Introduction

There are excellent resources available on the net, esp. the R FAQ.² However, for beginners or occasional users it might be too technical.

I’m assuming that you are running a 64 bit version of Windows (version 7 or later). If in doubt, right-click on Computer → Properties and under System / System type you will see whether it’s 32 or 64 bit. Although R comes in both flavours, I don’t recommend to run it on a 32 bit Operating System because you will be limited to 4 GB of memory – irrespective of how much RAM is installed on your machine. Furthermore, a 32 bit OS is no more supported by R 4.2.0 and later.

There are four possible scenarios:

1. In the ideal case you have local administrative privileges. Then you could install the 64 bit R to
   C:\Program Files. For details see below.
2. If not, you can install R to the default user location, which is
   C:\Users\UserName\AppData\Roaming. For details see below.
3. If your organization’s policy does not even allow that, you have to convince your boss that it’s just necessary to do your job.³

“I suppose it is tempting, if the only tool you have is a hammer,
to treat everything as if it were a nail.

4. If you are not successful in #3:
   • Explain that even most simple tasks (which may take you a minute) has to be outsourced. CDAs, time consuming paperwork to and fro, consultants’ ridiculous fees, etc.
     If this argument helps, return to #1 or #2.
   • If not, consider to find another employer (not wearing a tin foil hat).

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Download, Installation

Navigate to CRAN’s download site for Windows and click on the first link Download R x.y.z for Windows. The number x denotes a major, y a minor, and z a patch release.
If you didn’t change the location for downloaded files in your browser, the installer R-x.y.z-win.exe will be saved to C:\Users\UserName\Downloads.

Scenarios:

1. Right-click R-x.y.z-win.exe and select Run as Administrator. After providing your password, you will be asked by the installer which language should be used during the installation. This has nothing to do which language you will use later (see customization below).⁵
   After accepting the license, you will be asked for the location.

Fig. 1 Installation step 1.1

2. Click R-x.y.z-win.exe and you will be asked by the installer which language should be used during the installation. An information window appears.

Fig. 2 Installation step 2.1.

Fig. 3 Installation step 2.2.

Installation common to both scenarios:

In the next window select 64-bit User Installation (only for releases up to 4.1.3). It saves more than 50 MB of disk space, since the 32-bit Files are not needed on a 64 bit Windows.

Fig. 4a Installation step 3 (R ≤4.1.3).

Fig. 4b Installation step 3 (R ≥4.2.0).

In the next window change from the default ⦿ No to ⦿ Yes.

Fig. 5 Installation step 4.

In the next window change from the default ⦿ MDI to ⦿ SDI.

Fig. 6 Installation step 5.

In the next window keep the default ⦿ HTML help (which will open manual pages in your default browser). Only if you are visually impaired, change to ⦿ Plain text (for screen readers or a braille display).

Keep the Start menu Folder in the next window.

In the next window I suggest to create a desktop shortcut. Only if you want to keep different versions in parallel, don’t save the version in the registry.

Fig. 7 Installation step 6.

Hopefully the next window will look like this one:

Fig. 8 Completed Installation.

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Customization

Navigate to your installation folder (in my example \R\R-4.0.5 and doubleclick to open it. Doubleclick the folder etc. Open the file Rconsole in a plain text editor. Edit the options as you like.
Here are parts of mine:
font = TT Lucida Console (I don’t like Courier)
xconsole = 40 (moves the R-console 40px to the right)
yconsole = 30 (moves the R-console 30px down)
language = en (I’m on a German locale but prefer English in R)
background cornsilk
normaltext navy
usertext red

Once you are done, save the file. Click on the desktop shortcut to open the R console. With my customization version 4.4.2 looks like this:

Fig. 9 R Console.

In the menu bar click on Edit → GUI preferences… to check the results and adjust more if needed (e.g., on a high-resolution Retina display maybe you want a larger font size).

Mine again:

Fig. 10 GUI Configuration.

You can change any setting during an interactive session. That’s sometimes needed when you share your screen in a video conference.

For more customization edit the file Rprofile.site. Mine:

# To be consistant with the format on CRAN when creating package manuals
options(papersize="letter")
# Set the default help type
options(help_type="html")
# Change the default prompt from "> ", welcome,
# and don't ask stupid questions
options(prompt = "R> ", continue="+  ")
cat("Welcome at", date(), "\n")
utils::assignInNamespace(
  "q",
  function(save = "no", status = 0, runLast = TRUE) {
    .Internal(quit(save, status, runLast))
  }, "base"
)
# Change the system’s timezone to mine
Sys.setenv(TZ="Europe/Vienna")

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Packages, Libraries

There is some confusion about terminology.

• A package is a collection of R scripts for a specific purpose.
  It always contains manual pages (help for a specific function opening in the browser), a complete manual in PDF-format on CRAN, and may contain data, test-scripts, custom documentation, and/or vignettes giving background information and more detailed examples.
  Packages are hosted on CRAN (with October 2024 more than 21,600), Bioconductor, GitHub, SOURCEFORGE, …
  Pre-compiled packages can be downloaded as ZIP-files.
  Installation not from CRAN requires tools, C/C++ and Fortran compilers to built a package from the source code (provided in gzip-format) and is out of scope of this article.

• A library is a package already installed on your machine.
  Before you can use it, you have to attach it by executing the command library(foo), where foo is the name of the library.

Finding a suitable package is a cumbersome task. Google is your friend. Helpful are also the 41 CRAN Task Views listing packages by topic together with a short description.
However, these lists are maintained by volunteers and are not necessarily up to date:
PowerTOST⁶ and replicateBE⁷ are listed in the Task View Clinical Trial Design, Monitoring, and Ana­ly­sis, whereas Power2Stage⁸ and randomizeBE⁹ are not.

Before you download/install a certain package, I recommend to access its site at CRAN. The URL of packages has this pattern:
https://cran.r-project.org/package=foo, where foo is the name of the package. Inspect its ‘Reference Manual’ and possibly its ‘Vignettes’ to decide whether it will serve your purposes.

to get

+++++++++++ scaled (widened) ABEL +++++++++++
            Sample size estimation
   (simulation based on ANOVA evaluation)
---------------------------------------------
Study design: 2x2x4 (4 period full replicate)
log-transformed data (multiplicative model)
1e+05 studies for each step simulated.
alpha  = 0.05, target power = 0.8
CVw(T) = 0.4; CVw(R) = 0.4
True ratio = 0.9
ABE limits / PE constraint = 0.8 ... 1.25
EMA regulatory settings
- CVswitch            = 0.3
- cap on scABEL if CVw(R) > 0.5
- regulatory constant = 0.76
- pe constraint applied
Sample size search
 n     power
26   0.7587
28   0.7829
30   0.8066

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Installation

Once you found a package suitable for you task there are two options:

1. If you have local administrative privileges (i.e., R is installed at
   C:\Program Files\R\R-x.y.z), right-click on the desktop shortcut and select Run as Administrator, provide your password, and continue as described below.
2. If not, click on the desktop shortcut and continue as described below.

Open the R console and in the menu bar click on Packages → Install package(s)….

A window with a list of the 95 (with June 2024) CRAN mirrors opens:

Fig. 11 Top of list of CRAN mirrors.

I suggest to keep the default. The 0-Cloud is hosted by Posit and will initiate the download from a mirror close to you. Furthermore, it counts downloads, which is nice to know for the developers of packages (see the badges of PowerTOST on GitHub).

The next list is very long, since it contains all packages.

Fig. 12 Top of list of packages.

Scroll down to the one you want to install and click  OK .
If you want to install more than one, use  ctrl -click on each and confirm you selection with  OK  at the end.

As an example installing the package Power2Stage:⁸

Fig. 13 Successful installation.

Note that the ZIP-file comes with an MD5 checksum, which verifies the content. If you get an error, something went wrong in the download. Try it again.

Some packages depend¹⁰ on others.
Example for Power2Stage: It depends on the packages PowerTOST,⁶mvtnorm,¹¹ and cubature.¹² PowerTOST depends on cubature, which itself depends on Rcpp.¹³ Hence, in a new installation of Power2Stage four other packages will be installed as well. That’s not shown in the screenshot above because I have them already installed.

Now you can attach the library and show its manual in the browser.

library(Power2Stage)
help(p=Power2Stage)

Fig. 14 Attach and help.

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Update

It’s good practice to check regularly whether packages are updated. Whereas some ‘mature’ packages are considered stable by its maintainer and are updated maybe just once a year, others might be updated once a month.

To check whether your packages are up to date:

old.packages()

After specifying the mirror you will get a list showing the installed versions and the ones on the repository – if there are more recent ones (otherwise, you get just NULL). However, it does not tell whether the Windows-binaries (the ZIP-files) have already been built. You need special tools to build a package from the source-code. That’s not for beginners.

If you are as lazy as I am, you can automatically update all your outdated libraries:

update.packages(checkBuilt = TRUE, ask = FALSE)

Fig. 15 Update information.

Likely your list will be shorter (I have 900+ packages installed on my machines). Once the source code of a package is available, it takes up to one week till the Windows-binaries (the ZIP-files) are built on CRAN. That’s for experts (requiring the GNU compilers for C, C++, and Fortran). Therefore, in the next window

Fig. 16 Load and help.

click on the central button (the buttons will be labeled in your locale; on my German Windows    Nein    means ‘No’).

Only the Windows-binaries will be installed.

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remove.packages("foo")

Update 🇷

R is quite mature; it was originally developed by Ross Ihaka and Robert Gentleman in 1992.¹⁴ The first release was published in December 1997 and new versions are published every few months.

library(rversions)
rv                              <- r_versions()
rv$nickname[is.na(rv$nickname)] <- "none"
rv$date                         <- strftime(rv$date, format = "%Y-%m-%d")
rv                              <- rv[order(rv$date, decreasing = TRUE), ]
print(rv, row.names = FALSE, right = FALSE)
cat("1st digit: major release",
    "\n2nd digit: minor release",
    "\n3rd digit: patch")

#  version date       nickname                
#  4.4.2   2024-10-31 Pile of Leaves          
#  4.4.1   2024-06-14 Race for Your Life      
#  4.4.0   2024-04-24 Puppy Cup               
#  4.3.3   2024-02-29 Angel Food Cake         
#  4.3.2   2023-10-31 Eye Holes               
#  4.3.1   2023-06-16 Beagle Scouts           
#  4.3.0   2023-04-21 Already Tomorrow        
#  4.2.3   2023-03-15 Shortstop Beagle        
#  4.2.2   2022-10-31 Innocent and Trusting   
#  4.2.1   2022-06-23 Funny-Looking Kid       
#  4.2.0   2022-04-22 Vigorous Calisthenics   
#  4.1.3   2022-03-10 One Push-Up             
#  4.1.2   2021-11-01 Bird Hippie             
#  4.1.1   2021-08-10 Kick Things             
#  4.1.0   2021-05-18 Camp Pontanezen         
#  4.0.5   2021-03-31 Shake and Throw         
#  4.0.4   2021-02-15 Lost Library Book       
#  4.0.3   2020-10-10 Bunny-Wunnies Freak Out 
#  4.0.2   2020-06-22 Taking Off Again        
#  4.0.1   2020-06-06 See Things Now          
#  4.0.0   2020-04-24 Arbor Day               
#  3.6.3   2020-02-29 Holding the Windsock    
#  3.6.2   2019-12-12 Dark and Stormy Night   
#  3.6.1   2019-07-05 Action of the Toes      
#  3.6.0   2019-04-26 Planting of a Tree      
#  3.5.3   2019-03-11 Great Truth             
#  3.5.2   2018-12-20 Eggshell Igloo          
#  3.5.1   2018-07-02 Feather Spray           
#  3.5.0   2018-04-23 Joy in Playing          
#  3.4.4   2018-03-15 Someone to Lean On      
#  3.4.3   2017-11-30 Kite-Eating Tree        
#  3.4.2   2017-09-28 Short Summer            
#  3.4.1   2017-06-30 Single Candle           
#  3.4.0   2017-04-21 You Stupid Darkness     
#  3.3.3   2017-03-06 Another Canoe           
#  3.3.2   2016-10-31 Sincere Pumpkin Patch   
#  3.3.1   2016-06-21 Bug in Your Hair        
#  3.3.0   2016-05-03 Supposedly Educational  
#  3.2.5   2016-04-14 Very, Very Secure Dishes
#  3.2.4   2016-03-10 Very Secure Dishes      
#  3.2.3   2015-12-10 Wooden Christmas-Tree   
#  3.2.2   2015-08-14 Fire Safety             
#  3.2.1   2015-06-18 World-Famous Astronaut  
#  3.2.0   2015-04-16 Full of Ingredients     
#  3.1.3   2015-03-09 Smooth Sidewalk         
#  3.1.2   2014-10-31 Pumpkin Helmet          
#  3.1.1   2014-07-10 Sock it to Me           
#  3.1.0   2014-04-10 Spring Dance            
#  3.0.3   2014-03-06 Warm Puppy              
#  3.0.2   2013-09-25 Frisbee Sailing         
#  3.0.1   2013-05-16 Good Sport              
#  3.0.0   2013-04-03 Masked Marvel           
#  2.15.3  2013-03-01 Security Blanket        
#  2.15.2  2012-10-26 Trick or Treat          
#  2.15.1  2012-06-22 Roasted Marshmallows    
#  2.15.0  2012-03-30 Easter Beagle           
#  2.14.2  2012-02-29 Gift-Getting Season     
#  2.14.1  2011-12-22 December Snowflakes     
#  2.14.0  2011-10-31 Great Pumpkin           
#  2.13.2  2011-09-30 none                    
#  2.13.1  2011-07-08 none                    
#  2.13.0  2011-04-13 none                    
#  2.12.2  2011-02-25 none                    
#  2.12.1  2010-12-16 none                    
#  2.12.0  2010-10-15 none                    
#  2.11.1  2010-05-31 none                    
#  2.11.0  2010-04-22 none                    
#  2.10.1  2009-12-14 none                    
#  2.10.0  2009-10-26 none                    
#  2.9.2   2009-08-24 none                    
#  2.9.1   2009-06-26 none                    
#  2.9.0   2009-04-17 none                    
#  2.8.1   2008-12-22 none                    
#  2.8.0   2008-10-20 none                    
#  2.7.2   2008-08-25 none                    
#  2.7.1   2008-06-23 none                    
#  2.7.0   2008-04-22 none                    
#  2.6.2   2008-02-08 none                    
#  2.6.1   2007-11-26 none                    
#  2.6.0   2007-10-03 none                    
#  2.5.1   2007-06-28 none                    
#  2.5.0   2007-04-24 none                    
#  2.4.1   2006-12-18 none                    
#  2.4.0   2006-10-03 none                    
#  2.3.1   2006-06-01 none                    
#  2.3.0   2006-04-24 none                    
#  2.2.1   2005-12-20 none                    
#  2.2.0   2005-10-06 none                    
#  2.1.1   2005-06-20 none                    
#  2.1.0   2005-04-19 none                    
#  2.0.1   2004-11-15 none                    
#  2.0.0   2004-10-04 none                    
#  1.9.1   2004-06-21 none                    
#  1.9.0   2004-04-12 none                    
#  1.8.1   2003-11-21 none                    
#  1.8.0   2003-10-08 none                    
#  1.7.1   2003-06-16 none                    
#  1.7.0   2003-04-16 none                    
#  1.6.2   2003-01-10 none                    
#  1.6.1   2002-11-01 none                    
#  1.6.0   2002-10-01 none                    
#  1.5.1   2002-06-17 none                    
#  1.5.0   2002-04-29 none                    
#  1.4.1   2002-01-30 none                    
#  1.4     2001-12-19 none                    
#  1.3.1   2001-08-31 none                    
#  1.3     2001-06-22 none                    
#  1.2.3   2001-04-26 none                    
#  1.2.2   2001-02-26 none                    
#  1.2.1   2001-01-15 none                    
#  1.2     2000-12-15 none                    
#  1.1.1   2000-08-15 none                    
#  1.1     2000-06-15 none                    
#  1.0.1   2000-04-14 none                    
#  1.0     2000-02-29 none                    
#  0.99    2000-02-07 none                    
#  0.90.1  1999-12-15 none                    
#  0.90    1999-11-22 none                    
#  0.65.1  1999-10-06 none                    
#  0.65    1999-08-27 none                    
#  0.64.2  1999-07-02 none                    
#  0.64.1  1999-05-07 none                    
#  0.64    1999-04-07 none                    
#  0.63.3  1999-03-05 none                    
#  0.63.2  1999-01-11 none                    
#  0.63.1  1998-12-04 none                    
#  0.63    1998-11-13 none                    
#  0.62.4  1998-10-23 none                    
#  0.62.3  1998-08-28 none                    
#  0.62.2  1998-07-10 none                    
#  0.62.1  1998-06-15 none                    
#  0.62    1998-06-14 none                    
#  0.61.3  1998-05-02 none                    
#  0.61.2  1998-03-14 none                    
#  0.61.1  1998-01-10 none                    
#  0.61    1997-12-21 none                    
#  0.60    1997-12-04 none                    
# 1st digit: major release 
# 2nd digit: minor release 
# 3rd digit: patch

Changes are described in the ‘R News’ (see the current one).

At the latest when you attach an updated library (say, foo), you will get a warning:

Warning message:
package ‘foo’ was built under R version x.y.z

If x.y.z is higher than your version of R, its high time to update it.

First of all download and install the new release as described above. The installer will suggest to install to a folder with a different release-number than the one you have. Accept that (you can have different versions installed in parallel).

Navigate to the old installation’s sub-folder etc. Copy the file Rconsole (and Rprofile.site if you edited it) to the corresponding one in the new installation.

Once you have done that, navigate to your old installation and copy the entire library folder. Navigate to the new installation and paste it (i.e., overwrite its entire content).

Click (right-click if you have administrative privileges) the desktop shortcut of the new version and update all libraries as described above.

• You can keep different versions of R installed in parallel. That’s generally only required if a package was archived¹⁵ because it was not compatible with a later version and you still want to use it. An example is package bear,¹⁶ which requires 4.1.x for installation.¹⁷
  

There is a drawback of keeping different versions. Files in R’s native binary format .Rdata will always open in the latest version (unless you prevented saving the version number in the registry in Installation step 6 of all versions).

• If you don’t want to keep the previous version, navigate to the old installation and execute the file unins000.exe to remove it (including its desktop shortcut). However, the library folder will not be removed. Delete it, navigate one level up and delete the R-x.y.z folder as well.

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IDEs

In many companies the Integrated Development Environment RStudio is used. My personal views of its pros and cons:

• Pros
  • Automatic completion of arguments, spell and syntax check. Great, if you notoriusly – like me – type TREU¹⁸ instead of TRUE.
  • Straightforward installation and update of packages.
  • Support of the wonderful R Markdown, knitr,¹⁹ and pandoc.
  • Tools to build own packages with version control (locally and on GitHub)… I use it regularly myself.
• Cons
  • The graphics window is not optimal. See this example.
  • Whereas in Base R you can only have one version of a package installed, in RStudio you can keep different ones. Depending on the setup, it is possible that the first (which is not the most current one) will be used. This might lead to confusion.²⁰
  • Unless you develop packages, IMHO, it’s just over the top.

An alternative for neRds is Tinn-R.

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Validation

See R’s Software Development Life Cycle²¹ and its bug-tracking system.²² See also this document²³ about the acceptability of Base R in re­gu­lated environments. Note that ultimate responsibility for validation of any software (yes, of SAS as well…) lies in the hands of the user.^{24 25 26}

Generally in the respective ‘NEWS’-file the development of the package, bug-fixes, and introduction of new methods is documented (examples: PowerTOST, Power2Stage, replicateBE). Many packages contain test-scripts sup­port­ing users in validating their installations. The man-pages of packages contain examples of functions with expected results. Some packages contain vignettes with more detailed examples (examples: PowerTOST, replicateBE).

As an aside, statisticians of the U.S. FDA regularly use R themselves…

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