inst/docs/en/installation.md

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Installation

System requirements

• R ≥ 4.1.0
• Operating systems: Linux, macOS, Windows
• Suggested: a working C/C++ toolchain for compiling dependencies (usually already present)

Install from CRAN

install.packages("Rclade")

Install the development version

# install.packages("remotes")
remotes::install_github("zengzichao/Rclade")

Dependencies

Rclade imports: ape, ggtree, deeptime, ggplot2, rlang, stringr, tidytree, viridisLite.

Suggested packages (needed for some features): treeio, phangorn, RColorBrewer, cowplot, patchwork, shiny, optparse, yaml, testthat, knitr, rmarkdown.

Install suggested packages if you plan to use the Shiny app, CLI, or run tests:

install.packages(c("shiny", "optparse", "patchwork", "RColorBrewer",
                   "cowplot", "testthat", "rmarkdown", "knitr"))

Docker

A Dockerfile is provided in the repository for a reproducible environment:

docker build -t rclade .
docker run --rm -it rclade R -e 'library(Rclade); run_rclade_selftest()'

Verify the installation

library(Rclade)
run_rclade_selftest()

If all checks pass, you are ready to go. See Getting started.

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.