## R for Statistics and Graphics (Session 1)
## Mehmet Tevfik DORAK
## Web link: http://www.dorak.info/r

## This script is for installing all necessary R packages for this course (assuming R 4.0.0 or higher is already installed)
## If these are not already installed, please go ahead

## Open this file on R via Files/Open Script.. 
## Highlight the text in Section 1 and press CTRL + R; repeat this for each section (section 4b is for manual installation)

## During the process, if asked: .... Would you like a personal library instead? Say, YES
   ## Then, say YES to the suggested folder location (usually a subfolder within Documents folder)
## If asked, "Do you want to install from sources ....?" Say, NO

## Section 1 
## Select the mirror site to download the packages from: 
chooseCRANmirror()   # Select one of the sites and press OK
## Run the following command to downloadd and install all of those packages in one go:
install.packages(c("fBasics", "psych", "DataExplorer", "epiR", "rmeta", "pwr", "corrgram", "DescTools", "readxl", "xlsx", "plotrix", "pROC", "tidyverse", "ggthemes", "Rcmdr", "RColorBrewer", "grid", "animation", "ggdendro", "ctv", "survival", "survminer", "logspline", "quantmod", "caret"), dependencies = TRUE)

## Section 2 
install.packages(c("reshape2", "pastecs", "Hmisc", "moments", "ellipse", "gridExtra", "car", "wordcloud", "spatstat", "Rcpp", "magrittr", "tm", "SnowballC", "twitteR", "imager", "scales", "TSP", "magick", "patchwork", "datasets", "tibble", "stringr", "MASS", "HistData"), dependencies = TRUE)

## Section 3 (optional)
## If will be needed, install all packages related to phylogenetics or meta-analysis using the following commands:
library('ctv')
install.views("Phylogenetics")
install.views("MetaAnalysis")
install.views("Survival")
install.views("TeachingStatistics")

## Section 4a
# Make sure "devtools" is installed and up-to-date:
install.packages("devtools")
# Make sure "processx" is up-to-date:
install.packages("processx")
# Install "renotes"
install.packages("remotes") 

## Section 4b: MANUAL INSTALLATION
# Make sure Rtools.EXE is installed and up-to-date (check https://cran.r-project.org/bin/windows/Rtools)
  # Install the correct EXE file like any other Windows file and follow the instructions to complete its installation (by defining the PATH)

## Section 5
## Run the command below and see if additional downloads are necessary: 
library(Rcmdr)     # install any missing programs

## Section 6 (MANUAL download and installation)
## For manual installation of RTools. go to: https://cran.r-project.org/bin/windows/Rtools
## Download the recommended (green line) version of RTools like any other windows exe program 

## Section 7: Update Rccp as explained at:
   # https://rickpackblog.wordpress.com/2020/08/06/updating-rcpp-extprt_ptr-error (GitHub for Rcpp: https://github.com/RcppCore/Rcpp.git)

## For SWIRL courses to learn R in R:
install.packages("swirl")           # https://swirlstats.com 

# Installation of BioConductor (For R version 4.0.0 or higher)
# SEE: https://bioconductor.org/install
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

## Install the following multiple Bioconductor packages with a single command: 
BiocManager::install(c("GenomicFeatures", "GenomicRanges", "IRanges", "AnnotationDbi", "VariantAnnotation", "myvariant", "mygene", 
                       "GWASTools", "ReactomePA", "clusterProfiler"))

# At the end, make sure you have the most up-to-date version of all packages installed: 
  update.packages(ask='graphics',checkBuilt=TRUE) 

# Updating Bioconductor packages
  if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
  BiocManager::install()

# Last updated on 3 March 2021