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index.Rmd
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index.Rmd
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---
title: "Assembly of ecological communities: some theoretical explorations"
author: "Stefano Allesina"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: book.bib
biblio-style: apalike
link-citations: yes
description: "Lecture notes prepared for the ICTP Winter School on Quantitative Systems Biology: Quantitative Approaches in Ecosystem Ecology."
---
```{r, include=FALSE}
source("common_settings.R")
```
# Preliminaries {-}
## Goals {-}
- Brief overview of the history of the study of ecological assembly
- List the main issues that make the development of a theory of assembly difficult
- Make assumptions that remove the main obstacles
- Study top-down assembly, and show that in this way any endpoint of assembly is reachable
- Study bottom-up assembly, and the notion of an assembly graph
- Prove equivalence between bottom-up and top-down assembly for certain Lotka-Volterra models
- Outline next steps in the development of a theory of assembly
## Computing {-}
All the figures are generated at runtime, using `R` code that can be found in [this GitHub repository](https://github.com/StefanoAllesina/ICTP_Winter_School). Please make sure that the following libraries are installed:
- `deSolve` for integration of differential equations
- `tidyverse` for data manipulation and plotting
- `knitr` to compile this document
- `igraph` for visualizing networks
## Questions and answers {-}
If you have a question that prevents you from following the lecture, please unmute yourself and ask the question---other students are likely to have the same problem! If you are asking a question out of curiosity, or that can be discussed later, please put it in the chat. I will keep the last few minutes of each lecture for Q&A.