Launch Interactive Phylogeography Viewer — run_phylogeo

Creates a Shiny application with an interactive plotly visualization of continuous phylogeographic data. Hover over nodes to see labels, dates, and coordinates.

run_phylogeo_app(
  treedata,
  lon = "location2",
  lat = "location1",
  most_recent_sample = NULL,
  stream = TRUE,
  height_branches = "height_mean",
  height_hpd = "height_median",
  level = "0.80",
  ...
)

Arguments

treedata: A treedata object with phylogeographic annotations from treeio::read.beast()
lon: name of longitude column (default: "location2")
lat: name of latitude column (default: "location1")
most_recent_sample: Date, numeric year, or "YYYY-MM-DD" string for calibrating dates
stream: logical; whether to use stream plotting style (default TRUE)
height_branches: column for branch ages (default: "height_mean")
height_hpd: column for HPD ages (default: "height_median")
level: HPD level (default: "0.80")
...: Additional arguments passed to the app

Value

A Shiny app object (run with shiny::runApp or returns when run interactively)

Examples

if (FALSE) { # \dontrun{
library(treeio)
tree <- read.beast("path/to/beast.tree")
run_phylogeo_app(tree, most_recent_sample = "2019-06-15")
} # }