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1. About Cygwin

1.1. What is it?

1.2. What versions of Windows are supported?

1.3. Where can I get it?

1.4. Is it free software?

1.5. What version of Cygwin is this, anyway?

1.6. Who's behind the project?

1.1.

What is it?

Cygwin is a distribution of popular GNU and other Open Source tools running on Microsoft Windows. The core part is the Cygwin library which provides the POSIX system calls and environment these programs expect.

The Cygwin distribution contains thousands of packages from the Open Source world including most GNU tools, many BSD tools, an X server and a full set of X applications. If you're a developer you will find tools, headers and libraries allowing to write Windows console or GUI applications that make use of significant parts of the POSIX API. Cygwin allows easy porting of many Unix programs without the need for extensive changes to the source code. This includes configuring and building most of the available GNU or BSD software, including the packages included with the Cygwin distribution themselves. They can be used from one of the provided Unix shells like bash, tcsh or zsh.

1.2.

What versions of Windows are supported?

Cygwin can be expected to run on all modern, released versions of Windows. State January 2016 this includes Windows Vista, Windows Server 2008 and all later versions of Windows up to Windows 10 and Windows Server 2016. The 32 bit version of Cygwin also runs in the WOW64 32 bit environment on released 64 bit versions of Windows, the 64 bit version of course only on 64 bit Windows.

Keep in mind that Cygwin can only do as much as the underlying OS supports. Because of this, Cygwin will behave differently, and exhibit different limitations, on the various versions of Windows.

1.3.

Where can I get it?

The home page for the Cygwin project is https://cygwin.com/. There you should find everything you need for Cygwin, including links for download and setup, a current list of mirror sites, a User's Guide, an API Reference, mailing lists and archives.

You can find documentation for the individual GNU tools typically as man pages or info pages as part of the Cygwin net distribution. Additionally you can get the latest docs at http://www.gnu.org/manual.

1.4.

Is it free software?

Yes. Parts are GNU software (gcc, gas, ld, etc...), parts are covered by the standard X11 license, some of it is public domain, some of it was written by Red Hat (or the former Cygnus Solutions) and placed under the GPL. None of it is shareware. You don't have to pay anyone to use it but you should be sure to read the copyright section of the FAQ for more information on how the GNU General Public License may affect your use of these tools.

Note that when we say "free" we mean freedom, not price. The goal of such freedom is that the people who use a given piece of software should be able to change it to fit their needs, learn from it, share it with their friends, etc. The GPL or LGPL licenses allows you those freedoms, so it is free software.

1.5.

What version of Cygwin is this, anyway?

To find the version of the Cygwin DLL installed, you can use as on Linux or . Refer to each command's output and the Cygwin User's Guide for more information.

If you are looking for the version number for the whole Cygwin release, there is none. Each package in the Cygwin release has its own version. The packages in Cygwin are continually improving, thanks to the efforts of net volunteers who maintain the Cygwin binary ports. Each package has its own version numbers and its own release process.

So, how do you get the most up-to-date version of Cygwin? Easy. Just download the Cygwin Setup program by following the instructions here. The setup program will handle the task of updating the packages on your system to the latest version. For more information about using Cygwin's , see Setting Up Cygwin in the Cygwin User's Guide.

1.6.

Who's behind the project?

(Please note that if you have cygwin-specific questions, all of these people will appreciate it if you use the cygwin mailing lists rather than sending personal email.)

Corinna Vinschen is the current project lead. Corinna is a senior Red Hat engineer. Corinna is responsible for the Cygwin library and maintains a couple of packages, for instance OpenSSH, OpenSSL, and a lot more.

Yaakov Selkowitz is another Red Hat engineer working on the Cygwin project. He's the guy behind the current build and packaging system and maintains by far the most packages in the Cygwin distribution.

Jon Turney is developer and maintainer of the Cygwin X server and a couple of related packages.

The packages in the Net release are maintained by a large group of people; a complete list can be found here.

Please note that all of us working on Cygwin try to be as responsive as possible and deal with patches and questions as we get them, but realistically we don't have time to answer all of the email that is sent to the main mailing list. Making Net releases of the Win32 tools and helping people on the Net out is not our primary job function, so some email will have to go unanswered.

Many thanks to everyone using the tools for their many contributions in the form of advice, bug reports, and code fixes. Keep them coming!

2. Setting up Cygwin

2.1. What is the recommended installation procedure?

2.2. What about an automated Cygwin installation?

2.3. Does Setup accept command-line arguments?

2.4. Can I install Cygwin without administrator rights?

2.5. Why not install in C:\?

2.6. Can I use Cygwin Setup to get old versions of packages (like gcc-2.95)?

2.7. How does Cygwin secure the installation and update process?

2.8. What else can I do to ensure that my installation and updates are secure?

2.9. Is Cygwin Setup, or one of the packages, infected with a virus?

2.10. My computer hangs when I run Cygwin Setup!

2.11. What packages should I download? Where are 'make', 'gcc', 'vi', etc?

2.12. How do I just get everything?

2.13. How much disk space does Cygwin require?

2.14. How do I know which version I upgraded from?

2.15. What if setup fails?

2.16. My Windows logon name has a space in it, will this cause problems?

2.17. My HOME environment variable is not what I want.

2.18. How do I uninstall individual packages?

2.19. How do I uninstall a Cygwin service?

2.20. How do I uninstall all of Cygwin?

2.21. How do I install snapshots?

2.22. Can Cygwin Setup maintain a ``mirror''?

2.23. How can I make my own portable Cygwin on CD?

2.24. How do I save, restore, delete, or modify the Cygwin information stored in the registry?

2.1.

What is the recommended installation procedure?

There is only one recommended way to install Cygwin, which is to use the GUI installer setup-*.exe. It is flexible and easy to use. You can pick and choose the packages you wish to install, and update them individually. Full source code is available for all packages and tools. More information on using Cygwin Setup may be found at https://cygwin.com/cygwin-ug-net/setup-net.html.

If you do it any other way, you're on your own! If something doesn't work right for you, and it's not covered here or in the latest development snapshot at https://cygwin.com/snapshots/, then by all means report it to the mailing list.

For a searchable list of packages that can be installed with Cygwin, see https://cygwin.com/packages/.

2.2.

What about an automated Cygwin installation?

The Cygwin Setup program is designed to be interactive, but there are a few different ways to automate it. If you are deploying to multiple systems, the best way is to run through a full installation once, saving the entire downloaded package tree. Then, on target systems, run Cygwin Setup as a "Local Install" pointed at your downloaded package tree. You could do this non-interactively with the command line options , where your downloaded package tree is in (see the next FAQ for an explanation of those options.)

For other options, search the mailing lists with terms such as cygwin automated setup or automated cygwin install.

2.3.

Does Setup accept command-line arguments?

Yes, run or for a list.

2.4.

Can I install Cygwin without administrator rights?

Yes. The default installation requests administrator rights because this allows to set up the Cygwin environment so that all users can start a Cygwin shell out of the box. However, if you don't have administrator rights for your machine, and the admins don't want to install it for you, you can install Cygwin just for yourself by downloading setup-x86.exe (for a 32 bit install) or setup-x86_64.exe (for a 64 bit install) and then start it from the command line or via the "Run..." dialog from the start menu using the option, for instance:

2.5.

Why not install in C:\?

The Cygwin Setup program will prompt you for a "root" directory. The default is , but you can change it. You are urged not to choose something like (the root directory on the system drive) for your Cygwin root. If you do, then critical Cygwin system directories like , and could easily be corrupted by other (non-Cygwin) applications or packages that use , or . Perhaps there is no conflict now, but who knows what you might install in the future? It's also just good common sense to segregate your Cygwin "filesystems" from the rest of your Windows system disk.

(In the past, there had been genuine bugs that would cause problems for people who installed in , but we believe those are gone now.)

2.6.

Can I use Cygwin Setup to get old versions of packages (like gcc-2.95)?

Cygwin Setup can be used to install any packages that are on a Cygwin mirror, which usually includes one version previous to the current one. The complete list may be searched at https://cygwin.com/packages/. There is no complete archive of older packages. If you have a problem with the current version of a Cygwin package, please report it to the mailing list using the guidelines at https://cygwin.com/problems.html.

That said, if you really need an older package, you may be able to find an outdated or archival mirror by searching the web for an old package version (for example, ), but keep in mind that this older version will not be supported by the mailing list and that installing the older version will not help improve Cygwin.

2.7.

How does Cygwin secure the installation and update process?

Here is how Cygwin secures the installation and update process to counter man-in-the-middle (MITM) attacks:

Cygwin uses the cryptographic hash algorithm SHA-512 as of 2015-03-23. The earlier 2015-02-06 update of the setup program added support for SHA-512 (Cygwin previously used MD5). There are no known practical exploits of SHA-512 (SHA-512 is part of the widely-used SHA-2 suite of cryptographic hashes).

2.8.

What else can I do to ensure that my installation and updates are secure?

To best secure your installation and update process, download the setup program (32-bit) or (64-bit), and then check its signature (using a signature-checking tool you trust) using the Cygwin public key (https://cygwin.com/key/pubring.asc). This was noted on the front page for installing and updating.

If you use the actual Cygwin public key, and have an existing secure signature-checking process, you will counter many other attacks such as subversion of the Cygwin website and malicious certificates issued by untrustworthy certificate authorities (CAs). One challenge, of course, is ensuring that you have the actual Cygwin public key. You can increase confidence in the Cygwin public key by checking older copies of the Cygwin public key (to see if it's been the same over time). Another challenge is having a secure signature-checking process. You can use GnuPG to check signatures; if you have a trusted Cygwin installation you can install GnuPG. Otherwise, to check the signature you must use an existing trusted tool or install a signature-checking tool you can trust.

Not everyone will go through this additional effort, but we make it possible for those who want that extra confidence. We also provide automatic mechanisms (such as our use of HTTPS) for those with limited time and do not want to perform the signature checking on the setup program itself. Once the correct setup program is running, it will counter other attacks as described in https://cygwin.com/faq/faq.html#faq.setup.install-security.

2.9.

Is Cygwin Setup, or one of the packages, infected with a virus?

Unlikely. Unless you can confirm it, please don't report it to the mailing list. Anti-virus products have been known to detect false positives when extracting compressed tar archives. If this causes problems for you, consider disabling your anti-virus software when running . Read the next entry for a fairly safe way to do this.

2.10.

My computer hangs when I run Cygwin Setup!

Both Network Associates (formerly McAfee) and Norton anti-virus products have been reported to "hang" when extracting Cygwin tar archives. If this happens to you, consider disabling your anti-virus software when running Cygwin Setup. The following procedure should be a fairly safe way to do that:

This should be safe, but only if Cygwin Setup is not substituted by something malicious. See also https://cygwin.com/faq/faq.html#faq.setup.install-security for a description of how the Cygwin project counters man-in-the-middle (MITM) attacks.

See also https://cygwin.com/faq/faq.html#faq.using.bloda for a list of applications that have been known, at one time or another, to interfere with the normal functioning of Cygwin.

2.11.

What packages should I download? Where are 'make', 'gcc', 'vi', etc?

When using Cygwin Setup for the first time, the default is to install a minimal subset of all available packages. If you want anything beyond that, you will have to select it explicitly. See https://cygwin.com/packages/ for a searchable list of available packages, or use as described in the Cygwin User's Guide at https://cygwin.com/cygwin-ug-net/cygcheck.html.

If you want to build programs, of course you'll need , , and probably other packages from the ``Devel'' category. Text editors can be found under ``Editors''.

2.12.

How do I just get everything?

Long ago, the default was to install everything, much to the irritation of most users. Now the default is to install only a basic core of packages. Cygwin Setup is designed to make it easy to browse categories and select what you want to install or omit from those categories. It's also easy to install everything:

This procedure only works for packages that are currently available. There is no way to tell Cygwin Setup to install all packages by default from now on. As new packages become available that would not be installed by default, you have to repeat the above procedure to get them.

In general, a better method (in my opinion), is to:

2.13.

How much disk space does Cygwin require?

That depends, obviously, on what you've chosen to download and install. A full installation today is probably larger than 1 GB installed, not including the package archives themselves nor the source code.

After installation, the package archives remain in your ``Local Package Directory''. By default the location of . You may conserve disk space by deleting the subdirectories there. These directories will have very weird looking names, being encoded with their URLs (named ).

Of course, you can keep them around in case you want to reinstall a package. If you want to clean out only the outdated packages, Michael Chase has written a script called , available at in a Cygwin mirror.

2.14.

How do I know which version I upgraded from?

Detailed logs of the most recent Cygwin Setup session can be found in and less verbose information about prior actions is in .

2.15.

What if setup fails?

First, make sure that you are using the latest version of Cygwin Setup. The latest version is always available from the Cygwin Home Page at https://cygwin.com/.

If you are downloading from the Internet, setup will fail if it cannot download the list of mirrors at https://cygwin.com/mirrors.html. It could be that the network is too busy. Something similar could be the cause of a download site not working. Try another mirror, or try again later.

If setup refuses to download a package that you know needs to be upgraded, try deleting that package's entry from /etc/setup. If you are reacting quickly to an announcement on the mailing list, it could be that the mirror you are using doesn't have the latest copy yet. Try another mirror, or try again tomorrow.

If setup has otherwise behaved strangely, check the files and in ( by default). It may provide some clues as to what went wrong and why.

If you're still baffled, search the Cygwin mailing list for clues. Others may have the same problem, and a solution may be posted there. If that search proves fruitless, send a query to the Cygwin mailing list. You must provide complete details in your query: version of setup, options you selected, contents of setup.log and setup.log.full, what happened that wasn't supposed to happen, etc.

2.16.

My Windows logon name has a space in it, will this cause problems?

Most definitely yes! UNIX shells (and thus Cygwin) use the space character as a word delimiter. Under certain circumstances, it is possible to get around this with various shell quoting mechanisms, but you are much better off if you can avoid the problem entirely.

You have two choices:

2.17.

My environment variable is not what I want.

When starting Cygwin from Windows, is determined as follows:

When using Cygwin from a network login (via ssh for instance), is always taken from the passwd entry.

If your is set to a value such as /cygdrive/c, it is likely that it was set in Windows. Start a DOS Command Window and type "set HOME" to verify if this is the case.

Access to shared drives is often restricted when starting from the network, thus Domain users may wish to have a different in the Windows environment (on shared drive) than in Cygwin (on local drive). Note that ssh only considers the account information as retrieved by getpwnam(3), disregarding .

2.18.

How do I uninstall individual packages?

Run Cygwin Setup as you would to install packages. In the list of packages to install, browse the relevant category or click on the ``View'' button to get a full listing. Click on the cycle glyph until the action reads ``Uninstall''. Proceed by clicking ``Next''.

2.19.

How do I uninstall a Cygwin service?

2.20.

How do I uninstall all of Cygwin?

Setup has no automatic uninstall facility. The recommended method to remove all of Cygwin is as follows:

2.21.

How do I install snapshots?

First, are you sure you want to do this? Snapshots are risky. They have not been tested. Use them only if there is a feature or bugfix that you need to try, and you are willing to deal with any problems, or at the request of a Cygwin developer.

You cannot use Cygwin Setup to install a snapshot.

First, you will need to download the snapshot from the snapshots page at https://cygwin.com/snapshots/. Note the directory where you saved the snapshot tarball.

Before installing a snapshot, you must first Close all Cygwin applications, including shells and services (e.g., , ). You will not be able to replace if any Cygwin process is running. You may have to restart Windows to clear the DLL from memory (beware of automatic service startup).

Most of the downloaded snapshot can be installed using . Cygwin won't be able to update (because it's used by itself), but it should succeed with everything else. If you are only installing the DLL snapshot, skip the first tar command. Open a shell (it should be the only running Cygwin process) and issue the following commands:

Exit the bash shell, and use Explorer or the Windows command shell to first rename to and then move to (assuming you installed Cygwin in ).

The operative word in trying the snapshots is "trying". If you notice a problem with the snapshot that was not present in the release DLL (what we call a "regression"), please report it to the Cygwin mailing list (see https://cygwin.com/problems.html for problem reporting guidelines). If you wish to go back to the older version of the DLL, again, close all Cygwin processes, delete , and rename back to (again assuming that your "" is ). To restore the rest of the snapshot files, reinstall the "" package using Setup.

2.22.

Can Cygwin Setup maintain a ``mirror''?

NO. Cygwin Setup cannot do this for you. Use a tool designed for this purpose. See http://rsync.samba.org/, http://www.gnu.org/software/wget/ for utilities that can do this for you. For more information on setting up a custom Cygwin package server, see the Cygwin Setup homepage at https://sourceware.org/cygwin-apps/setup.html.

2.23.

How can I make my own portable Cygwin on CD?

While some users have successfully done this, for example Indiana University's XLiveCD http://racinfo.indiana.edu/research/xlivecd.php, there is no easy way to do it. Full instructions for constructing a portable Cygwin on CD by hand can be found on the mailing list at https://www.cygwin.com/ml/cygwin/2003-07/msg01117.html (Thanks to fergus at bonhard dot uklinux dot net for these instructions.) Please note that these instructions are very old and are referring to the somewhat different setup of a Cygwin 1.5.x release. As soon as somebody set this up for recent Cygwin releases, we might add this information here.

2.24.

How do I save, restore, delete, or modify the Cygwin information stored in the registry?

Cygwin doesn't store anything important in the registry anymore for quite some time. There's no reason to save, restore or delete it.

3. Further Resources

3.1. Where's the documentation?

3.2. What Cygwin mailing lists can I join?

3.3. What if I have a problem? (Or: Why won't you/the mailing list answer my questions?)

3.1.

Where's the documentation?

If you have installed Cygwin, you can find lots of documentation in . Some packages have Cygwin specific instructions in a file . In addition, many packages ship with standard documentation, which you can find in or by using the or tools. (Hint: use to list what man pages the package includes.) Some older packages still keep their documentation in instead of .

There are links to quite a lot of documentation on the main Cygwin project web page, https://cygwin.com/, including this FAQ. Be sure to at least read any 'Release Notes' or 'Readme' or 'read this' links on the main web page, if there are any.

There is a comprehensive Cygwin User's Guide at https://cygwin.com/cygwin-ug-net/cygwin-ug-net.html and an API Reference at https://cygwin.com/cygwin-api/cygwin-api.html.

You can find documentation for the individual GNU tools at http://www.gnu.org/manual/.

3.2.

What Cygwin mailing lists can I join?

Comprehensive information about the Cygwin mailing lists can be found at https://cygwin.com/lists.html.

3.3.

What if I have a problem? (Or: Why won't you/the mailing list answer my questions?)

Comprehensive information about reporting problems with Cygwin can be found at https://cygwin.com/problems.html.

4. Using Cygwin

4.1. Why can't my application locate cygncurses-8.dll? or cygintl-3.dll? or cygreadline6.dll? or ...?

4.2. Starting a new terminal window is slow. What's going on?

4.3. Why is Cygwin suddenly so slow?

4.4. Why can't my services access network shares?

4.5. How should I set my PATH?

4.6. Bash (or another shell) says "command not found", but it's right there!

4.7. How do I convert between Windows and UNIX paths?

4.8. Why doesn't bash read my .bashrc file on startup?

4.9. How can I get bash filename completion to be case insensitive?

4.10. Can I use paths/filenames containing spaces in them?

4.11. Why can't I cd into a shortcut to a directory?

4.12. I'm having basic problems with find. Why?

4.13. Why doesn't su work?

4.14. Why doesn't man -k, apropos or whatis work?

4.15. Why doesn't chmod work?

4.16. Why doesn't my shell script work?

4.17. How do I print under Cygwin?

4.18. Why don't international (Unicode) characters work?

4.19. My application prints international characters but I only see gray boxes

4.20. Is it OK to have multiple copies of the DLL?

4.21. I read the above but I want to bundle Cygwin with a product, and ship it to customer sites. How can I do this without conflicting with any Cygwin installed by the user?

4.22. Can I bundle Cygwin with my product for free?

4.23. But doesn't that mean that if some application installs an older Cygwin DLL on top of a newer DLL, my application will break?

4.24. Why isn't package XYZ available in Cygwin?

4.25. Why is the Cygwin package of XYZ so out of date?

4.26. How can I access other drives?

4.27. How can I copy and paste into Cygwin console windows?

4.28. What firewall should I use with Cygwin?

4.29. How can I share files between Unix and Windows?

4.30. Is Cygwin case-sensitive??

4.31. What about DOS special filenames?

4.32. When it hangs, how do I get it back?

4.33. Why the weird directory structure?

4.34. How do anti-virus programs like Cygwin?

4.35. Is there a Cygwin port of GNU Emacs?

4.36. Is there a Cygwin port of XEmacs?

4.37. Why don't some of my old symlinks work anymore?

4.38. Why don't symlinks work on Samba-mounted filesystems?

4.39. Why does public key authentication with ssh fail after updating to Cygwin 1.7.34 or later?

4.40. Why is my .rhosts file not recognized by rlogin anymore after updating to Cygwin 1.7.34?

4.41. Why do my files have extra permissions after updating to Cygwin 1.7.34?

4.42. Why do my Tk programs not work anymore?

4.43. What applications have been found to interfere with Cygwin?

4.44. How do I fix fork() failures?

4.45. How do I fix find_fast_cwd warnings?

4.1.

Why can't my application locate cygncurses-8.dll? or cygintl-3.dll? or cygreadline6.dll? or ...?

Well, something has gone wrong somehow...

To repair the damage, you must run Cygwin Setup again, and re-install the package which provides the missing DLL package.

If you already installed the package at one point, Cygwin Setup won't show the option to install the package by default. In the ``Select packages to install'' dialog, click on the button. This lists all packages, even those that are already installed. Scroll down to locate the missing package, for instance . Click on the ``cycle'' glyph until it says ``Reinstall''. Continue with the installation.

For a detailed explanation of the general problem, and how to extend it to other missing DLLs and identify their containing packages, see https://cygwin.com/ml/cygwin/2002-01/msg01619.html.

4.2.

Starting a new terminal window is slow. What's going on?

There are many possible causes for this.

If your terminal windows suddenly began starting slowly after a Cygwin upgrade, it may indicate issues in the authentication setup.

For almost all its lifetime, Cygwin has used Unix-like and files to mirror the contents of the Windows SAM and AD databases. Although these files can still be used, since Cygwin 1.7.34, new installations now use the SAM/AD databases directly.

To switch to the new method, move these two files out of the way and restart the Cygwin terminal. That runs Cygwin in its new default mode.

If you are on a system that isn't using AD domain logins, this makes Cygwin use the native Windows SAM database directly, which may be faster than the old method involving and such. At worst, it will only be a bit slower. (The speed difference you see depends on which benchmark you run.) For the AD case, it can be slower than the old method, since it is trading a local file read for a network request. Version 1.7.35 will reduce the number of AD server requests the DLL makes relative to 1.7.34, with the consequence that you will now have to alter in order to change your Cygwin home directory, instead of being able to change it from the AD configuration.

If you are still experiencing very slow shell startups, there are a number of other things you can look into:

If none of the above helps, the best troubleshooting method is to run your startup scripts in debug mode. Right-click your Cygwin Terminal icon, go to Properties, and edit the command. It should be something like C:\cygwin\bin\mintty.exe -i /Cygwin-Terminal.ico -. Assuming you are using Bash for your login shell, change it to C:\cygwin\bin\mintty /bin/bash -lx then try running Cygwin Terminal again. The option tells Bash to write every command it runs to the terminal before launching it. If the terminal immediately starts filling with lines of text but then pauses, the line where the output paused is your clue as to what's going on. The Cygwin DLL proper probably isn't the cause of the slowdown in this case, since those delays happen before the first line of text appears in the terminal.

4.3.

Why is Cygwin suddenly so slow?

If suddenly every command takes a very long time, then something is probably attempting to access a network share. You may have the obsolete notation in your PATH or startup files. Using means to contact the network server, which will slow things down tremendously if it does not exist.

4.4.

Why can't my services access network shares?

If your service is one of those which switch the user context (sshd, inetd, etc), then it depends on the method used to switch to another user. This problem as well as its solution is described in detail in the Cygwin User's Guide, see https://cygwin.com/cygwin-ug-net/ntsec.html.

Workarounds include using public network share that does not require authentication (for non-critical files), providing your password to a net use command, or running the service as your own user with (see for more information).

4.5.

How should I set my PATH?

This is done for you in the file /etc/profile, which is sourced by bash when you start it from the Desktop or Start Menu shortcut, created by . The line is

Effectively, this prepends /usr/local/bin and /usr/bin to your Windows system path. If you choose to reset your PATH, say in $HOME/.bashrc, or by editing etc/profile directly, then you should follow this rule. You must have in your PATH before any Windows system directories. (And you must not omit the Windows system directories!) Otherwise you will likely encounter all sorts of problems running Cygwin applications.

If you're using another shell than bash (say, tcsh), the mechanism is the same, just the names of the login scripts are different.

4.6.

Bash (or another shell) says "command not found", but it's right there!

If you compile a program, you might find that you can't run it:

Unlike the Windows default behaviour, Unix shells like bash do not look for programs in (the current directory) by default. You can add to your PATH (see above), but this is not recommended (at least on UNIX) for security reasons. Just tell bash where to find it, when you type it on the command line:

4.7.

How do I convert between Windows and UNIX paths?

Use the 'cygpath' utility. Type '' for information. For example (on my installation):

Note that bash interprets the backslash '\' as an escape character, so you must type it twice in the bash shell if you want it to be recognized as such.

4.8.

Why doesn't bash read my .bashrc file on startup?

Your .bashrc is read from your home directory specified by the HOME environment variable. It uses /.bashrc if HOME is not set. So you need to set HOME (and the home dir in your passwd account information) correctly.

4.9.

How can I get bash filename completion to be case insensitive?

Add the following to your file:

and add the following to your file:

4.10.

Can I use paths/filenames containing spaces in them?

Cygwin does support spaces in filenames and paths. That said, some utilities that use the library may not, since files don't typically contain spaces in Unix. If you stumble into problems with this, you will need to either fix the utilities or stop using spaces in filenames used by Cygwin tools.

In particular, bash interprets space as a word separator. You would have to quote a filename containing spaces, or escape the space character. For example:

or

4.11.

Why can't I cd into a shortcut to a directory?

Cygwin does not follow MS Windows Explorer Shortcuts (*.lnk files). It sees a shortcut as a regular file and this you cannot "cd" into it.

Cygwin is also capable to create POSIX symlinks as Windows shortcuts (see the CYGWIN environment variable option "winsymlinks"), but these shortcuts are different from shortcuts created by native Windows applications. Windows applications can usually make use of Cygwin shortcuts but not vice versa. This is by choice. The reason is that Windows shortcuts may contain a bunch of extra information which would get lost, if, for example, Cygwin tar archives and extracts them as symlinks.

Changing a Cygwin shortcut in Windows Explorer usually changes a Cygwin shortcut into a Windows native shortcut. Afterwards, Cygwin will not recognize it as symlink anymore.

4.12.

I'm having basic problems with find. Why?

Make sure you are using the find that came with Cygwin and that you aren't picking up the Win32 find command instead. You can verify that you are getting the right one by doing a "type find" in bash.

If the path argument to find, including current directory (default), is itself a symbolic link, then find will not traverse it unless you specify the option. This behavior is different than most other UNIX implementations, but is not likely to change.

If find does not seem to be producing enough results, or seems to be missing out some directories, you may be experiencing a problem with one of find's optimisations. The absence of and directories on some filesystems, such as DVD-R UDF, can confuse find. See the documentation for the option in the man page.

4.13.

Why doesn't work?

The command has been in and out of Cygwin distributions, but it has not been ported to Cygwin and has never worked. It is currently installed as part of the sh-utils, but again, it does not work.

You should rather install and use as a replacement.

For some technical background into why doesn't work, read https://www.cygwin.com/ml/cygwin/2003-06/msg00897.html and related messages.

4.14.

Why doesn't , or work?

Before you can use , or , you must create the whatis database. Just run the command

(it may take a few minutes to complete).

4.15.

Why doesn't work?

If you're using FAT32 instead of NTFS, will fail since FAT32 does not provide any permission information. You should really consider converting the drive to NTFS with . FAT and FAT32 are barely good enough for memory cards or USB sticks to exchange pictures...

For other cases, understand that Cygwin attempts to show UNIX permissions based on the security features of Windows, so the Windows ACLs are likely the source of your problem. See the Cygwin User's Guide at https://cygwin.com/cygwin-ug-net/ntsec.html for more information on how Cygwin maps Windows permissions.

4.16.

Why doesn't my shell script work?

There are two basic problems you might run into. One is the fact that /bin/sh is really bash. It could be missing some features you might expect in /bin/sh, if you are used to /bin/sh actually being zsh (MacOS X "Panther") or ksh (Tru64).

Or, it could be a permission problem, and Cygwin doesn't understand that your script is executable. On NTFS or NFS just make the script executable using . However, may not work due to restrictions of the filesystem (see FAQ entry above). In this case Cygwin must read the contents of files to determine if they are executable. If your script does not start with

(or any path to a script interpreter, it does not have to be /bin/sh) then Cygwin will not know it is an executable script. The Bourne shell idiom

also works.

Note that you can use the filesystem flag in to force Cygwin to treat all files under the mount point as executable. This can be used for individual files as well as directories. Then Cygwin will not bother to read files to determine whether they are executable.

4.17.

How do I print under Cygwin?

lpr is available in the cygutils package. Some usage hints are available courtesy of Rodrigo Medina.

Jason Tishler has written a couple of messages that explain how to use a2ps (for nicely formatted text in PostScript) and ghostscript (to print PostScript files on non-PostScript Windows printers). Start at https://cygwin.com/ml/cygwin/2001-04/msg00657.html. Note that these are old mails and a2ps as well as file are long available as part of the Cygwin distribution.

Alternatively, you can use the Windows print command. Type

for usage instructions (note the must be escaped from the shell).

Finally, you can simply cat the file to the printer's share name:

You may need to press the formfeed button on your printer or append the formfeed character to your file.

4.18.

Why don't international (Unicode) characters work?

Internationalization is a complex issue. The short answer is that Cygwin relies on the setting of the setting of LANG/LC_xxx environment variables. The long answer can be found in the User's Guide in the section Internationalization

Cygwin uses UTF-8 by default. To use a different character set, you need to set the LC_ALL, LC_CTYPE or LANG environment variables.

4.19.

My application prints international characters but I only see gray boxes

In the case of Cygwin programs, this likely means that the character set as determined by the LC_ALL, LC_CTYPE or LANG environment variables does not match the one set on the Text page of the Cygwin Terminal's options. Setting the locale in the terminal's options will set the LANG variable accordingly.

Non-Cygwin programs in the Cygwin Terminal do not usually take heed of the locale environment variables. Instead, they often use the so-called console codepage, which can be determined with the command cmd /c chcp followed by the appropriate Windows codepage number. The codepage number for Cygwin's default UTF-8 character set is 65001.

4.20.

Is it OK to have multiple copies of the DLL?

Yes, as long as they are used in strictly separated installations.

The Cygwin DLL has to handle various sharing situations between multiple processes. It has to keep a process table. It has to maintain a mount table which is based on the installation path of the Cygwin DLL.

For that reason, the Cygwin DLL maintains shared resources based on a hash value created from its own installation path. Each Cygwin DLL on the machine constitutes a Cygwin installation, with the directory the Cygwin DLL resides in treated as "/bin", the parent directory as "/".

Therefore, you can install two or more separate Cygwin distros on a single machine. Each of these installations use their own Cygwin DLL, and they don't share the default POSIX paths, nor process tables, nor any other shared resource used to maintain the installation.

However, a clean separation requires that you don't try to run executables of one Cygwin installation from processes running in another Cygwin installation. This may or may not work, but the chances that the result is not what you expect are pretty high.

If you get the error "shared region is corrupted" or "shared region version mismatch" it means you have multiple versions of cygwin1.dll running at the same time which conflict with each other. Apart from mixing executables of different Cygwin installations, this could also happen if you have one a single Cygwin installation, for example, if you update the Cygwin package without exiting all Cygwin apps (including services like sshd) beforehand.

The only DLL that is sanctioned by the Cygwin project is the one that you get by running setup-x86.exe or setup-x86_64.exe, installed in a directory controlled by this program. If you have other versions on your system and desire help from the cygwin project, you should delete or rename all DLLs that are not installed by .

Table of Contents

This is an introduction to R (“GNU S”), a language and environment for statistical computing and graphics. R is similar to the award-winning¹ S system, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...).

This manual provides information on data types, programming elements, statistical modelling and graphics.

This manual is for R, version 4.0.2 (2020-06-22).

Copyright © 1990 W. N. Venables
Copyright © 1992 W. N. Venables & D. M. Smith
Copyright © 1997 R. Gentleman & R. Ihaka
Copyright © 1997, 1998 M. Maechler
Copyright © 1999–2018 R Core Team

Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies.

Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one.

Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.

Preface

This introduction to R is derived from an original set of notes describing the S and S-PLUS environments written in 1990–2 by Bill Venables and David M. Smith when at the University of Adelaide. We have made a number of small changes to reflect differences between the R and S programs, and expanded some of the material.

We would like to extend warm thanks to Bill Venables (and David Smith) for granting permission to distribute this modified version of the notes in this way, and for being a supporter of R from way back.

Comments and corrections are always welcome. Please address email correspondence to R-help@R-project.org.

Suggestions to the reader

Most R novices will start with the introductory session in Appendix A. This should give some familiarity with the style of R sessions and more importantly some instant feedback on what actually happens.

Many users will come to R mainly for its graphical facilities. See Graphics, which can be read at almost any time and need not wait until all the preceding sections have been digested.

1 Introduction and preliminaries

1.1 The R environment

R is an integrated suite of software facilities for data manipulation, calculation and graphical display. Among other things it has

• an effective data handling and storage facility,
• a suite of operators for calculations on arrays, in particular matrices,
• a large, coherent, integrated collection of intermediate tools for data analysis,
• graphical facilities for data analysis and display either directly at the computer or on hardcopy, and
• a well developed, simple and effective programming language (called ‘S’) which includes conditionals, loops, user defined recursive functions and input and output facilities. (Indeed most of the system supplied functions are themselves written in the S language.)

The term “environment” is intended to characterize it as a fully planned and coherent system, rather than an incremental accretion of very specific and inflexible tools, as is frequently the case with other data analysis software.

R is very much a vehicle for newly developing methods of interactive data analysis. It has developed rapidly, and has been extended by a large collection of packages. However, most programs written in R are essentially ephemeral, written for a single piece of data analysis.

1.2 Related software and documentation

R can be regarded as an implementation of the S language which was developed at Bell Laboratories by Rick Becker, John Chambers and Allan Wilks, and also forms the basis of the S-PLUS systems.

The evolution of the S language is characterized by four books by John Chambers and coauthors. For R, the basic reference is The New S Language: A Programming Environment for Data Analysis and Graphics by Richard A. Becker, John M. Chambers and Allan R. Wilks. The new features of the 1991 release of S are covered in Statistical Models in S edited by John M. Chambers and Trevor J. Hastie. The formal methods and classes of the methods package are based on those described in Programming with Data by John M. Chambers. See References, for precise references.

There are now a number of books which describe how to use R for data analysis and statistics, and documentation for S/S-PLUS can typically be used with R, keeping the differences between the S implementations in mind. See What documentation exists for R? in The R statistical system FAQ.

1.3 R and statistics

Our introduction to the R environment did not mention statistics, yet many people use R as a statistics system. We prefer to think of it of an environment within which many classical and modern statistical techniques have been implemented. A few of these are built into the base R environment, but many are supplied as packages. There are about 25 packages supplied with R (called “standard” and “recommended” packages) and many more are available through the family of Internet sites (via https://CRAN.R-project.org) and elsewhere. More details on packages are given later (see Packages).

Most classical statistics and much of the latest methodology is available for use with R, but users may need to be prepared to do a little work to find it.

There is an important difference in philosophy between S (and hence R) and the other main statistical systems. In S a statistical analysis is normally done as a series of steps, with intermediate results being stored in objects. Thus whereas SAS and SPSS will give copious output from a regression or discriminant analysis, R will give minimal output and store the results in a fit object for subsequent interrogation by further R functions.

1.4 R and the window system

The most convenient way to use R is at a graphics workstation running a windowing system. This guide is aimed at users who have this facility. In particular we will occasionally refer to the use of R on an X window system although the vast bulk of what is said applies generally to any implementation of the R environment.

Most users will find it necessary to interact directly with the operating system on their computer from time to time. In this guide, we mainly discuss interaction with the operating system on UNIX machines. If you are running R under Windows or macOS you will need to make some small adjustments.

Setting up a workstation to take full advantage of the customizable features of R is a straightforward if somewhat tedious procedure, and will not be considered further here. Users in difficulty should seek local expert help.

1.5 Using R interactively

When you use the R program it issues a prompt when it expects input commands. The default prompt is ‘’, which on UNIX might be the same as the shell prompt, and so it may appear that nothing is happening. However, as we shall see, it is easy to change to a different R prompt if you wish. We will assume that the UNIX shell prompt is ‘’.

In using R under UNIX the suggested procedure for the first occasion is as follows:

1. Create a separate sub-directory, say , to hold data files on which you will use R for this problem. This will be the working directory whenever you use R for this particular problem.
2. Start the R program with the command
3. At this point R commands may be issued (see later).
4. To quit the R program the command is

   At this point you will be asked whether you want to save the data from your R session. On some systems this will bring up a dialog box, and on others you will receive a text prompt to which you can respond , or (a single letter abbreviation will do) to save the data before quitting, quit without saving, or return to the R session. Data which is saved will be available in future R sessions.

Further R sessions are simple.

1. Make the working directory and start the program as before:
2. Use the R program, terminating with the command at the end of the session.

To use R under Windows the procedure to follow is basically the same. Create a folder as the working directory, and set that in the field in your R shortcut. Then launch R by double clicking on the icon.

1.6 An introductory session

Readers wishing to get a feel for R at a computer before proceeding are strongly advised to work through the introductory session given in A sample session.

1.7 Getting help with functions and features

R has an inbuilt help facility similar to the facility of UNIX. To get more information on any specific named function, for example , the command is

An alternative is

For a feature specified by special characters, the argument must be enclosed in double or single quotes, making it a “character string”: This is also necessary for a few words with syntactic meaning including , and .

Either form of quote mark may be used to escape the other, as in the string . Our convention is to use double quote marks for preference.

On most R installations help is available in format by running

which will launch a Web browser that allows the help pages to be browsed with hyperlinks. On UNIX, subsequent help requests are sent to the -based help system. The ‘Search Engine and Keywords’ link in the page loaded by is particularly useful as it is contains a high-level concept list which searches though available functions. It can be a great way to get your bearings quickly and to understand the breadth of what R has to offer.

The command (alternatively ) allows searching for help in various ways. For example,

Try for details and more examples.

The examples on a help topic can normally be run by

Windows versions of R have other optional help systems: use

for further details.

1.8 R commands, case sensitivity, etc.

Technically R is an expression language with a very simple syntax. It is case sensitive as are most UNIX based packages, so and are different symbols and would refer to different variables. The set of symbols which can be used in R names depends on the operating system and country within which R is being run (technically on the locale in use). Normally all alphanumeric symbols are allowed² (and in some countries this includes accented letters) plus ‘’ and ‘’, with the restriction that a name must start with ‘’ or a letter, and if it starts with ‘’ the second character must not be a digit. Names are effectively unlimited in length.

Elementary commands consist of either expressions or assignments. If an expression is given as a command, it is evaluated, printed (unless specifically made invisible), and the value is lost. An assignment also evaluates an expression and passes the value to a variable but the result is not automatically printed.

Commands are separated either by a semi-colon (‘’), or by a newline. Elementary commands can be grouped together into one compound expression by braces (‘’ and ‘’). Comments can be put almost³ anywhere, starting with a hashmark (‘’), everything to the end of the line is a comment.

If a command is not complete at the end of a line, R will give a different prompt, by default

on second and subsequent lines and continue to read input until the command is syntactically complete. This prompt may be changed by the user. We will generally omit the continuation prompt and indicate continuation by simple indenting.

Command lines entered at the console are limited⁴ to about 4095 bytes (not characters).

1.9 Recall and correction of previous commands

Under many versions of UNIX and on Windows, R provides a mechanism for recalling and re-executing previous commands. The vertical arrow keys on the keyboard can be used to scroll forward and backward through a command history. Once a command is located in this way, the cursor can be moved within the command using the horizontal arrow keys, and characters can be removed with the key or added with the other keys. More details are provided later: see The command-line editor.

The recall and editing capabilities under UNIX are highly customizable. You can find out how to do this by reading the manual entry for the readline library.

Alternatively, the Emacs text editor provides more general support mechanisms (via , Emacs Speaks Statistics) for working interactively with R. See R and Emacs in The R statistical system FAQ.

1.10 Executing commands from or diverting output to a file

If commands⁵ are stored in an external file, say in the working directory , they may be executed at any time in an R session with the command

For Windows Source is also available on the File menu. The function ,

will divert all subsequent output from the console to an external file, . The command

restores it to the console once again.

1.11 Data permanency and removing objects

The entities that R creates and manipulates are known as objects. These may be variables, arrays of numbers, character strings, functions, or more general structures built from such components.

During an R session, objects are created and stored by name (we discuss this process in the next section). The R command

(alternatively, ) can be used to display the names of (most of) the objects which are currently stored within R. The collection of objects currently stored is called the workspace.

To remove objects the function is available:

All objects created during an R session can be stored permanently in a file for use in future R sessions. At the end of each R session you are given the opportunity to save all the currently available objects. If you indicate that you want to do this, the objects are written to a file called ⁶ in the current directory, and the command lines used in the session are saved to a file called .

When R is started at later time from the same directory it reloads the workspace from this file. At the same time the associated commands history is reloaded.

It is recommended that you should use separate working directories for analyses conducted with R. It is quite common for objects with names and to be created during an analysis. Names like this are often meaningful in the context of a single analysis, but it can be quite hard to decide what they might be when the several analyses have been conducted in the same directory.

2 Simple manipulations; numbers and vectors

2.1 Vectors and assignment

R operates on named data structures. The simplest such structure is the numeric vector, which is a single entity consisting of an ordered collection of numbers. To set up a vector named , say, consisting of five numbers, namely 10.4, 5.6, 3.1, 6.4 and 21.7, use the R command

This is an assignment statement using the function which in this context can take an arbitrary number of vector arguments and whose value is a vector got by concatenating its arguments end to end.⁷

A number occurring by itself in an expression is taken as a vector of length one.

Notice that the assignment operator (‘’), which consists of the two characters ‘’ (“less than”) and ‘’ (“minus”) occurring strictly side-by-side and it ‘points’ to the object receiving the value of the expression. In most contexts the ‘’ operator can be used as an alternative.

Assignment can also be made using the function . An equivalent way of making the same assignment as above is with:

The usual operator, , can be thought of as a syntactic short-cut to this.

Assignments can also be made in the other direction, using the obvious change in the assignment operator. So the same assignment could be made using

If an expression is used as a complete command, the value is printed and lost⁸. So now if we were to use the command

the reciprocals of the five values would be printed at the terminal (and the value of , of course, unchanged).

The further assignment

would create a vector with 11 entries consisting of two copies of with a zero in the middle place.

2.2 Vector arithmetic

Vectors can be used in arithmetic expressions, in which case the operations are performed element by element. Vectors occurring in the same expression need not all be of the same length. If they are not, the value of the expression is a vector with the same length as the longest vector which occurs in the expression. Shorter vectors in the expression are recycled as often as need be (perhaps fractionally) until they match the length of the longest vector. In particular a constant is simply repeated. So with the above assignments the command

generates a new vector of length 11 constructed by adding together, element by element, repeated 2.2 times, repeated just once, and repeated 11 times.

The elementary arithmetic operators are the usual , , , and for raising to a power. In addition all of the common arithmetic functions are available. , , , , , , and so on, all have their usual meaning. and select the largest and smallest elements of a vector respectively. is a function whose value is a vector of length two, namely . is the number of elements in , gives the total of the elements in , and their product.

Two statistical functions are which calculates the sample mean, which is the same as , and which gives

or sample variance. If the argument to is an n-by-p matrix the value is a p-by-p sample covariance matrix got by regarding the rows as independent p-variate sample vectors.

returns a vector of the same size as with the elements arranged in increasing order; however there are other more flexible sorting facilities available (see or which produce a permutation to do the sorting).

Note that and select the largest and smallest values in their arguments, even if they are given several vectors. The parallel maximum and minimum functions and return a vector (of length equal to their longest argument) that contains in each element the largest (smallest) element in that position in any of the input vectors.

For most purposes the user will not be concerned if the “numbers” in a numeric vector are integers, reals or even complex. Internally calculations are done as double precision real numbers, or double precision complex numbers if the input data are complex.

To work with complex numbers, supply an explicit complex part. Thus

will give and a warning, but

will do the computations as complex numbers.

2.3 Generating regular sequences

R has a number of facilities for generating commonly used sequences of numbers. For example is the vector . The colon operator has high priority within an expression, so, for example is the vector . Put and compare the sequences and .

The construction may be used to generate a sequence backwards.

The function is a more general facility for generating sequences. It has five arguments, only some of which may be specified in any one call. The first two arguments, if given, specify the beginning and end of the sequence, and if these are the only two arguments given the result is the same as the colon operator. That is is the same vector as .

Arguments to , and to many other R functions, can also be given in named form, in which case the order in which they appear is irrelevant. The first two arguments may be named and ; thus , and are all the same as . The next two arguments to may be named and , which specify a step size and a length for the sequence respectively. If neither of these is given, the default is assumed.

For example

generates in the vector . Similarly

generates the same vector in .

The fifth argument may be named , which is normally used as the only argument to create the sequence , or the empty sequence if the vector is empty (as it can be).

A related function is which can be used for replicating an object in various complicated ways. The simplest form is

which will put five copies of end-to-end in . Another useful version is

which repeats each element of five times before moving on to the next.

2.4 Logical vectors

As well as numerical vectors, R allows manipulation of logical quantities. The elements of a logical vector can have the values , , and (for “not available”, see below). The first two are often abbreviated as and , respectively. Note however that and are just variables which are set to and by default, but are not reserved words and hence can be overwritten by the user. Hence, you should always use and .

Logical vectors are generated by conditions. For example

sets as a vector of the same length as with values corresponding to elements of where the condition is not met and where it is.

The logical operators are , , , , for exact equality and for inequality. In addition if and are logical expressions, then is their intersection (“and”), is their union (“or”), and is the negation of .

Logical vectors may be used in ordinary arithmetic, in which case they are coerced into numeric vectors, becoming and becoming . However there are situations where logical vectors and their coerced numeric counterparts are not equivalent, for example see the next subsection.

2.5 Missing values

In some cases the components of a vector may not be completely known. When an element or value is “not available” or a “missing value” in the statistical sense, a place within a vector may be reserved for it by assigning it the special value . In general any operation on an becomes an . The motivation for this rule is simply that if the specification of an operation is incomplete, the result cannot be known and hence is not available.

The function gives a logical vector of the same size as with value if and only if the corresponding element in is .

Notice that the logical expression is quite different from since is not really a value but a marker for a quantity that is not available. Thus is a vector of the same length as all of whose values are as the logical expression itself is incomplete and hence undecidable.

Note that there is a second kind of “missing” values which are produced by numerical computation, the so-called Not a Number, , values. Examples are

or

which both give since the result cannot be defined sensibly.

In summary, is both for and values. To differentiate these, is only for s.

Missing values are sometimes printed as when character vectors are printed without quotes.

2.6 Character vectors

Character quantities and character vectors are used frequently in R, for example as plot labels. Where needed they are denoted by a sequence of characters delimited by the double quote character, e.g., , .

Character strings are entered using either matching double () or single () quotes, but are printed using double quotes (or sometimes without quotes). They use C-style escape sequences, using as the escape character, so is entered and printed as , and inside double quotes is entered as . Other useful escape sequences are , newline, , tab and , backspace—see for a full list.

Character vectors may be concatenated into a vector by the function; examples of their use will emerge frequently.

The function takes an arbitrary number of arguments and concatenates them one by one into character strings. Any numbers given among the arguments are coerced into character strings in the evident way, that is, in the same way they would be if they were printed. The arguments are by default separated in the result by a single blank character, but this can be changed by the named argument, , which changes it to , possibly empty.

For example

makes into the character vector

Note particularly that recycling of short lists takes place here too; thus is repeated 5 times to match the sequence . ⁹

2.7 Index vectors; selecting and modifying subsets of a data set

Subsets of the elements of a vector may be selected by appending to the name of the vector an index vector in square brackets. More generally any expression that evaluates to a vector may have subsets of its elements similarly selected by appending an index vector in square brackets immediately after the expression.

Such index vectors can be any of four distinct types.

1. A logical vector. In this case the index vector is recycled to the same length as the vector from which elements are to be selected. Values corresponding to in the index vector are selected and those corresponding to are omitted. For example
   > y <- x[!is.na(x)]

   creates (or re-creates) an object which will contain the non-missing values of , in the same order. Note that if has missing values, will be shorter than . Also

   > (x+1)[(!is.na(x)) & x>0] -> z

   creates an object and places in it the values of the vector for which the corresponding value in was both non-missing and positive.

2. A vector of positive integral quantities. In this case the values in the index vector must lie in the set {1, 2, …, }. The corresponding elements of the vector are selected and concatenated, in that order, in the result. The index vector can be of any length and the result is of the same length as the index vector. For example is the sixth component of and

   selects the first 10 elements of (assuming is not less than 10). Also

   > c("x","y")[rep(c(1,2,2,1), times=4)]

   (an admittedly unlikely thing to do) produces a character vector of length 16 consisting of repeated four times.

3. A vector of negative integral quantities. Such an index vector specifies the values to be excluded rather than included. Thus

   gives all but the first five elements of .

4. A vector of character strings. This possibility only applies where an object has a attribute to identify its components. In this case a sub-vector of the names vector may be used in the same way as the positive integral labels in item 2 further above.
   > fruit <- c(5, 10, 1, 20) > names(fruit) <- c("orange", "banana", "apple", "peach") > lunch <- fruit[c("apple","orange")]

   The advantage is that alphanumeric names are often easier to remember than numeric indices. This option is particularly useful in connection with data frames, as we shall see later.

An indexed expression can also appear on the receiving end of an assignment, in which case the assignment operation is performed only on those elements of the vector. The expression must be of the form as having an arbitrary expression in place of the vector name does not make much sense here.

For example

replaces any missing values in by zeros and

has the same effect as

2.8 Other types of objects

Vectors are the most important type of object in R, but there are several others which we will meet more formally in later sections.

• matrices or more generally arrays are multi-dimensional generalizations of vectors. In fact, they are vectors that can be indexed by two or more indices and will be printed in special ways. See Arrays and matrices.
• factors provide compact ways to handle categorical data. See Factors.
• lists are a general form of vector in which the various elements need not be of the same type, and are often themselves vectors or lists. Lists provide a convenient way to return the results of a statistical computation. See Lists.
• data frames are matrix-like structures, in which the columns can be of different types. Think of data frames as ‘data matrices’ with one row per observational unit but with (possibly) both numerical and categorical variables. Many experiments are best described by data frames: the treatments are categorical but the response is numeric. See Data frames.
• functions are themselves objects in R which can be stored in the project’s workspace. This provides a simple and convenient way to extend R. See Writing your own functions.

3 Objects, their modes and attributes

3.1 Intrinsic attributes: mode and length

The entities R operates on are technically known as objects. Examples are vectors of numeric (real) or complex values, vectors of logical values and vectors of character strings. These are known as “atomic” structures since their components are all of the same type, or mode, namely numeric¹⁰, complex, logical, character and raw.

Vectors must have their values all of the same mode. Thus any given vector must be unambiguously either logical, numeric, complex, character or raw. (The only apparent exception to this rule is the special “value” listed as for quantities not available, but in fact there are several types of ). Note that a vector can be empty and still have a mode. For example the empty character string vector is listed as and the empty numeric vector as .

R also operates on objects called lists, which are of mode list. These are ordered sequences of objects which individually can be of any mode. lists are known as “recursive” rather than atomic structures since their components can themselves be lists in their own right.

The other recursive structures are those of mode function and expression. Functions are the objects that form part of the R system along with similar user written functions, which we discuss in some detail later. Expressions as objects form an advanced part of R which will not be discussed in this guide, except indirectly when we discuss formulae used with modeling in R.

By the mode of an object we mean the basic type of its fundamental constituents. This is a special case of a “property” of an object. Another property of every object is its length. The functions and can be used to find out the mode and length of any defined structure ¹¹.

Further properties of an object are usually provided by , see Getting and setting attributes. Because of this, mode and length are also called “intrinsic attributes” of an object.

For example, if is a complex vector of length 100, then in an expression is the character string and is .

R caters for changes of mode almost anywhere it could be considered sensible to do so, (and a few where it might not be). For example with

we could put

after which is the character vector . A further coercion, or change of mode, reconstructs the numerical vector again:

Now and are the same.¹² There is a large collection of functions of the form for either coercion from one mode to another, or for investing an object with some other attribute it may not already possess. The reader should consult the different help files to become familiar with them.

3.2 Changing the length of an object

An “empty” object may still have a mode. For example

makes an empty vector structure of mode numeric. Similarly is a empty character vector, and so on. Once an object of any size has been created, new components may be added to it simply by giving it an index value outside its previous range. Thus

now makes a vector of length 3, (the first two components of which are at this point both ). This applies to any structure at all, provided the mode of the additional component(s) agrees with the mode of the object in the first place.

This automatic adjustment of lengths of an object is used often, for example in the function for input. (see The scan() function.)

Conversely to truncate the size of an object requires only an assignment to do so. Hence if is an object of length 10, then

makes it an object of length 5 consisting of just the former components with even index. (The old indices are not retained, of course.) We can then retain just the first three values by

and vectors can be extended (by missing values) in the same way.

3.3 Getting and setting attributes

The function returns a list of all the non-intrinsic attributes currently defined for that object. The function can be used to select a specific attribute. These functions are rarely used, except in rather special circumstances when some new attribute is being created for some particular purpose, for example to associate a creation date or an operator with an R object. The concept, however, is very important.

Some care should be exercised when assigning or deleting attributes since they are an integral part of the object system used in R.

When it is used on the left hand side of an assignment it can be used either to associate a new attribute with or to change an existing one. For example

allows R to treat as if it were a 10-by-10 matrix.

3.4 The class of an object

All objects in R have a class, reported by the function . For simple vectors this is just the mode, for example , , or , but , , and are other possible values.

A special attribute known as the class of the object is used to allow for an object-oriented style¹³ of programming in R. For example if an object has class , it will be printed in a certain way, the function will display it graphically in a certain way, and other so-called generic functions such as will react to it as an argument in a way sensitive to its class.

To remove temporarily the effects of class, use the function . For example if has the class then

will print it in data frame form, which is rather like a matrix, whereas

will print it as an ordinary list. Only in rather special situations do you need to use this facility, but one is when you are learning to come to terms with the idea of class and generic functions.

Generic functions and classes will be discussed further in Object orientation, but only briefly.

4 Ordered and unordered factors

A factor is a vector object used to specify a discrete classification (grouping) of the components of other vectors of the same length. R provides both ordered and unordered factors. While the “real” application of factors is with model formulae (see Contrasts), we here look at a specific example.

4.1 A specific example

Suppose, for example, we have a sample of 30 tax accountants from all the states and territories of Australia¹⁴ and their individual state of origin is specified by a character vector of state mnemonics as

Notice that in the case of a character vector, “sorted” means sorted in alphabetical order.

A factor is similarly created using the function:

The function handles factors slightly differently from other objects:

To find out the levels of a factor the function can be used.

4.2 The function and ragged arrays

To continue the previous example, suppose we have the incomes of the same tax accountants in another vector (in suitably large units of money)

To calculate the sample mean income for each state we can now use the special function :

giving a means vector with the components labelled by the levels

The function is used to apply a function, here , to each group of components of the first argument, here , defined by the levels of the second component, here ¹⁵, as if they were separate vector structures. The result is a structure of the same length as the levels attribute of the factor containing the results. The reader should consult the help document for more details.

Suppose further we needed to calculate the standard errors of the state income means. To do this we need to write an R function to calculate the standard error for any given vector. Since there is an builtin function to calculate the sample variance, such a function is a very simple one liner, specified by the assignment:

(Writing functions will be considered later in Writing your own functions. Note that R’s a builtin function is something different.) After this assignment, the standard errors are calculated by

and the values calculated are then

As an exercise you may care to find the usual 95% confidence limits for the state mean incomes. To do this you could use once more with the function to find the sample sizes, and the function to find the percentage points of the appropriate t-distributions. (You could also investigate R’s facilities for t-tests.)

The function