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Install_required_packages.R
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# BIO9905MERG1_V21
# 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")