 276 downloads 10 exports 35 dependencies

Last updated 1 years agofrom:00ff991035. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 23 2025
R-4.5-winOKFeb 23 2025
R-4.5-macOKFeb 23 2025
R-4.5-linuxOKFeb 23 2025
R-4.4-winOKFeb 23 2025
R-4.4-macOKFeb 23 2025
R-4.3-winOKFeb 23 2025
R-4.3-macOKFeb 23 2025

Exports:clInitializeTernaryQuartsclInitializeTernarySplitsclPlotAverageQuartetsclPlotAverageSplitsclPlotBestAverageSplitsclPlotQuartetsclPlotSplitsclPlotTheseAverageQuartetsclPlotTheseAverageSplitsclPlotTheseBestAverageSplits

Dependencies:base64encbslibcachemclicommonmarkcrayondigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmemoisemimePlotToolspromisesR6rappdirsRcppRcppHungarianrlangsassshinysourcetoolsspTernarywithrxtable

Analysing Congreve & Lamsdell matrices

Martin R. Smith [email protected]

Rendered fromConduct-analyses.Rmdusingknitr::rmarkdownon Feb 23 2025.

Last update: 2024-02-29
Started: 2018-11-29

Resolution and accuracy in Congreve & Lamsdell matrices

Martin R. Smith [email protected]

Rendered fromCompare-methods.Rmdusingknitr::rmarkdownon Feb 23 2025.

Last update: 2024-02-22
Started: 2018-11-28

Node support efficacy in Congreve & Lamsdell matrices

Martin R. Smith [email protected]

Rendered fromCompare-node-supports.Rmdusingknitr::rmarkdownon Feb 23 2025.

Last update: 2019-12-19
Started: 2018-11-28

Readme and manuals

Help Manual

Help pageTopics
Consistency indicesclCI
Default colours for analyses.clColours
Initialize ternary plots for quartet plottingclInitializeTernaryQuarts clInitializeTernarySplits
100 simulated data matricesclMatrices clPhyDat
Plot resultsclPlotAverageQuartets clPlotAverageSplits clPlotBestAverageSplits clPlotQuartets clPlotSplits clPlotTheseAverageQuartets clPlotTheseAverageSplits clPlotTheseBestAverageSplits
Tree topology for matrix simulationclReferenceTree
Congreve and Lamsdell tree distancesclBootFreqPartitions clBootFreqQuartets clBootGcPartitions clBootGcQuartets clBremPartitions clBremQuartets clJackFreqPartitions clJackFreqQuartets clJackGcPartitions clJackGcQuartets clMkvPartitions clMkvQuartets clResults