spatial-phy-workshop

This repo includes materials for the Workshop on Spatial Phylogenetics held from June 5--7 2023 at the ForBio Research School in Biosystematics, Oslo, Norway

All materials by Joel Nitta

Slides

Day 1: Assembling Spatial and Genetic Data

Day 2: Applications of Spatial Phylogenetics

Tutorials

Day 1: Obtaining occurrence and phylogeny data in R

Day 2: Spatial phylogenetics in R with canaper

Software requirements

Cloud

If you don't want to install anything locally or are unable to install some of the required software, you can run the code in your browser.

NOTE: If you use this method, do not save any sensitive information in the RStudio session (passwords, etc.). The binder is a public, open system and you should not consider it a secure place to store private data.

Click the "launch binder" button below:

Local install

This workshop requires installation of R, RStudio, and several R packages.

You can install the required packages by running the following code in R:

install.packages(
  c(
    "canaper",
    "CoordinateCleaner",
    "phyloregion",
    "rgbif",
    "rnaturalearth",
    "sf",
    "tidyverse")
  )

install.packages(
  "rnaturalearthhires",
  repos = "https://ropensci.r-universe.dev",
  type = "source")

install.packages(
  "ftolr",
  repos = c(
    "https://joelnitta.r-universe.dev/",
    "https://cran.rstudio.com/"
  ),
  dep = TRUE)

Or, you can clone this repository, open this folder in RStudio, and use renv to install the packages at the versions used when creating the workshop materials:

# Install renv first if necessary
install.packages("renv")
renv::restore()

Deployment

To deploy the rendered slides, run quarto publish.

License

CC BY 4.0