R Markdown File

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  • R Markdown supports dozens of static and dynamic output formats including HTML, PDF, MS Word, Beamer, HTML5 slides, Tufte-style handouts, books.
  • Video created by????????????????????????? For the course '???????????????????????????' This week we cover some of the core tools for developing reproducible documents. We cover the literate.
  • The GPL in other formats: plain text, Texinfo, LaTeX, standalone HTML, ODF, Docbook v4 or v5, reStructuredText, Markdown, and RTF. GPLv3 logos to use with your project; Old versions of the GNU GPL; What to do if you see a possible GPL violation.
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GNU General Public License

This video takes an R Markdown file that was created in advance to walk through some basic biomaRt commands in R. Designed for Tools for Genome.

  • The GPL in other formats: plain text, Texinfo, LaTeX, standalone HTML, ODF, Docbook v4 or v5, reStructuredText, Markdown, and RTF.
  • GPLv3 logos to use with your project

GNU GENERAL PUBLIC LICENSE

Version 3, 29 June 2007

Copyright © 2007 Free Software Foundation, Inc. <https://fsf.org/>

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

Preamble

The GNU General Public License is a free, copyleft license forsoftware and other kinds of works.

The licenses for most software and other practical works are designedto take away your freedom to share and change the works. By contrast,the GNU General Public License is intended to guarantee your freedom toshare and change all versions of a program--to make sure it remains freesoftware for all its users. We, the Free Software Foundation, use theGNU General Public License for most of our software; it applies also toany other work released this way by its authors. You can apply it toyour programs, too.

When we speak of free software, we are referring to freedom, notprice. Our General Public Licenses are designed to make sure that youhave the freedom to distribute copies of free software (and charge forthem if you wish), that you receive source code or can get it if youwant it, that you can change the software or use pieces of it in newfree programs, and that you know you can do these things.

To protect your rights, we need to prevent others from denying youthese rights or asking you to surrender the rights. Therefore, you havecertain responsibilities if you distribute copies of the software, or ifyou modify it: responsibilities to respect the freedom of others.

For example, if you distribute copies of such a program, whethergratis or for a fee, you must pass on to the recipients the samefreedoms that you received. You must make sure that they, too, receiveor can get the source code. And you must show them these terms so theyknow their rights.

Developers that use the GNU GPL protect your rights with two steps:(1) assert copyright on the software, and (2) offer you this Licensegiving you legal permission to copy, distribute and/or modify it.

For the developers' and authors' protection, the GPL clearly explainsthat there is no warranty for this free software. For both users' andauthors' sake, the GPL requires that modified versions be marked aschanged, so that their problems will not be attributed erroneously toauthors of previous versions.

Some devices are designed to deny users access to install or runmodified versions of the software inside them, although the manufacturercan do so. This is fundamentally incompatible with the aim ofprotecting users' freedom to change the software. The systematicpattern of such abuse occurs in the area of products for individuals touse, which is precisely where it is most unacceptable. Therefore, wehave designed this version of the GPL to prohibit the practice for thoseproducts. If such problems arise substantially in other domains, westand ready to extend this provision to those domains in future versionsof the GPL, as needed to protect the freedom of users.

Finally, every program is threatened constantly by software patents.States should not allow patents to restrict development and use ofsoftware on general-purpose computers, but in those that do, we wish toavoid the special danger that patents applied to a free program couldmake it effectively proprietary. To prevent this, the GPL assures thatpatents cannot be used to render the program non-free.

The precise terms and conditions for copying, distribution andmodification follow.

TERMS AND CONDITIONS

0. Definitions.

“This License” refers to version 3 of the GNU General Public License.

“Copyright” also means copyright-like laws that apply to other kinds ofworks, such as semiconductor masks.

“The Program” refers to any copyrightable work licensed under thisLicense. Each licensee is addressed as “you”. “Licensees” and“recipients” may be individuals or organizations.

To “modify” a work means to copy from or adapt all or part of the workin a fashion requiring copyright permission, other than the making of anexact copy. The resulting work is called a “modified version” of theearlier work or a work “based on” the earlier work.

A “covered work” means either the unmodified Program or a work basedon the Program.

To “propagate” a work means to do anything with it that, withoutpermission, would make you directly or secondarily liable forinfringement under applicable copyright law, except executing it on acomputer or modifying a private copy. Propagation includes copying,distribution (with or without modification), making available to thepublic, and in some countries other activities as well.

To “convey” a work means any kind of propagation that enables otherparties to make or receive copies. Mere interaction with a user througha computer network, with no transfer of a copy, is not conveying.

An interactive user interface displays “Appropriate Legal Notices”to the extent that it includes a convenient and prominently visiblefeature that (1) displays an appropriate copyright notice, and (2)tells the user that there is no warranty for the work (except to theextent that warranties are provided), that licensees may convey thework under this License, and how to view a copy of this License. Ifthe interface presents a list of user commands or options, such as amenu, a prominent item in the list meets this criterion.

1. Source Code.

The “source code” for a work means the preferred form of the workfor making modifications to it. Update chrome on macbook air. “Object code” means any non-sourceform of a work.

A “Standard Interface” means an interface that either is an officialstandard defined by a recognized standards body, or, in the case ofinterfaces specified for a particular programming language, one thatis widely used among developers working in that language.

The “System Libraries” of an executable work include anything, otherthan the work as a whole, that (a) is included in the normal form ofpackaging a Major Component, but which is not part of that MajorComponent, and (b) serves only to enable use of the work with thatMajor Component, or to implement a Standard Interface for which animplementation is available to the public in source code form. A“Major Component”, in this context, means a major essential component(kernel, window system, and so on) of the specific operating system(if any) on which the executable work runs, or a compiler used toproduce the work, or an object code interpreter used to run it.

The “Corresponding Source” for a work in object code form means allthe source code needed to generate, install, and (for an executablework) run the object code and to modify the work, including scripts tocontrol those activities. However, it does not include the work'sSystem Libraries, or general-purpose tools or generally available freeprograms which are used unmodified in performing those activities butwhich are not part of the work. For example, Corresponding Sourceincludes interface definition files associated with source files forthe work, and the source code for shared libraries and dynamicallylinked subprograms that the work is specifically designed to require,such as by intimate data communication or control flow between thosesubprograms and other parts of the work.

The Corresponding Source need not include anything that userscan regenerate automatically from other parts of the CorrespondingSource.

The Corresponding Source for a work in source code form is thatsame work.

2. Basic Permissions.

All rights granted under this License are granted for the term ofcopyright on the Program, and are irrevocable provided the statedconditions are met. This License explicitly affirms your unlimitedpermission to run the unmodified Program. The output from running acovered work is covered by this License only if the output, given itscontent, constitutes a covered work. This License acknowledges yourrights of fair use or other equivalent, as provided by copyright law.

You may make, run and propagate covered works that you do notconvey, without conditions so long as your license otherwise remainsin force. You may convey covered works to others for the sole purposeof having them make modifications exclusively for you, or provide youwith facilities for running those works, provided that you comply withthe terms of this License in conveying all material for which you donot control copyright. Those thus making or running the covered worksfor you must do so exclusively on your behalf, under your directionand control, on terms that prohibit them from making any copies ofyour copyrighted material outside their relationship with you.

Conveying under any other circumstances is permitted solely underthe conditions stated below. Sublicensing is not allowed; section 10makes it unnecessary.

3. Protecting Users' Legal Rights From Anti-Circumvention Law.

No covered work shall be deemed part of an effective technologicalmeasure under any applicable law fulfilling obligations under article11 of the WIPO copyright treaty adopted on 20 December 1996, orsimilar laws prohibiting or restricting circumvention of suchmeasures.

When you convey a covered work, you waive any legal power to forbidcircumvention of technological measures to the extent such circumventionis effected by exercising rights under this License with respect tothe covered work, and you disclaim any intention to limit operation ormodification of the work as a means of enforcing, against the work'susers, your or third parties' legal rights to forbid circumvention oftechnological measures.

4. Conveying Verbatim Copies.

You may convey verbatim copies of the Program's source code as youreceive it, in any medium, provided that you conspicuously andappropriately publish on each copy an appropriate copyright notice;keep intact all notices stating that this License and anynon-permissive terms added in accord with section 7 apply to the code;keep intact all notices of the absence of any warranty; and give allrecipients a copy of this License along with the Program.

You may charge any price or no price for each copy that you convey,and you may offer support or warranty protection for a fee.

5. Conveying Modified Source Versions.

You may convey a work based on the Program, or the modifications toproduce it from the Program, in the form of source code under theterms of section 4, provided that you also meet all of these conditions:

  • a) The work must carry prominent notices stating that you modified it, and giving a relevant date.
  • b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7. This requirement modifies the requirement in section 4 to “keep intact all notices”.
  • c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it.
  • d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so.

A compilation of a covered work with other separate and independentworks, which are not by their nature extensions of the covered work,and which are not combined with it such as to form a larger program,in or on a volume of a storage or distribution medium, is called an“aggregate” if the compilation and its resulting copyright are notused to limit the access or legal rights of the compilation's usersbeyond what the individual works permit. Inclusion of a covered workin an aggregate does not cause this License to apply to the otherparts of the aggregate.

6. Conveying Non-Source Forms.

You may convey a covered work in object code form under the termsof sections 4 and 5, provided that you also convey themachine-readable Corresponding Source under the terms of this License,in one of these ways:

  • a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange.
  • b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge.
  • c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b.
  • d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements.
  • e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d.

A separable portion of the object code, whose source code is excludedfrom the Corresponding Source as a System Library, need not beincluded in conveying the object code work.

A “User Product” is either (1) a “consumer product”, which means anytangible personal property which is normally used for personal, family,or household purposes, or (2) anything designed or sold for incorporationinto a dwelling. In determining whether a product is a consumer product,doubtful cases shall be resolved in favor of coverage. For a particularproduct received by a particular user, “normally used” refers to atypical or common use of that class of product, regardless of the statusof the particular user or of the way in which the particular useractually uses, or expects or is expected to use, the product. A productis a consumer product regardless of whether the product has substantialcommercial, industrial or non-consumer uses, unless such uses representthe only significant mode of use of the product.

“Installation Information” for a User Product means any methods,procedures, authorization keys, or other information required to installand execute modified versions of a covered work in that User Product froma modified version of its Corresponding Source. The information mustsuffice to ensure that the continued functioning of the modified objectcode is in no case prevented or interfered with solely becausemodification has been made.

If you convey an object code work under this section in, or with, orspecifically for use in, a User Product, and the conveying occurs aspart of a transaction in which the right of possession and use of theUser Product is transferred to the recipient in perpetuity or for afixed term (regardless of how the transaction is characterized), theCorresponding Source conveyed under this section must be accompaniedby the Installation Information. But this requirement does not applyif neither you nor any third party retains the ability to installmodified object code on the User Product (for example, the work hasbeen installed in ROM).

The requirement to provide Installation Information does not include arequirement to continue to provide support service, warranty, or updatesfor a work that has been modified or installed by the recipient, or forthe User Product in which it has been modified or installed. Access to anetwork may be denied when the modification itself materially andadversely affects the operation of the network or violates the rules andprotocols for communication across the network.

Corresponding Source conveyed, and Installation Information provided,in accord with this section must be in a format that is publiclydocumented (and with an implementation available to the public insource code form), and must require no special password or key forunpacking, reading or copying.

7. Additional Terms.

“Additional permissions” are terms that supplement the terms of thisLicense by making exceptions from one or more of its conditions.Additional permissions that are applicable to the entire Program shallbe treated as though they were included in this License, to the extentthat they are valid under applicable law. If additional permissionsapply only to part of the Program, that part may be used separatelyunder those permissions, but the entire Program remains governed bythis License without regard to the additional permissions.

When you convey a copy of a covered work, you may at your optionremove any additional permissions from that copy, or from any part ofit. (Additional permissions may be written to require their ownremoval in certain cases when you modify the work.) You may placeadditional permissions on material, added by you to a covered work,for which you have or can give appropriate copyright permission.

Notwithstanding any other provision of this License, for material youadd to a covered work, you may (if authorized by the copyright holders ofthat material) supplement the terms of this License with terms:

  • a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or
  • b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or
  • c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or
  • d) Limiting the use for publicity purposes of names of licensors or authors of the material; or
  • e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or
  • f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors.

All other non-permissive additional terms are considered “furtherrestrictions” within the meaning of section 10. If the Program as youreceived it, or any part of it, contains a notice stating that it isgoverned by this License along with a term that is a furtherrestriction, you may remove that term. If a license document containsa further restriction but permits relicensing or conveying under thisLicense, you may add to a covered work material governed by the termsof that license document, provided that the further restriction doesnot survive such relicensing or conveying.

If you add terms to a covered work in accord with this section, youmust place, in the relevant source files, a statement of theadditional terms that apply to those files, or a notice indicatingwhere to find the applicable terms.

Additional terms, permissive or non-permissive, may be stated in theform of a separately written license, or stated as exceptions;the above requirements apply either way.

8. Termination.

You may not propagate or modify a covered work except as expresslyprovided under this License. Any attempt otherwise to propagate ormodify it is void, and will automatically terminate your rights underthis License (including any patent licenses granted under the thirdparagraph of section 11).

However, if you cease all violation of this License, then yourlicense from a particular copyright holder is reinstated (a)provisionally, unless and until the copyright holder explicitly andfinally terminates your license, and (b) permanently, if the copyrightholder fails to notify you of the violation by some reasonable meansprior to 60 days after the cessation.

Moreover, your license from a particular copyright holder isreinstated permanently if the copyright holder notifies you of theviolation by some reasonable means, this is the first time you havereceived notice of violation of this License (for any work) from thatcopyright holder, and you cure the violation prior to 30 days afteryour receipt of the notice.

Termination of your rights under this section does not terminate thelicenses of parties who have received copies or rights from you underthis License. If your rights have been terminated and not permanentlyreinstated, you do not qualify to receive new licenses for the samematerial under section 10.

9. Acceptance Not Required for Having Copies.

You are not required to accept this License in order to receive orrun a copy of the Program. Ancillary propagation of a covered workoccurring solely as a consequence of using peer-to-peer transmissionto receive a copy likewise does not require acceptance. However,nothing other than this License grants you permission to propagate ormodify any covered work. These actions infringe copyright if you donot accept this License. Therefore, by modifying or propagating acovered work, you indicate your acceptance of this License to do so.

10. Automatic Licensing of Downstream Recipients.

Each time you convey a covered work, the recipient automaticallyreceives a license from the original licensors, to run, modify andpropagate that work, subject to this License. You are not responsiblefor enforcing compliance by third parties with this License.

An “entity transaction” is a transaction transferring control of anorganization, or substantially all assets of one, or subdividing anorganization, or merging organizations. If propagation of a coveredwork results from an entity transaction, each party to thattransaction who receives a copy of the work also receives whateverlicenses to the work the party's predecessor in interest had or couldgive under the previous paragraph, plus a right to possession of theCorresponding Source of the work from the predecessor in interest, ifthe predecessor has it or can get it with reasonable efforts.

You may not impose any further restrictions on the exercise of therights granted or affirmed under this License. For example, you maynot impose a license fee, royalty, or other charge for exercise ofrights granted under this License, and you may not initiate litigation(including a cross-claim or counterclaim in a lawsuit) alleging thatany patent claim is infringed by making, using, selling, offering forsale, or importing the Program or any portion of it.

11. Patents.

A “contributor” is a copyright holder who authorizes use under thisLicense of the Program or a work on which the Program is based. Thework thus licensed is called the contributor's “contributor version”.

A contributor's “essential patent claims” are all patent claimsowned or controlled by the contributor, whether already acquired orhereafter acquired, that would be infringed by some manner, permittedby this License, of making, using, or selling its contributor version,but do not include claims that would be infringed only as aconsequence of further modification of the contributor version. Forpurposes of this definition, “control” includes the right to grantpatent sublicenses in a manner consistent with the requirements ofthis License.

Create R Markdown File

Each contributor grants you a non-exclusive, worldwide, royalty-freepatent license under the contributor's essential patent claims, tomake, use, sell, offer for sale, import and otherwise run, modify andpropagate the contents of its contributor version.

In the following three paragraphs, a “patent license” is any expressagreement or commitment, however denominated, not to enforce a patent(such as an express permission to practice a patent or covenant not tosue for patent infringement). To “grant” such a patent license to aparty means to make such an agreement or commitment not to enforce apatent against the party.

If you convey a covered work, knowingly relying on a patent license,and the Corresponding Source of the work is not available for anyoneto copy, free of charge and under the terms of this License, through apublicly available network server or other readily accessible means,then you must either (1) cause the Corresponding Source to be soavailable, or (2) arrange to deprive yourself of the benefit of thepatent license for this particular work, or (3) arrange, in a mannerconsistent with the requirements of this License, to extend the patentlicense to downstream recipients. “Knowingly relying” means you haveactual knowledge that, but for the patent license, your conveying thecovered work in a country, or your recipient's use of the covered workin a country, would infringe one or more identifiable patents in thatcountry that you have reason to believe are valid.

If, pursuant to or in connection with a single transaction orarrangement, you convey, or propagate by procuring conveyance of, acovered work, and grant a patent license to some of the partiesreceiving the covered work authorizing them to use, propagate, modifyor convey a specific copy of the covered work, then the patent licenseyou grant is automatically extended to all recipients of the coveredwork and works based on it.

A patent license is “discriminatory” if it does not include withinthe scope of its coverage, prohibits the exercise of, or isconditioned on the non-exercise of one or more of the rights that arespecifically granted under this License. You may not convey a coveredwork if you are a party to an arrangement with a third party that isin the business of distributing software, under which you make paymentto the third party based on the extent of your activity of conveyingthe work, and under which the third party grants, to any of theparties who would receive the covered work from you, a discriminatorypatent license (a) in connection with copies of the covered workconveyed by you (or copies made from those copies), or (b) primarilyfor and in connection with specific products or compilations thatcontain the covered work, unless you entered into that arrangement,or that patent license was granted, prior to 28 March 2007.

Nothing in this License shall be construed as excluding or limitingany implied license or other defenses to infringement that mayotherwise be available to you under applicable patent law.

12. No Surrender of Others' Freedom.

If conditions are imposed on you (whether by court order, agreement orotherwise) that contradict the conditions of this License, they do notexcuse you from the conditions of this License. If you cannot convey acovered work so as to satisfy simultaneously your obligations under thisLicense and any other pertinent obligations, then as a consequence you maynot convey it at all. For example, if you agree to terms that obligate youto collect a royalty for further conveying from those to whom you conveythe Program, the only way you could satisfy both those terms and thisLicense would be to refrain entirely from conveying the Program.

13. Use with the GNU Affero General Public License.

Notwithstanding any other provision of this License, you havepermission to link or combine any covered work with a work licensedunder version 3 of the GNU Affero General Public License into a singlecombined work, and to convey the resulting work. The terms of thisLicense will continue to apply to the part which is the covered work,but the special requirements of the GNU Affero General Public License,section 13, concerning interaction through a network will apply to thecombination as such.

14. Revised Versions of this License.

The Free Software Foundation may publish revised and/or new versions ofthe GNU General Public License from time to time. Such new versions willbe similar in spirit to the present version, but may differ in detail toaddress new problems or concerns.

Each version is given a distinguishing version number. If theProgram specifies that a certain numbered version of the GNU GeneralPublic License “or any later version” applies to it, you have theoption of following the terms and conditions either of that numberedversion or of any later version published by the Free SoftwareFoundation. If the Program does not specify a version number of theGNU General Public License, you may choose any version ever publishedby the Free Software Foundation.

If the Program specifies that a proxy can decide which futureversions of the GNU General Public License can be used, that proxy'spublic statement of acceptance of a version permanently authorizes youto choose that version for the Program.

Later license versions may give you additional or differentpermissions. However, no additional obligations are imposed on anyauthor or copyright holder as a result of your choosing to follow alater version.

15. Disclaimer of Warranty.

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BYAPPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHTHOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTYOF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULARPURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAMIS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OFALL NECESSARY SERVICING, REPAIR OR CORRECTION.

16. Limitation of Liability.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITINGWILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYSTHE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANYGENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THEUSE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OFDATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRDPARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OFSUCH DAMAGES.

17. Interpretation of Sections 15 and 16.

If the disclaimer of warranty and limitation of liability providedabove cannot be given local legal effect according to their terms,reviewing courts shall apply local law that most closely approximatesan absolute waiver of all civil liability in connection with theProgram, unless a warranty or assumption of liability accompanies acopy of the Program in return for a fee.

END OF TERMS AND CONDITIONS

How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatestpossible use to the public, the best way to achieve this is to make itfree software which everyone can redistribute and change under these terms.

To do so, attach the following notices to the program. It is safestto attach them to the start of each source file to most effectivelystate the exclusion of warranty; and each file should have at leastthe “copyright” line and a pointer to where the full notice is found.

Also add information on how to contact you by electronic and paper mail.

If the program does terminal interaction, make it output a shortnotice like this when it starts in an interactive mode:

The hypothetical commands `show w' and `show c' should show the appropriateparts of the General Public License. Of course, your program's commandsmight be different; for a GUI interface, you would use an “about box”.

You should also get your employer (if you work as a programmer) or school,if any, to sign a “copyright disclaimer” for the program, if necessary.For more information on this, and how to apply and follow the GNU GPL, see<https://www.gnu.org/licenses/>.

The GNU General Public License does not permit incorporating your programinto proprietary programs. If your program is a subroutine library, youmay consider it more useful to permit linking proprietary applications withthe library. If this is what you want to do, use the GNU Lesser GeneralPublic License instead of this License. But first, please read<https://www.gnu.org/licenses/why-not-lgpl.html>.

  1. Understand what RMarkdown is and why you should use it
  2. Learn how to construct an RMarkdown file
  3. Export an RMarkdown file into many file formats

R Markdown allows you to create documents that serve as a neat record of your analysis. In the world of reproducible research, we want other researchers to easily understand what we did in our analysis, otherwise nobody can be certain that you analysed your data properly. You might choose to create an RMarkdown document as an appendix to a paper or project assignment that you are doing, upload it to an online repository such as Github, or simply to keep as a personal record so you can quickly look back at your code and see what you did. RMarkdown presents your code alongside its output (graphs, tables, etc.) with conventional text to explain it, a bit like a notebook.

RMarkdown makes use of Markdown syntax. Markdown is a very simple ‘markup’ language which provides methods for creating documents with headers, images, links etc. from plain text files, while keeping the original plain text file easy to read. You can convert Markdown documents to many other file types like .html or .pdf to display the headers, images etc.

When you create an RMarkdown file (.Rmd), you use conventional Markdown syntax alongside chunks of code written in R (or other programming languages!). When you knit the RMarkdown file, the Markdown formatting and the R code are evaluated, and an output file (HTML, PDF, etc) is produced.

To see what RMarkdown is capable of, have a look at this undergraduate dissertation, which gives a concise log of their statistical analysis, or the completed demo RMarkdown file for this tutorial.

Markdown

All the resources for this tutorial, including some helpful cheatsheets can be downloaded from this repository. Download by clicking on Code -> Download ZIP, then unzipping the archive in a folder you will use for this tutorial.

Read through this tutorial and use the information you learn along the way to convert the tutorial R script (RMarkdown_Tutorial.R), which you can find in the repo, into a well commented, logically structured R Markdown (.Rmd) document. Afterwards, there are some challenge scripts that you can convert to .Rmd documents. If you want, you could also try converting one of your own R scripts.

Haven’t used R or RStudio before? No worries! Check out our Intro to R and RStudio tutorial, then come back here to master RMarkdown!

To get RMarkdown working in RStudio, the first thing you need is the rmarkdown package, which you can get from CRAN by running the following commands in R or RStudio:

To create a new RMarkdown file (.Rmd), select File -> New File -> R Markdown.._ in RStudio, then choose the file type you want to create. For now we will focus on a .htmlDocument, which can be easily converted to other file types later.

The newly created .Rmd file comes with basic instructions, but we want to create our own RMarkdown script, so go ahead and delete everything in the example file.

Now save the .Rmd file to the repository you downloaded earlier from Github.

Now open the RMarkdown_Tutorial.R practice script from the repository you downloaded earlier in another tab in RStudio and use the instructions below to help you convert this script into a coherent RMarkdown document, bit by bit.

If you have any of your own R scripts that you would like to make into an R Markdown document, you can also use those!

At the top of any RMarkdown script is a YAML header section enclosed by ---. By default this includes a title, author, date and the file type you want to output to. Many other options are available for different functions and formatting, see here for .html options and here for .pdf options. Rules in the header section will alter the whole document. Have a flick through quickly to familiarise yourself with the sorts of things you can alter by adding an option to the YAML header.

Insert something like this at the top of your new .Rmd script:

By default, the title, author, date and output format are printed at the top of your .html document. This is the minimum you should put in your header section.

Now that we have our first piece of content, we can test the .Rmd file by compiling it to .html. To compile your .Rmd file into a .html document, you should press the Knit button in the taskbar:

By default, RStudio opens a separate preview window to display the output of your .Rmd file. If you want the output to be displayed in the Viewer window in RStudio (the same window where you would see plotted figures / packages / file paths), select “View in Pane” from the drop down menu that appears when you click on the Knit button in the taskbar, or in the Settings gear icon drop down menu next to the Knit button.

A preview appears, and a .html file is also saved to the same folder where you saved your .Rmd file.

You can use regular markdown rules in your R Markdown document. Once you knit your document, the output will display text formatted according to the following simple rules.

Formatting Text

Here are a few common formatting commands:

*Italic*

Italic

**Bold**

Bold

This is `code` in text

This is code in text

# Header 1

## Header 2

Header 2

Note that when a # symbol is placed inside a code chunk it acts as a normal R comment, but when placed in text it controls the header size.

* Unordered list item

  • Unordered list item
  • 1. Ordered list item

    1. Ordered list item

    [Link](https://www.google.com)

    $A = pi times r^{2}$

    The $ symbols tells R markdown to use LaTeX equation syntax.

    To practice this, try writing some formatted text in your .Rmd document and producing a .html page using the “Knit” button.

    Below the YAML header is the space where you will write your code, accompanying explanation and any outputs. Code that is included in your .Rmd document should be enclosed by three backwards apostrophes ``` (grave accents!). These are known as code chunks and look like this:

    You can quickly insert a code chunk in RStudio using a button in the toolbar:

    Inside the curly brackets is a space where you can assign rules for that code chunk. The code chunk above says that the code is R code. We’ll get onto some other curly brace rules later.

    Have a go at grabbing some code from the example R script and inserting it into a code chunk in your .Rmd document.

    You can run an individual chunk of code at any time by clicking on the small green arrow:

    The output of the code will appear just beneath the code chunk.

    More on Code Chunks

    It’s important to remember when you are creating an RMarkdown file that if you want to run code that refers to an object, for example:

    you must include instructions showing what dataframe is, just like in a normal R script. For example:

    Or if you are loading a dataframe from a .csv file, you must include the code in the .Rmd:

    Similarly, if you are using any packages in your analysis, you will have to load them in the .Rmd file using library() as in a normal R script.

    Hiding code chunks

    If you don’t want the code of a particular code chunk to appear in the final document, but still want to show the output (e.g. a plot), then you can include echo = FALSE in the code chunk instructions.

    Similarly, you might want to create an object, but not include both the code and the output in the final .html file. To do this you can use, include = FALSE. Be aware though, when making reproducible research it’s often not a good idea to completely hide some part of your analysis:

    In some cases, when you load packages into RStudio, various warning messages such as “Warning: package ‘dplyr’ was built under R version 3.4.4” might appear. If you do not want these warning messages to appear, you can use warning = FALSE.

    REMEMBER: R Markdown doesn’t pay attention to anything you have loaded in other R scripts, you MUST load all objects and packages in the R Markdown script.

    More Code Chunk Instructions

    RuleExample
    (default)
    Function
    evaleval=TRUEIs the code run and the results included in the output?
    includeinclude=TRUEAre the code and the results included in the output?
    echoecho=TRUEIs the code displayed alongside the results?
    warningwarning=TRUEAre warning messages displayed?
    errorerror=FALSEAre error messages displayed?
    messagemessage=TRUEAre messages displayed?
    tidytidy=FALSEIs the code reformatted to make it look “tidy”?
    resultsresults='markup' How are results treated?
    'hide' = no results
    'asis' = results without formatting
    'hold' = results only compiled at end of chunk (use if many commands act on one object)
    cachecache=FALSEAre the results cached for future renders?
    commentcomment='##'What character are comments prefaced with?
    fig.width, fig.heightfig.width=7What width/height (in inches) are the plots?
    fig.alignfig.align='left''left' 'right' 'center'

    Inserting Figures

    Inserting a graph into RMarkdown is easy, the more energy-demanding aspect might be adjusting the formatting.

    By default, RMarkdown will place graphs by maximising their height, while keeping them within the margins of the page and maintaining aspect ratio. If you have a particularly tall figure, this can mean a really huge graph. In the following example we modify the dimensions of the figure we created above. To manually set the figure dimensions, you can insert an instruction into the curly braces:

    Inserting Tables

    Standard R Markdown

    While R Markdown can print the contents of a data frame easily by enclosing the name of the data frame in a code chunk:

    this can look a bit messy, especially with data frames with a lot of columns. Including a formal table requires more effort.

    kable() function from knitr package

    The most aesthetically pleasing and simple table formatting function I have found is kable() in the knitr package. The first argument tells kable to make a table out of the object dataframe and that numbers should have two significant figures. Remember to load the knitr package in your .Rmd file as well.

    pander function from pander package

    If you want a bit more control over the content of your table you can use pander() in the pander package. Imagine I want the 3rd column to appear in italics:

    Find more info on pander here.

    Manually creating tables using markdown syntax

    You can also manually create small tables using markdown syntax. This should be put outside of any code chunks.

    For example:

    will create something that looks like this:

    PlantTemp.Growth
    A200.65
    B200.95
    C200.15

    The :-----: tells markdown that the line above should be treated as a header and the lines below should be treated as the body of the table. Text alignment of the columns is set by the position of ::

    SyntaxAlignment
    `:----:`Centre
    `:-----`Left
    `-----:`Right
    `------`Auto

    Creating tables from model outputs

    Using tidy() from the package broom, we are able to create tables of our model outputs, and insert these tables into our markdown file. The example below shows a simple example linear model, where the summary output table can be saved as a new R object and then added into the markdown file.

    By using warning=FALSE as an argument, any warnings produced will be outputted in the console when knitting but will not appear in the produced document.

    Creating .pdf documents for printing in A4 requires a bit more fiddling around. RStudio uses another document compiling system called LaTeX to make .pdf documents.

    The easiest way to use LaTeX is to install the TinyTex distribution from within RStudio. First, restart your R session (Session -> Restart R), then run these line in the console:

    Becoming familiar with LaTeX will give you a lot more options to make your R Markdown .pdf look pretty, as LaTeX commands are mostly compatible with R Markdown, though some googling is often required.

    To compile a .pdf instead of a .html document, change output: from html_document to pdf_document, or use the dropdown menu from the “Knit” button:

    Common problems when compiling a .pdf

    • Text is running off the page

    Add a global_options argument at the start of your .Rmd file:

    This code chunk won’t be displayed in the final document due to the include = FALSE call and should be placed immediately after the YAML header to affect everything below that.

    tidy.opts = list(width.cutoff = 60) defines the margin cutoff point and wraps text to the next line. Play with the value to get it right.

    • I lose my syntax highlighting

    Use the xelatex engine to compile your .pdf:

    By default, R markdown uses the base LaTeX engine to compile pdfs, but this may limit certain options when it comes to formatting. There are lots of other engines to play around with as well.

    • My page margins are too big/small

    Add a geometry argument to the YAML header

    geometry is a LaTeX command.

    • My plot/table/code is split over two pages

    R Markdown File Choose

    Add a page break before the dodgy element:

    • I want to change the font

    Add a font argument to your header section

    mainfont is a LaTeX command.

    Have a go yourself

    At this point, if you haven’t been following through already, have a go at converting the tutorial R script (RMarkdown_Tutorial.R) into a .Rmd document using the information above as a guide.

    Remember that a good R markdown document should provide a reproducible log of your code, properly commented, with subtitles, comments and code relevant output so the reader knows what is going on.

    RMarkdown outputs to a non-interactive file format like .html or .pdf. When presenting your code, this means you have to make a choice, do you want interactive but messy looking code (.Rmd) or non-interactive but neat looking code (.html, .pdf)? R notebooks provide a file format that combines the interactivity of a .Rmd file with the attractiveness of .html output.

    R notebooks output to the imaginatively named .nb.html format. .nb.html files can be loaded into a web browser to see the output, or loaded into a code editor like RStudio to see the code. You are able to interactively select which code chunks to hide or show code chunks.

    Notebooks use the same syntax as .Rmd files so it is easy to copy and paste the script from a .Rmd into a Notebook. To create a new R Notebook file, select File -> New File -> R Notebook. Create a notebook from your newly created .Rmd file by copying and pasting the script. If you choose to copy and paste the script, make sure that under your YAML header, output: html_notebook instead of output: html_document.

    Alternatively, to turn any existing .Rmd file into an R notebook, add html_notebook: default under the output: argument in the YAML header. If you have more than one output document type, the “Knit” button will only produce the first type. You can use the dropdown menu form the Knit button to produce one of the other types.

    To output to .nb.html, first make sure all your code chunks have been run:

    then click Preview:

    Notice that with R Notebooks you can still output to .html or .pdf, the same as a .Rmd file.

    R notebooks have only been around for about a couple of years so they’re not perfect yet, but may replace R markdown in the future for many applications.

    Difference between RMarkdown and RNotebooks

    R Markdown documents are ‘knitted’, while R Notebooks are ‘previewed’.

    Although the notebook preview looks similar to the knitted markdown document, the notebook preview does not execute any code chunks, but only shows you a rendered copy of the Markdown output of your document along with the most recent chunk output. The preview is also generated automatically whenever the notebook is saved. This would be especially useful if we have the preview showing in the Viewer window next to the console. This means that in R Notebooks, we are able to visually assess the output as we develop the document without having to knit the whole document again.

    For example, with the following code chunk example (from the RMarkdown_Tutorial.R practice script), we are creating a table of species richness for each taxonomic group.

    R Markdown File Example

    To bring up the table output, we can add richness, pander(richness), kable(richness) to the end of that code chunk. If we had initially forgotten to add in either one of those functions, the table would not have been produced in both the knitted markdown document and the notebook preview. Imagine that we are now editing the R Markdown document / R Notebook document to include this function to bring up the table in the outputted document.

    For RMarkdown: we would type in pander(richness), run that specific code chunk, and then have to click the Knit button in the taskbar to knit the whole document again.

    For R Notebooks, we type in pander(richness), run that specific code chunk, and save the document, and the preview in the Viewer window would be updated on its own - there is no need to click the Preview button in the taskbar and run the code for the whole document.

    Note: R Markdown Notebooks are only available in RStudio 1.0 or higher.

    Bonus task!

    Either in a small group or on your own, convert one of the three demo R scripts into a well commented and easy to follow R Markdown document, or R Markdown Notebook. The files (RMarkdown_Demo_1.R, RMarkdown_Demo_2.R, RMarkdown_Demo_3.R) can be found in the repo you downloaded earlier.

    1. You are familiar with the Markdown syntax and code chunk rules.
    2. You can include figures and tables in your Markdown reports.
    3. You can create RMarkdown files and export them to pdf or html files.


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    How To Create An R Markdown File

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