In wardfont/edcpR: Ecological Data Collection and Processing Package

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(edcpR)

Part 1

# First update package
library(edcpR)
data(varespec_s6, package = "edcpR")
data(varechem_s6, package = "edcpR")

PCA

• Perform a PCA on the environmental data and plot the results.
• TIP: vegan package
• Extract the eigen values and calculate the amount of variation explained by each axis.

Part 2

PCoA

• Repeat the same tasks with the PCoA
• TIP: ape package
• TIP: gowdis() function from FD package

Part 3

NMDS

• Perform a NMDS on the species data. Which dissimilarity index should be used?
• TIP: metaMDS function from vegan package
• Try to plot the results and add the environmental vairables to the plot
• TIP: envfit function from vegan package

Assignment

There is NO assignment for this week's session:

• Combined assigned for the session on ordination and classification
• Online after the session on classification (December 9th)

Remember to upload Assignment 4 (Relationships & Comparing Means) by next week: December 2nd, 12 pm (= at noon!)

wardfont/edcpR documentation built on Dec. 23, 2021, 5:07 p.m.