CA

Assignment 6

Author

AJ Smit

Published

June 28, 2020

Submit a R script wherein you provide answers to Questions 1–3 by no later than 8:00 tomorrow. Label the script as follows: BCB743_<Name>_<Surname>_Assignment_6.R, e.g. BCB743_AJ_Smit_Assignment_6.R.

Refer to the Correspondence Analysis lecture material to see the questions in context.

Assignment 6 Questions

Question 1. How would you explain the patterns seen in the four panels of the above figure?

Question 2. Apply approaches taken from the analysis shown immediately above to these datasets: 1. bird communities along elevation gradient in Yushan Mountain, Taiwan; 2. alpine plant communities in Aravo, France.

Question 3. Discuss the patterns observed, and explain the ordination diagrams with particular reference to how the species are influenced by the major environmental drivers.

Question 4 (Bonus) For bonus marks that could earn you 120/100, please see if you can recreate the bottom right figure for the species ‘Cogo’ using ggplot2. This will require digging deep into the ordination and ordisurf objects, creating dataframes for each layer of data, and assembling the graph manually.

Reuse

CC BY-NC-SA 4.0

Citation

BibTeX citation:

@online{smit,_a._j.2020,
  author = {Smit, A. J., and Smit, AJ},
  title = {CA},
  date = {2020-06-28},
  url = {http://tangledbank.netlify.app/slides/BCB743_09-ca.html},
  langid = {en}
}

For attribution, please cite this work as:

Smit, A. J., Smit A (2020) CA. http://tangledbank.netlify.app/slides/BCB743_09-ca.html.

---
title: "CA"
subtitle: "Assignment 6"  
author: 
  - "AJ Smit"
date: '2020/06/28 (updated: `r Sys.Date()`)'
output:
  xaringan::moon_reader:
    css:
      - default
      - "default-fonts.css"
      - ki
      - "uwc_logo.css"
    yolo: false
    self_contained: TRUE  
    lib_dir: libs
    nature:
      highlightStyle: idea
      highlightLines: true
      highlightLanguage: r
      countIncrementalSlides: false
      ratio: 16:9
---

```{r setup, include = FALSE, echo = FALSE} 
library(tidyverse)
library(ggpubr)
knitr::opts_chunk$set(echo = TRUE,
                      comment = "R>",
                      message = FALSE,
                      warning = FALSE,
                      include = TRUE,
                      fig.retina = 3,
                      fig.width = 6,
                      fig.height = 3.6,
                      fig.align = "center")
```

Submit a R script wherein you provide answers to Questions 1--3 by no later than 8:00 tomorrow. Label the script as follows: **`BCB743_<Name>_<Surname>_Assignment_6.R`**, e.g. **`BCB743_AJ_Smit_Assignment_6.R`**.

Refer to the [Correspondence Analysis lecture material](https://ajsmit.netlify.app/quantecol/chapters/09-ca/) to see the questions in context.

---

### Assignment 6 Questions

> **Question 1.** How would you explain the patterns seen in the four panels of the above figure?
>
> **Question 2.** Apply approaches taken from the analysis shown immediately above to these datasets: 1. [bird communities along elevation gradient in Yushan Mountain, Taiwan](https://www.davidzeleny.net/anadat-r/doku.php/en:data:ybirds); 2. [alpine plant communities in Aravo, France](https://www.davidzeleny.net/anadat-r/doku.php/en:data:aravo).
>
> **Question 3.** Discuss the patterns observed, and explain the ordination diagrams with particular reference to how the species are influenced by the major environmental drivers.
>
> **Question 4 (Bonus)** For bonus marks that could earn you 120/100, please see if you can recreate the bottom right figure for the species 'Cogo' using **ggplot2**. This will require digging deep into the ordination and ordisurf objects, creating dataframes for each layer of data, and assembling the graph manually.