Package: phylepic 0.2.0

Carl Suster

phylepic: Combined Visualisation of Phylogenetic and Epidemiological Data

A collection of utilities and 'ggplot2' extensions to assist with visualisations in genomic epidemiology. This includes the 'phylepic' chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included 'ggplot2' extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.

Authors:Carl Suster [aut, cre], Western Sydney Local Health District, NSW Health [cph]

phylepic_0.2.0.tar.gz
phylepic_0.2.0.tar.gz(r-4.5-noble)phylepic_0.2.0.tar.gz(r-4.4-noble)
phylepic_0.2.0.tgz(r-4.4-emscripten)phylepic_0.2.0.tgz(r-4.3-emscripten)
phylepic.pdf |phylepic.html
phylepic/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/cidm-ph/phylepic/issues

20 exports 0.09 score 58 dependencies

Last updated 16 days agofrom:5341505b5f52acf268e8902ece3621a7025fb770

Exports:coord_treeCoordTreecreate_tree_layoutdrop.cladegeom_calendargeom_node_text_filledGeomCalendarGeomTextFilledoob_infinitephylepicplot_barsplot_calendarplot_epicurveplot_treescale_x_weekstat_weekstat_week_2dStatWeekStatWeek2dweek_breaks

Dependencies:apecachemclicolorspacecowplotcpp11digestdplyrfansifarverfastmapforcatsgenericsggforceggnewscaleggplot2ggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr

phylepic charts: combining phylogenetic trees with epidemic curves

Rendered fromphylepic.Rmdusingknitr::rmarkdownon Jun 01 2024.

Last update: 2024-06-01
Started: 2024-06-01