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.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'))

Peer review:

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

Datasets:

On CRAN:

10 exports 0.84 score 35 dependencies 1 scripts 227 downloads

Last updated 7 months agofrom:00ff991035. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-winOKAug 27 2024
R-4.5-linuxOKAug 27 2024
R-4.4-winOKAug 27 2024
R-4.4-macOKAug 27 2024
R-4.3-winOKAug 27 2024
R-4.3-macOKAug 27 2024

Exports:clInitializeTernaryQuartsclInitializeTernarySplitsclPlotAverageQuartetsclPlotAverageSplitsclPlotBestAverageSplitsclPlotQuartetsclPlotSplitsclPlotTheseAverageQuartetsclPlotTheseAverageSplitsclPlotTheseBestAverageSplits

Dependencies:base64encbslibcachemclicommonmarkcrayondigestfastmapfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmemoisemimePlotToolspromisesR6rappdirsRcppRcppHungarianrlangsassshinysourcetoolsspTernarywithrxtable

Analysing Congreve & Lamsdell matrices

Martin R. Smith [email protected]

Rendered fromConduct-analyses.Rmdusingknitr::rmarkdownon Aug 27 2024.

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 Aug 27 2024.

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 Aug 27 2024.

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