In wardfont/edcpR: Ecological Data Collection and Processing Package

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

library(edcpR)

Part 1

library(vegan)
data("BCI", package = "vegan")

• Alfa diversity
• Calculate species richness, shannon and simpson indices
  • TIP: vegan package
• Calculate corresponding evenness indices
  • TIP: use formulas provided in the lecture slides
• Calculate corresponding Hill numbers
  • TIP: tsallis() function
• Plot relationships between different alfa diversity measures

Part 2

• Beta diversity
• Calculate pairwise beta diversity
  • TIP: betadiver()
• Partition beta diversity in nestedness and turnover components
  • TIP: betapart package
  • TIP: tranform to presence/abscence data!
• Calculate multiple site beta diversity

Part 3

• Gamma diversity
• Calculate chao estimators for the BCI dataset
  • TIP: specpool()
• An old dataset has the following Chao estimators: Chao = 280 (SE = 11.5)
  • Did we lose or gain species?

Part 4

library(FD)
data("tussock", package = "FD")

• Functional diversity
• Calculate the functional diversity indices from the Tussock dataset:
  • TIP: tussock dataset from FD package
  • TIP: dbFD()

Assignment 3

Access the assignment:

vignette("assignment-3", package = "edcpR")

Remember to upload everything before November 3rd, 12 am (= at noon!).

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