Package: mixtree 0.0.1

mixtree: A Statistical Framework for Comparing Sets of Trees

Apply hypothesis testing methods to assess differences between sets of trees.

Authors:Cyril Geismar [aut, cre, cph]

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mixtree.pdf |mixtree.html✨
mixtree/json (API)

# Install 'mixtree' in R:

install.packages('mixtree', repos = c('https://cygei.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cygei/mixtree/issues

Pkgdown site:https://cygei.github.io

On CRAN:

4.70 score 8 exports 147 dependencies

Last updated 1 months agofrom:de3662b1ac. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 06 2025
R-4.5-win	OK	Mar 06 2025
R-4.5-mac	OK	Mar 06 2025
R-4.5-linux	OK	Mar 06 2025
R-4.4-win	OK	Mar 06 2025
R-4.4-mac	OK	Mar 06 2025
R-4.4-linux	OK	Mar 06 2025
R-4.3-win	OK	Mar 06 2025
R-4.3-mac	OK	Mar 06 2025

Exports:abouheif euclidean kendall make_tree patristic shuffle_graph_ids tree_test validate_tree

Dependencies:ade4 adegenet adegraphics ape askpass base64enc bbmle bdsmatrix boot bslib cachem cellranger cli cluster clusterGeneration coda codetools colorspace combinat commonmark cpp11 crayon crosstalk curl data.table deldir DEoptim digest distory doParallel dotCall64 dplyr DT ellipse evaluate expm fansi farver fastmap fastmatch fields fontawesome foreach fs generics ggplot2 glue googleVis gtable highr hms htmltools htmlwidgets httpuv httr igraph interp isoband iterators jpeg jquerylib jsonlite KernSmooth knitr labeling lamW later lattice latticeExtra lazyeval lifecycle Luminescence magrittr maps markdown MASS Matrix matrixStats mclust memoise mgcv mime minpack.lm mnormt munsell mvtnorm nlme numDeriv openssl optimParallel permute phangorn phytools pillar pixmap pkgconfig plyr png prettyunits progress promises quadprog R6 rappdirs RCarb RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel readxl rematch reshape2 rgl rhandsontable rlang RLumShiny rmarkdown sass scales scatterD3 scatterplot3d segmented seqinr shape shiny shinyBS shinydashboard sourcetools sp spam stringi stringr sys tibble tidyselect tinytex treespace utf8 vctrs vegan viridisLite withr xfun XML xtable yaml

mixtree

Cyril Geismar

Rendered frommixtree.Rmdusingknitr::rmarkdownon Mar 06 2025.

Last update: 2025-02-24
Started: 2025-02-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute the Abouheif distance matrix	abouheif
Calculate the Euclidean distance between two distance matrices.	euclidean
Compute the Kendall distance matrix	kendall
Generate a Transmission Tree	make_tree
Compute the Patristic distance matrix	patristic
Shuffle Node IDs in a Graph	shuffle_graph_ids
Test Differences Between Sets of Transmission Trees	tree_test
Validate a Transmission Tree	validate_tree

Usage by other packages (reverse dependencies)