We will use R (version 4.0.5 or later) and Rstudio (version 1.4.1 or later) in this course.
Everybody should download and install R (https://www.r-project.org/), Rstudio (https://www.rstudio.com/) and the required packages before the course starts.
It is preferable that you have all packages installed before the course starts. For those of you having trouble with installing the packages, we will provide some help Monday afternoon, 4pm, but we will not be able to provide comprehensive IT-service though.
Content of required packages:
# Please make sure that you have the required R packages installed.
# You can get a list of the package already installed on your computer s by executing
installed.packages()
# in R alternatively you can just run the installation for each package
# to make sure that you have the latest version.
# Run these installation commands line-by-line in R (or Rstudio)
# and answer yesif you are asked to update any previously installed pakages:
install.packages("readr") # To read and write files
install.packages("readxl") # To read excel files
install.packages("dplyr") # To manipulate dataframes
install.packages("tibble") # To work with data frames
install.packages("tidyr") # To work with data frames
install.packages("stringr") # To manipulate strings
install.packages("ggplot2") # To do plots
install.packages("tidyverse") # To manipulate and visualize data
install.packages("Matrix") # Manipulation of large matrices
install.packages("wTO") # Newtork analysis
install.packages("igraph") # Network analysis
#install.packages("standardize")
install.packages("vegan")
install.packages("magrittr")
install.packages("spaa") # Installs the ecological package spaa
install.packages("compositions") # To work with compositional data
install.packages("zCompositions") # To work with compositional data
install.packages("devtools") # Developer tools
install.packages("mixOmics") # Multivariate methods
install.packages("ape") # Phylogenetic tools
install.packages("recluster") # Clustering tools
install.packages("dendextend") # To work with dendrograms
install.packages("corrplot") # makes nice correlation plots
install.packages("RcmdrMisc") # diverse tools
install.packages("devtools")
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(c("dada2", "phyloseq","Biostrings","PCAtools"))
BiocManager::install("microbiome")
#BiocManager::install("SpiecEasi") #Network construction
# Network packages
library(devtools)
install_github("zdk123/SpiecEasi")
devtools::install_github("pr2database/pr2database") # Installs directly from github resources that are not in R repos
devtools::install_github("GuillemSalazar/EcolUtils") # Installs other tools for ecological analyses
devtools::install_github('fawda123/ggord')
# This package might cause a problem. Here are some possible solutions:
# https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/
# https://stackoverflow.com/questions/37776377/error-when-installing-an-r-package-from-github-could-not-find-build-tools-neces
# For timing processes
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("muscle")