treesinspace

Exploring the Effects of Ecological Parameters on the Spatial Structure of Genealogies

Welcome to the treesinspace package. This will supply everything needed to reproduce the analyses and figures included in the manuscript. The code was written by M. Ianni-Ravn (mianniravn@uchicago.edu), with abundant help from Martin Petr and the rest of the Racimo lab at UCPH. The project extensively makes use of the R package slendr (current version at https://cran.r-project.org/web/packages/slendr/index.html). This will be installed, if not already present, when opening this R project.

Installation

To get going, please clone this repository:

git clone https://github.com/mkiravn/treesinspace.git

Once this has installed, please open the treesinspace.Rproj project. This will load all necessary modules.

Navigating the package

The new_scripts directory contains files needed for the analysis. Namely:

exploration.R: exploring the effects of dispersal distribution, competition distance and mating distance.
diffusion.R: comparing a theoretical model of mate choice to simulated results. This also uses data from data/ThirdSidePDF.tsv, produced by thirdsidepdf.nb.
estimation.R: investigating the accuracy of ML estimation of $\sigma$ under a brownian motion model
illustration.R: a visualisation of the effects of competition and mate choice scale.

These scripts will output figures into a figs directory, and label them with the current date.