Diversity Analysis

Handout - Mahendra Mariadassou

Exercises

## Create new working directory
dir.create("Diversity"); setwd("Diversity")

## Download the R script for the exercises
mm1.url <- "https://www.gdc-docs.ethz.ch/MDA/scripts/script_with_solutions_v200128.R"
utils::download.file(mm1.url, destfile = "diversity.R")
file.edit("diversity.R")

Reports

➜ Report for dataset Ravel et al. 2011
➜ Report for dataset Chaillou et al. 2015

Functions

install.packages("remotes")
remotes::install_github("mahendra-mariadassou/phyloseq-extended", ref = "dev")

In case the download from github does not work, you can get the function directly from the support site: 

# functions.url <- "https://www.gdc-docs.ethz.ch/MDA/scripts/graphical_methods.R"
# utils::download.file(functions.url, destfile = "graphical_methods.R")
# source("graphical_methods.R")

Data Sets

biom.url <- "https://www.gdc-docs.ethz.ch/MDA/data/biom.zip"
utils::download.file(biom.url, destfile = "biom.zip")
unzip("biom.zip")

chaillou.url <- "https://www.gdc-docs.ethz.ch/MDA/data/Chaillou2015.zip"
utils::download.file(chaillou.url, destfile = "Chaillou2015.zip")
unzip("Chaillou2015.zip")

mach.url <- "https://www.gdc-docs.ethz.ch/MDA/data/mach.zip"
utils::download.file(mach.url, destfile = "mach.zip")
unzip("mach.zip")

manual.url <- "https://www.gdc-docs.ethz.ch/MDA/data/manual.zip"
utils::download.file(manual.url, destfile = "manual.zip")
unzip("manual.zip")

morton.url <- "https://www.gdc-docs.ethz.ch/MDA/data/Morton.zip"
utils::download.file(morton.url, destfile = "Morton.zip")
unzip("Morton.zip")

ravel.url <- "https://www.gdc-docs.ethz.ch/MDA/data/ravel.zip"
utils::download.file(ravel.url, destfile = "ravel.zip")
unzip("ravel.zip")