Setting up RStudio on Ubuntu (UCSF PHDI)

RStudio_MPROJECT_setup.md

Installing packages in RStudio on Ubuntu

This document covers installing packages on RStudio server (Ubuntu).

System Specs

Currently using:

Release 16.04.5 LTS (Xenial Xerus) 64-bit
Kernel Linux 4.4.0-134-generic x86_64
MATE 1.12.1

And

RStudio Version 1.1.456 
Mozilla/5.0 

Follow the directions on this post.

Run In Terminal

These get run in the terminal (password required):

sudo apt-get install software-properties-common python-software-properties
sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
sudo apt-get update
sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev
sudo apt-get install libxml2-dev
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libfreetype6-dev

Install R on Ubuntu 16.04

1. Add R repository First, we’ve got to add a line to our /etc/apt/sources.list file. This can be accomplished with the following. Note the “xenial” in the line, indicating Ubuntu 16.04. If you have a different version, just change that.

sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list

This returned the following:

deb http://cran.rstudio.com/bin/linux/ubuntu xenial/

Add R to Ubuntu Keyring

gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -

I did not do the following steps:

Install R-Base Most Linux users should be familiar with the old… sudo apt-get update sudo apt-get install r-base r-base-dev

Install R packages

Run the following code, need ~ 10 min to install all these packages.

This gets run in the RStudio source file.

    # options for loading form CRAN
    options("repos" = c(CRAN = "http://cran.rstudio.com/"))
    # packages to install
    install.packages(c("fs",
                       "mdsr",
                       "data.table", 
                       "knitr", 
                       "RCurl", 
                       "XML", 
                       "ggmap", 
                       "raster", 
                       "openair", 
                       "rasterVis", 
                       "viridisLite", 
                       "sf", 
                       "geomnet", 
                       "ggrepel", 
                       "showtext", 
                       "geosphere", 
                       "kableExtra", 
                       "ggsn", 
                       "tidyverse", 
                       "magrittr", 
                       "readxl",
                       "haven",
                       "jsonlite",
                       "httr",
                       "rvest",
                       "DBI",
                       "readODS",   # Import ODS (OpenDocument Spreadsheet", into R as a data
                       "rmatio",    # Reading and writing Matlab MAT files from R
                       "readxl",   # reading excel sheets into R
                       "lubridate",
                       "hms",
                       "blob",
                       "reshape",   # flexibly reshape data with melt and cast
                       "reshape2",  # again
                       "magrittr",
                       "glue",
                       "GGally",
                       "gganimate",
                       "ggExtra",
                       "ggfittext",
                       "ggformula",
                       "ggridges",
                       "ggnetwork",
                       "ggvis",
                       "ggrepel",
                       "ggtern",
                       "ggthemes",
                       "ggmap",     # ggmap for maps
                       "gcookbook", # package contains data sets used in r graphics cookbook"
                       "lattice",  # lattice package
                       "timevis",   # create rich and fully interactive timeline visualizations
                       "tidymodels",
                       "ISLR",      # introduction to statistical learning package
                       "e1071",     # misc functions from dept of stats, prob theory group
                       "memisc",    # tools for managing survey data presentation of analysis
                       "Hmisc",     # contains many functions useful for data analysis,
                       "LOGIT",     # functions, data and code for PGLR
                       "caret",     # model data
                       "broom",     # data frames for messy output of built-in functions in R
                       "faraway",   # linear models in R
                       "AppliedPredictiveModeling", # applied predicitive modeling book
                       "regtools",  # regression tools
                       "skimr",     # tiny histograms
                       "janitor",   # crosstabs and nice tables
                       "tableone",    # create tables
                       "urltools",  # A toolkit for all URL-handling needs
                       "csvy",      # import and export csv data with a yaml metadata header
                       "feather",   # access a feather store like a data frame
                       "fst",       # read and write data frames at high speed.
                       "datapasta", # easy copy and paste
                       "gutenbergr",  # download and process public domain works in project
                       "tidytext",    # text manipulation/modeling (tidy approach",
                       "scales",      # commas
                       "stringi",     # string manipulation
                       "xtable",      # coerce data to latex and html tables
                       "rmdformats",  # formatting Rmd files
                       "rmdHelpers",  # helpers
                       "furniture",   # crosstabulations of variables
                       "styler",      # style code easily
                       "nycflights13", # the infamous flights data
                       "Lahman",      # data tables from the 'Sean Lahman Baseball Database'
                       "Ecdat",       # data sets for econometrics
                       "HistData",    # data sets from the history of statistics and data viz
                       "fivethirtyeight", # data sets from http://fivethirtyeight.com/
                       "DBI", # provides connection to DBMS with a “front-end” and a “back-end”
                       "RMySQL", # MySQL driver for DBI
                       "RMariaDB", # MariaDB driver for DBI
                       "RPostgreSQL")) # PostgreSQL driver for DBI