https://github.com/csiro/phylocontrol-geninput

Generate inputs for PhyloControl app

https://github.com/csiro/phylocontrol-geninput

Repository

Generate inputs for PhyloControl app

readme.Rmd

---
output: github_document
editor: visual
---



```{r, include = FALSE}
  knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    out.width = "100%"
)
```

# `phylocontrol-geninput`



[![Lifecycle: stable](https://lifecycle.r-lib.org/articles/figures/lifecycle-stable.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)



A phylogeny and spatial data visualisation interface for risk analysis and decision support in weed biological control.

## Introduction

PhyloControl is a user-friendly visualisation tool to aid biocontrol researchers in their decision-making during risk analysis. Thorough host-specificity testing is crucial to minimise the risk of off-target damage by biocontrol agents to native and economically important plant species. To facilitate this, host test lists need to be developed from an understanding of evolutionary relationships. The process of obtaining a host test list is currently not standardised, and the manual steps may be time-consuming and challenging, introducing risks if taxonomic associations with the target weeds are uncertain or if the taxonomy of potential non-target species is poorly resolved. PhyloControl integrates taxonomic data, molecular data, spatial data, and plant traits in an intuitive interactive interface, empowering biocontrol practitioners to summarise, visualise, and analyse data efficiently.

This repository, [`phylocontrol-geninput`](https://github.com/csiro/phylocontrol-geninput), contains the four Quarto notebooks to generate inputs for the R Shiny visualisation application. The application is available from the [`phylocontrol-viz` repository](https://github.com/csiro/phylocontrol.viz) and contains the source code for the `{phylocontrol.viz}` package.







## Install and run

To run these Quarto notebooks, clone this repository to your local computer and open the `.qmd` files using RStudio to edit and run them. Each notebook is self-contained and can be run independently. This allows users to skip steps if you already have input data from other sources.

## Key outputs from each notebook

**`1_Species_list.qmd`**

A csv file containing a list of scientific names of the target weed and related species e.g. `Erigeron_species_list.csv`

**`2_Occurrences.qmd`**

A csv file of point occurrence data containing the key columns 'species', 'decimalLatitude', 'decimalLongitude', and 'country' e.g. `Erigeron_occurrences.csv`

**`3_Species_distribution_modelling.qmd`**

A `sdm/` folder containing folders `maxent_results/` and/or `climatch_results/`. There is another directory indicating the climate layers used e.g. `chelsa2.1_bio/` which then contains a folder for each species run. Key outputs for visualisation are the grid files e.g. `maxent_predict.grd` and `climatch_predict.grd` and in the case of MaxEnt, the `maxent_thresholds.csv` file.

**`4_Sequences_and_phylogenomics.qmd`**

A phylogenetic tree in Newick format e.g. `Erigeron.tre`. It should be outgroup rooted.

It is recommended to copy the output files needed for the PhyloControl visualisation application into a separate directory set up specifically for the visualisation app which contains a folder for each study group e.g. `App_data/Erigeron/`.







You can also optionally add a text file containing the default target weed as well as a csv file containing traits to visualise with heatmaps. For an example of this directory structure, have a look at the App_data folder in the [supplementary data for the manuscript](https://data.csiro.au/collection/csiro:64365).

## Demo server

Try out the [demo version of the visualisation application](https://shiny.csiro.au/phylocontrol-viz-demo/).

## Code of Conduct

Please note that this project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

## Citing PhyloControl

The PhyloControl paper is published in *Biological Control*.

> Stephanie H. Chen, Lauren Stevens, Ben Gooden, Michelle A. Rafter, Nunzio Knerr, Peter H. Thrall, Louise Ord, Alexander N. Schmidt-Lebuhn (2025). PhyloControl: a phylogeny visualisation platform for risk analysis in weed biological control. *Biological Control*. DOI: [10.1016/j.biocontrol.2025.105859](https://doi.org/10.1016/j.biocontrol.2025.105859 "Persistent link using digital object identifier")

Owner

Citation (CITATION.cff)

# This CITATION.cff reference content was generated from Zotero.
message: "If you use this software, please cite it as below."
title: "PhyloControl: A phylogeny visualisation platform for risk analysis in weed biological control"
type: journalArticle
issn: 1049-9644
journal: Biological Control
pages: 105859
volume: 209
url: https://www.sciencedirect.com/science/article/pii/S1049964425001690
keywords: 
- Biological control
- Phylogenetics
- Species distribution modelling
- Weeds
authors: 
- family-names: Chen
  given-names: Stephanie H.
- family-names: Stevens
  given-names: Lauren
- family-names: Gooden
  given-names: Ben
- family-names: Rafter
  given-names: Michelle A.
- family-names: Knerr
  given-names: Nunzio
- family-names: Thrall
  given-names: Peter H.
- family-names: Ord
  given-names: Louise
- family-names: Schmidt-Lebuhn
  given-names: Alexander N.
date-published: 2025-07-30
doi: 10.1016/j.biocontrol.2025.105859

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