diff --git a/.Rbuildignore b/.Rbuildignore index 91114bf..578242c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,9 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +.github +aws +docs +scripts +app.R +LICENSE +^LICENSE\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index 6b4bb68..50db4a6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,31 +1,37 @@ Package: straf -Title: STR Analysis For Forensics -Version: 1.5.0 +Title: STR Analysis for Forensics +Version: 2.0.0 Authors@R: person(given = "Alexandre", family = "Gouy", role = c("aut", "cre"), - email = "alexandre.gouy@protonmail.com") -Description: straf is a Shiny application to perform STR / microsatellite data analysis. -License: `use_gpl3_license()` + email = "alexandre.gouy@protonmail.com", + comment = c(ORCID = "0000-0002-2478-8475")) +Description: A 'shiny' application to perform Short Tandem Repeats (STRs, also + known as microsatellites) data analysis. The application allows one to + compute forensic parameters, population genetics indices, and investigate + population structure through various methods and generate relevant data + visualisations. It also implements file conversion to other popular formats. +Depends: R (>= 3.5.0) +License: GPL-3 Encoding: UTF-8 -LazyData: true +BugReports: https://github.com/agouy/straf/issues Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.1.9000 Imports: shiny (>= 1.5.0), + shinyWidgets, colourpicker, DT, plotly, - shinyWidgets, - ade4, - adegenet, - pegas, - hierfstat, - car, openxlsx, reshape2, dplyr, tidyr, ggplot2, - ggrepel + ggrepel, + car, + ade4, + adegenet, + pegas, + hierfstat diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 31da8df..0000000 --- a/LICENSE +++ /dev/null @@ -1,623 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - 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 for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. By contrast, -the GNU General Public License is intended to guarantee your freedom to -share and change all versions of a program--to make sure it remains free -software for all its users. We, the Free Software Foundation, use the -GNU General Public License for most of our software; it applies also to -any other work released this way by its authors. You can apply it to -your programs, too. - - When we speak of free software, we are referring to freedom, not -price. Our General Public Licenses are designed to make sure that you -have the freedom to distribute copies of free software (and charge for -them if you wish), that you receive source code or can get it if you -want it, that you can change the software or use pieces of it in new -free programs, and that you know you can do these things. - - To protect your rights, we need to prevent others from denying you -these rights or asking you to surrender the rights. Therefore, you have -certain responsibilities if you distribute copies of the software, or if -you modify it: responsibilities to respect the freedom of others. - - For example, if you distribute copies of such a program, whether -gratis or for a fee, you must pass on to the recipients the same -freedoms that you received. You must make sure that they, too, receive -or can get the source code. And you must show them these terms so they -know 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 License -giving you legal permission to copy, distribute and/or modify it. - - For the developers' and authors' protection, the GPL clearly explains -that there is no warranty for this free software. For both users' and -authors' sake, the GPL requires that modified versions be marked as -changed, so that their problems will not be attributed erroneously to -authors of previous versions. - - Some devices are designed to deny users access to install or run -modified versions of the software inside them, although the manufacturer -can do so. This is fundamentally incompatible with the aim of -protecting users' freedom to change the software. The systematic -pattern of such abuse occurs in the area of products for individuals to -use, which is precisely where it is most unacceptable. Therefore, we -have designed this version of the GPL to prohibit the practice for those -products. If such problems arise substantially in other domains, we -stand ready to extend this provision to those domains in future versions -of 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 of -software on general-purpose computers, but in those that do, we wish to -avoid the special danger that patents applied to a free program could -make it effectively proprietary. To prevent this, the GPL assures that -patents cannot be used to render the program non-free. - - The precise terms and conditions for copying, distribution and -modification 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 of -works, such as semiconductor masks. - - "The Program" refers to any copyrightable work licensed under this -License. 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 work -in a fashion requiring copyright permission, other than the making of an -exact copy. The resulting work is called a "modified version" of the -earlier work or a work "based on" the earlier work. - - A "covered work" means either the unmodified Program or a work based -on the Program. - - To "propagate" a work means to do anything with it that, without -permission, would make you directly or secondarily liable for -infringement under applicable copyright law, except executing it on a -computer or modifying a private copy. Propagation includes copying, -distribution (with or without modification), making available to the -public, and in some countries other activities as well. - - To "convey" a work means any kind of propagation that enables other -parties to make or receive copies. Mere interaction with a user through -a 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 visible -feature that (1) displays an appropriate copyright notice, and (2) -tells the user that there is no warranty for the work (except to the -extent that warranties are provided), that licensees may convey the -work under this License, and how to view a copy of this License. If -the interface presents a list of user commands or options, such as a -menu, a prominent item in the list meets this criterion. - - 1. Source Code. - - The "source code" for a work means the preferred form of the work -for making modifications to it. "Object code" means any non-source -form of a work. - - A "Standard Interface" means an interface that either is an official -standard defined by a recognized standards body, or, in the case of -interfaces specified for a particular programming language, one that -is widely used among developers working in that language. - - The "System Libraries" of an executable work include anything, other -than the work as a whole, that (a) is included in the normal form of -packaging a Major Component, but which is not part of that Major -Component, and (b) serves only to enable use of the work with that -Major Component, or to implement a Standard Interface for which an -implementation 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 to -produce the work, or an object code interpreter used to run it. - - The "Corresponding Source" for a work in object code form means all -the source code needed to generate, install, and (for an executable -work) run the object code and to modify the work, including scripts to -control those activities. However, it does not include the work's -System Libraries, or general-purpose tools or generally available free -programs which are used unmodified in performing those activities but -which are not part of the work. For example, Corresponding Source -includes interface definition files associated with source files for -the work, and the source code for shared libraries and dynamically -linked subprograms that the work is specifically designed to require, -such as by intimate data communication or control flow between those -subprograms and other parts of the work. - - The Corresponding Source need not include anything that users -can regenerate automatically from other parts of the Corresponding -Source. - - The Corresponding Source for a work in source code form is that -same work. - - 2. Basic Permissions. - - All rights granted under this License are granted for the term of -copyright on the Program, and are irrevocable provided the stated -conditions are met. This License explicitly affirms your unlimited -permission to run the unmodified Program. The output from running a -covered work is covered by this License only if the output, given its -content, constitutes a covered work. This License acknowledges your -rights of fair use or other equivalent, as provided by copyright law. - - You may make, run and propagate covered works that you do not -convey, without conditions so long as your license otherwise remains -in force. You may convey covered works to others for the sole purpose -of having them make modifications exclusively for you, or provide you -with facilities for running those works, provided that you comply with -the terms of this License in conveying all material for which you do -not control copyright. Those thus making or running the covered works -for you must do so exclusively on your behalf, under your direction -and control, on terms that prohibit them from making any copies of -your copyrighted material outside their relationship with you. - - Conveying under any other circumstances is permitted solely under -the conditions stated below. Sublicensing is not allowed; section 10 -makes it unnecessary. - - 3. Protecting Users' Legal Rights From Anti-Circumvention Law. - - No covered work shall be deemed part of an effective technological -measure under any applicable law fulfilling obligations under article -11 of the WIPO copyright treaty adopted on 20 December 1996, or -similar laws prohibiting or restricting circumvention of such -measures. - - When you convey a covered work, you waive any legal power to forbid -circumvention of technological measures to the extent such circumvention -is effected by exercising rights under this License with respect to -the covered work, and you disclaim any intention to limit operation or -modification of the work as a means of enforcing, against the work's -users, your or third parties' legal rights to forbid circumvention of -technological measures. - - 4. Conveying Verbatim Copies. - - You may convey verbatim copies of the Program's source code as you -receive it, in any medium, provided that you conspicuously and -appropriately publish on each copy an appropriate copyright notice; -keep intact all notices stating that this License and any -non-permissive terms added in accord with section 7 apply to the code; -keep intact all notices of the absence of any warranty; and give all -recipients 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 to -produce it from the Program, in the form of source code under the -terms 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 independent -works, 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 not -used to limit the access or legal rights of the compilation's users -beyond what the individual works permit. Inclusion of a covered work -in an aggregate does not cause this License to apply to the other -parts of the aggregate. - - 6. Conveying Non-Source Forms. - - You may convey a covered work in object code form under the terms -of sections 4 and 5, provided that you also convey the -machine-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 excluded -from the Corresponding Source as a System Library, need not be -included in conveying the object code work. - - A "User Product" is either (1) a "consumer product", which means any -tangible personal property which is normally used for personal, family, -or household purposes, or (2) anything designed or sold for incorporation -into a dwelling. In determining whether a product is a consumer product, -doubtful cases shall be resolved in favor of coverage. For a particular -product received by a particular user, "normally used" refers to a -typical or common use of that class of product, regardless of the status -of the particular user or of the way in which the particular user -actually uses, or expects or is expected to use, the product. A product -is a consumer product regardless of whether the product has substantial -commercial, industrial or non-consumer uses, unless such uses represent -the 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 install -and execute modified versions of a covered work in that User Product from -a modified version of its Corresponding Source. The information must -suffice to ensure that the continued functioning of the modified object -code is in no case prevented or interfered with solely because -modification has been made. - - If you convey an object code work under this section in, or with, or -specifically for use in, a User Product, and the conveying occurs as -part of a transaction in which the right of possession and use of the -User Product is transferred to the recipient in perpetuity or for a -fixed term (regardless of how the transaction is characterized), the -Corresponding Source conveyed under this section must be accompanied -by the Installation Information. But this requirement does not apply -if neither you nor any third party retains the ability to install -modified object code on the User Product (for example, the work has -been installed in ROM). - - The requirement to provide Installation Information does not include a -requirement to continue to provide support service, warranty, or updates -for a work that has been modified or installed by the recipient, or for -the User Product in which it has been modified or installed. Access to a -network may be denied when the modification itself materially and -adversely affects the operation of the network or violates the rules and -protocols for communication across the network. - - Corresponding Source conveyed, and Installation Information provided, -in accord with this section must be in a format that is publicly -documented (and with an implementation available to the public in -source code form), and must require no special password or key for -unpacking, reading or copying. - - 7. Additional Terms. - - "Additional permissions" are terms that supplement the terms of this -License by making exceptions from one or more of its conditions. -Additional permissions that are applicable to the entire Program shall -be treated as though they were included in this License, to the extent -that they are valid under applicable law. If additional permissions -apply only to part of the Program, that part may be used separately -under those permissions, but the entire Program remains governed by -this License without regard to the additional permissions. - - When you convey a copy of a covered work, you may at your option -remove any additional permissions from that copy, or from any part of -it. (Additional permissions may be written to require their own -removal in certain cases when you modify the work.) You may place -additional 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 you -add to a covered work, you may (if authorized by the copyright holders of -that 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 "further -restrictions" within the meaning of section 10. If the Program as you -received it, or any part of it, contains a notice stating that it is -governed by this License along with a term that is a further -restriction, you may remove that term. If a license document contains -a further restriction but permits relicensing or conveying under this -License, you may add to a covered work material governed by the terms -of that license document, provided that the further restriction does -not survive such relicensing or conveying. - - If you add terms to a covered work in accord with this section, you -must place, in the relevant source files, a statement of the -additional terms that apply to those files, or a notice indicating -where to find the applicable terms. - - Additional terms, permissive or non-permissive, may be stated in the -form 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 expressly -provided under this License. Any attempt otherwise to propagate or -modify it is void, and will automatically terminate your rights under -this License (including any patent licenses granted under the third -paragraph of section 11). - - However, if you cease all violation of this License, then your -license from a particular copyright holder is reinstated (a) -provisionally, unless and until the copyright holder explicitly and -finally terminates your license, and (b) permanently, if the copyright -holder fails to notify you of the violation by some reasonable means -prior to 60 days after the cessation. - - Moreover, your license from a particular copyright holder is -reinstated permanently if the copyright holder notifies you of the -violation by some reasonable means, this is the first time you have -received notice of violation of this License (for any work) from that -copyright holder, and you cure the violation prior to 30 days after -your receipt of the notice. - - Termination of your rights under this section does not terminate the -licenses of parties who have received copies or rights from you under -this License. If your rights have been terminated and not permanently -reinstated, you do not qualify to receive new licenses for the same -material under section 10. - - 9. Acceptance Not Required for Having Copies. - - You are not required to accept this License in order to receive or -run a copy of the Program. Ancillary propagation of a covered work -occurring solely as a consequence of using peer-to-peer transmission -to receive a copy likewise does not require acceptance. However, -nothing other than this License grants you permission to propagate or -modify any covered work. These actions infringe copyright if you do -not accept this License. Therefore, by modifying or propagating a -covered 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 automatically -receives a license from the original licensors, to run, modify and -propagate that work, subject to this License. You are not responsible -for enforcing compliance by third parties with this License. - - An "entity transaction" is a transaction transferring control of an -organization, or substantially all assets of one, or subdividing an -organization, or merging organizations. If propagation of a covered -work results from an entity transaction, each party to that -transaction who receives a copy of the work also receives whatever -licenses to the work the party's predecessor in interest had or could -give under the previous paragraph, plus a right to possession of the -Corresponding Source of the work from the predecessor in interest, if -the predecessor has it or can get it with reasonable efforts. - - You may not impose any further restrictions on the exercise of the -rights granted or affirmed under this License. For example, you may -not impose a license fee, royalty, or other charge for exercise of -rights granted under this License, and you may not initiate litigation -(including a cross-claim or counterclaim in a lawsuit) alleging that -any patent claim is infringed by making, using, selling, offering for -sale, or importing the Program or any portion of it. - - 11. Patents. - - A "contributor" is a copyright holder who authorizes use under this -License of the Program or a work on which the Program is based. The -work thus licensed is called the contributor's "contributor version". - - A contributor's "essential patent claims" are all patent claims -owned or controlled by the contributor, whether already acquired or -hereafter acquired, that would be infringed by some manner, permitted -by this License, of making, using, or selling its contributor version, -but do not include claims that would be infringed only as a -consequence of further modification of the contributor version. For -purposes of this definition, "control" includes the right to grant -patent sublicenses in a manner consistent with the requirements of -this License. - - Each contributor grants you a non-exclusive, worldwide, royalty-free -patent license under the contributor's essential patent claims, to -make, use, sell, offer for sale, import and otherwise run, modify and -propagate the contents of its contributor version. - - In the following three paragraphs, a "patent license" is any express -agreement or commitment, however denominated, not to enforce a patent -(such as an express permission to practice a patent or covenant not to -sue for patent infringement). To "grant" such a patent license to a -party means to make such an agreement or commitment not to enforce a -patent 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 anyone -to copy, free of charge and under the terms of this License, through a -publicly available network server or other readily accessible means, -then you must either (1) cause the Corresponding Source to be so -available, or (2) arrange to deprive yourself of the benefit of the -patent license for this particular work, or (3) arrange, in a manner -consistent with the requirements of this License, to extend the patent -license to downstream recipients. "Knowingly relying" means you have -actual knowledge that, but for the patent license, your conveying the -covered work in a country, or your recipient's use of the covered work -in a country, would infringe one or more identifiable patents in that -country that you have reason to believe are valid. - - If, pursuant to or in connection with a single transaction or -arrangement, you convey, or propagate by procuring conveyance of, a -covered work, and grant a patent license to some of the parties -receiving the covered work authorizing them to use, propagate, modify -or convey a specific copy of the covered work, then the patent license -you grant is automatically extended to all recipients of the covered -work and works based on it. - - A patent license is "discriminatory" if it does not include within -the scope of its coverage, prohibits the exercise of, or is -conditioned on the non-exercise of one or more of the rights that are -specifically granted under this License. You may not convey a covered -work if you are a party to an arrangement with a third party that is -in the business of distributing software, under which you make payment -to the third party based on the extent of your activity of conveying -the work, and under which the third party grants, to any of the -parties who would receive the covered work from you, a discriminatory -patent license (a) in connection with copies of the covered work -conveyed by you (or copies made from those copies), or (b) primarily -for and in connection with specific products or compilations that -contain 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 limiting -any implied license or other defenses to infringement that may -otherwise 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 or -otherwise) that contradict the conditions of this License, they do not -excuse you from the conditions of this License. If you cannot convey a -covered work so as to satisfy simultaneously your obligations under this -License and any other pertinent obligations, then as a consequence you may -not convey it at all. For example, if you agree to terms that obligate you -to collect a royalty for further conveying from those to whom you convey -the Program, the only way you could satisfy both those terms and this -License 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 have -permission to link or combine any covered work with a work licensed -under version 3 of the GNU Affero General Public License into a single -combined work, and to convey the resulting work. The terms of this -License 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 the -combination as such. - - 14. Revised Versions of this License. - - The Free Software Foundation may publish revised and/or new versions of -the GNU General Public License from time to time. Such new versions will -be similar in spirit to the present version, but may differ in detail to -address new problems or concerns. - - Each version is given a distinguishing version number. If the -Program specifies that a certain numbered version of the GNU General -Public License "or any later version" applies to it, you have the -option of following the terms and conditions either of that numbered -version or of any later version published by the Free Software -Foundation. If the Program does not specify a version number of the -GNU General Public License, you may choose any version ever published -by the Free Software Foundation. - - If the Program specifies that a proxy can decide which future -versions of the GNU General Public License can be used, that proxy's -public statement of acceptance of a version permanently authorizes you -to choose that version for the Program. - - Later license versions may give you additional or different -permissions. However, no additional obligations are imposed on any -author or copyright holder as a result of your choosing to follow a -later version. - - 15. Disclaimer of Warranty. - - THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY -APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT -HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY -OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, -THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR -PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM -IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF -ALL NECESSARY SERVICING, REPAIR OR CORRECTION. - - 16. Limitation of Liability. - - IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING -WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS -THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY -GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE -USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF -DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD -PARTIES 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 OF -SUCH DAMAGES. - - 17. Interpretation of Sections 15 and 16. - - If the disclaimer of warranty and limitation of liability provided -above cannot be given local legal effect according to their terms, -reviewing courts shall apply local law that most closely approximates -an absolute waiver of all civil liability in connection with the -Program, unless a warranty or assumption of liability accompanies a -copy of the Program in return for a fee. - - END OF TERMS AND CONDITIONS - - diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..995cc06 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,595 @@ +GNU General Public License +========================== + +_Version 3, 29 June 2007_ +_Copyright © 2007 Free Software Foundation, Inc. <>_ + +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 for software and other +kinds of works. + +The licenses for most software and other practical works are designed to take away +your freedom to share and change the works. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change all versions of a +program--to make sure it remains free software for all its users. We, the Free +Software Foundation, use the GNU General Public License for most of our software; it +applies also to any other work released this way by its authors. You can apply it to +your programs, too. + +When we speak of free software, we are referring to freedom, not price. Our General +Public Licenses are designed to make sure that you have the freedom to distribute +copies of free software (and charge for them if you wish), that you receive source +code or can get it if you want it, that you can change the software or use pieces of +it in new free programs, and that you know you can do these things. + +To protect your rights, we need to prevent others from denying you these rights or +asking you to surrender the rights. Therefore, you have certain responsibilities if +you distribute copies of the software, or if you modify it: responsibilities to +respect the freedom of others. + +For example, if you distribute copies of such a program, whether gratis or for a fee, +you must pass on to the recipients the same freedoms that you received. You must make +sure that they, too, receive or can get the source code. And you must show them these +terms so they know 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 License giving you legal permission +to copy, distribute and/or modify it. + +For the developers' and authors' protection, the GPL clearly explains that there is +no warranty for this free software. For both users' and authors' sake, the GPL +requires that modified versions be marked as changed, so that their problems will not +be attributed erroneously to authors of previous versions. + +Some devices are designed to deny users access to install or run modified versions of +the software inside them, although the manufacturer can do so. This is fundamentally +incompatible with the aim of protecting users' freedom to change the software. The +systematic pattern of such abuse occurs in the area of products for individuals to +use, which is precisely where it is most unacceptable. Therefore, we have designed +this version of the GPL to prohibit the practice for those products. If such problems +arise substantially in other domains, we stand ready to extend this provision to +those domains in future versions of 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 of software on general-purpose +computers, but in those that do, we wish to avoid the special danger that patents +applied to a free program could make it effectively proprietary. To prevent this, the +GPL assures that patents cannot be used to render the program non-free. + +The precise terms and conditions for copying, distribution and modification 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 of +works, such as semiconductor masks. + +“The Program” refers to any copyrightable work licensed under this +License. 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 work in +a fashion requiring copyright permission, other than the making of an exact copy. The +resulting work is called a “modified version” of the earlier work or a +work “based on” the earlier work. + +A “covered work” means either the unmodified Program or a work based on +the Program. + +To “propagate” a work means to do anything with it that, without +permission, would make you directly or secondarily liable for infringement under +applicable copyright law, except executing it on a computer or modifying a private +copy. Propagation includes copying, distribution (with or without modification), +making available to the public, and in some countries other activities as well. + +To “convey” a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through a 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 visible feature that **(1)** +displays an appropriate copyright notice, and **(2)** tells the user that there is no +warranty for the work (except to the extent that warranties are provided), that +licensees may convey the work under this License, and how to view a copy of this +License. If the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + +### 1. Source Code + +The “source code” for a work means the preferred form of the work for +making modifications to it. “Object code” means any non-source form of a +work. + +A “Standard Interface” means an interface that either is an official +standard defined by a recognized standards body, or, in the case of interfaces +specified for a particular programming language, one that is widely used among +developers working in that language. + +The “System Libraries” of an executable work include anything, other than +the work as a whole, that **(a)** is included in the normal form of packaging a Major +Component, but which is not part of that Major Component, and **(b)** serves only to +enable use of the work with that Major Component, or to implement a Standard +Interface for which an implementation 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 to produce the work, or an object code +interpreter used to run it. + +The “Corresponding Source” for a work in object code form means all the +source code needed to generate, install, and (for an executable work) run the object +code and to modify the work, including scripts to control those activities. However, +it does not include the work's System Libraries, or general-purpose tools or +generally available free programs which are used unmodified in performing those +activities but which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for the work, and +the source code for shared libraries and dynamically linked subprograms that the work +is specifically designed to require, such as by intimate data communication or +control flow between those subprograms and other parts of the work. + +The Corresponding Source need not include anything that users can regenerate +automatically from other parts of the Corresponding Source. + +The Corresponding Source for a work in source code form is that same work. + +### 2. Basic Permissions + +All rights granted under this License are granted for the term of copyright on the +Program, and are irrevocable provided the stated conditions are met. This License +explicitly affirms your unlimited permission to run the unmodified Program. The +output from running a covered work is covered by this License only if the output, +given its content, constitutes a covered work. This License acknowledges your rights +of fair use or other equivalent, as provided by copyright law. + +You may make, run and propagate covered works that you do not convey, without +conditions so long as your license otherwise remains in force. You may convey covered +works to others for the sole purpose of having them make modifications exclusively +for you, or provide you with facilities for running those works, provided that you +comply with the terms of this License in conveying all material for which you do not +control copyright. Those thus making or running the covered works for you must do so +exclusively on your behalf, under your direction and control, on terms that prohibit +them from making any copies of your copyrighted material outside their relationship +with you. + +Conveying under any other circumstances is permitted solely under the conditions +stated below. Sublicensing is not allowed; section 10 makes it unnecessary. + +### 3. Protecting Users' Legal Rights From Anti-Circumvention Law + +No covered work shall be deemed part of an effective technological measure under any +applicable law fulfilling obligations under article 11 of the WIPO copyright treaty +adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention +of such measures. + +When you convey a covered work, you waive any legal power to forbid circumvention of +technological measures to the extent such circumvention is effected by exercising +rights under this License with respect to the covered work, and you disclaim any +intention to limit operation or modification of the work as a means of enforcing, +against the work's users, your or third parties' legal rights to forbid circumvention +of technological measures. + +### 4. Conveying Verbatim Copies + +You may convey verbatim copies of the Program's source code as you receive it, in any +medium, provided that you conspicuously and appropriately publish on each copy an +appropriate copyright notice; keep intact all notices stating that this License and +any non-permissive terms added in accord with section 7 apply to the code; keep +intact all notices of the absence of any warranty; and give all recipients 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 to produce it from +the Program, in the form of source code under the terms 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 independent works, 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 not used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work in an aggregate +does not cause this License to apply to the other parts of the aggregate. + +### 6. Conveying Non-Source Forms + +You may convey a covered work in object code form under the terms of sections 4 and +5, provided that you also convey the machine-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 excluded from the +Corresponding Source as a System Library, need not be included in conveying the +object code work. + +A “User Product” is either **(1)** a “consumer product”, which +means any tangible personal property which is normally used for personal, family, or +household purposes, or **(2)** anything designed or sold for incorporation into a +dwelling. In determining whether a product is a consumer product, doubtful cases +shall be resolved in favor of coverage. For a particular product received by a +particular user, “normally used” refers to a typical or common use of +that class of product, regardless of the status of the particular user or of the way +in which the particular user actually uses, or expects or is expected to use, the +product. A product is a consumer product regardless of whether the product has +substantial commercial, industrial or non-consumer uses, unless such uses represent +the 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 install and execute +modified versions of a covered work in that User Product from a modified version of +its Corresponding Source. The information must suffice to ensure that the continued +functioning of the modified object code is in no case prevented or interfered with +solely because modification has been made. + +If you convey an object code work under this section in, or with, or specifically for +use in, a User Product, and the conveying occurs as part of a transaction in which +the right of possession and use of the User Product is transferred to the recipient +in perpetuity or for a fixed term (regardless of how the transaction is +characterized), the Corresponding Source conveyed under this section must be +accompanied by the Installation Information. But this requirement does not apply if +neither you nor any third party retains the ability to install modified object code +on the User Product (for example, the work has been installed in ROM). + +The requirement to provide Installation Information does not include a requirement to +continue to provide support service, warranty, or updates for a work that has been +modified or installed by the recipient, or for the User Product in which it has been +modified or installed. Access to a network may be denied when the modification itself +materially and adversely affects the operation of the network or violates the rules +and protocols for communication across the network. + +Corresponding Source conveyed, and Installation Information provided, in accord with +this section must be in a format that is publicly documented (and with an +implementation available to the public in source code form), and must require no +special password or key for unpacking, reading or copying. + +### 7. Additional Terms + +“Additional permissions” are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. Additional +permissions that are applicable to the entire Program shall be treated as though they +were included in this License, to the extent that they are valid under applicable +law. If additional permissions apply only to part of the Program, that part may be +used separately under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option remove any +additional permissions from that copy, or from any part of it. (Additional +permissions may be written to require their own removal in certain cases when you +modify the work.) You may place additional 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 you add to a +covered work, you may (if authorized by the copyright holders of that 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 “further +restrictions” within the meaning of section 10. If the Program as you received +it, or any part of it, contains a notice stating that it is governed by this License +along with a term that is a further restriction, you may remove that term. If a +license document contains a further restriction but permits relicensing or conveying +under this License, you may add to a covered work material governed by the terms of +that license document, provided that the further restriction does not survive such +relicensing or conveying. + +If you add terms to a covered work in accord with this section, you must place, in +the relevant source files, a statement of the additional terms that apply to those +files, or a notice indicating where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the form 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 expressly provided under +this License. Any attempt otherwise to propagate or modify it is void, and will +automatically terminate your rights under this License (including any patent licenses +granted under the third paragraph of section 11). + +However, if you cease all violation of this License, then your license from a +particular copyright holder is reinstated **(a)** provisionally, unless and until the +copyright holder explicitly and finally terminates your license, and **(b)** permanently, +if the copyright holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + +Moreover, your license from a particular copyright holder is reinstated permanently +if the copyright holder notifies you of the violation by some reasonable means, this +is the first time you have received notice of violation of this License (for any +work) from that copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + +Termination of your rights under this section does not terminate the licenses of +parties who have received copies or rights from you under this License. If your +rights have been terminated and not permanently reinstated, you do not qualify to +receive new licenses for the same material under section 10. + +### 9. Acceptance Not Required for Having Copies + +You are not required to accept this License in order to receive or run a copy of the +Program. Ancillary propagation of a covered work occurring solely as a consequence of +using peer-to-peer transmission to receive a copy likewise does not require +acceptance. However, nothing other than this License grants you permission to +propagate or modify any covered work. These actions infringe copyright if you do not +accept this License. Therefore, by modifying or propagating a covered 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 automatically receives a license +from the original licensors, to run, modify and propagate that work, subject to this +License. You are not responsible for enforcing compliance by third parties with this +License. + +An “entity transaction” is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an organization, or +merging organizations. If propagation of a covered work results from an entity +transaction, each party to that transaction who receives a copy of the work also +receives whatever licenses to the work the party's predecessor in interest had or +could give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if the predecessor +has it or can get it with reasonable efforts. + +You may not impose any further restrictions on the exercise of the rights granted or +affirmed under this License. For example, you may not impose a license fee, royalty, +or other charge for exercise of rights granted under this License, and you may not +initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging +that any patent claim is infringed by making, using, selling, offering for sale, or +importing the Program or any portion of it. + +### 11. Patents + +A “contributor” is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The work thus +licensed is called the contributor's “contributor version”. + +A contributor's “essential patent claims” are all patent claims owned or +controlled by the contributor, whether already acquired or hereafter acquired, that +would be infringed by some manner, permitted by this License, of making, using, or +selling its contributor version, but do not include claims that would be infringed +only as a consequence of further modification of the contributor version. For +purposes of this definition, “control” includes the right to grant patent +sublicenses in a manner consistent with the requirements of this License. + +Each contributor grants you a non-exclusive, worldwide, royalty-free patent license +under the contributor's essential patent claims, to make, use, sell, offer for sale, +import and otherwise run, modify and propagate the contents of its contributor +version. + +In the following three paragraphs, a “patent license” is any express +agreement or commitment, however denominated, not to enforce a patent (such as an +express permission to practice a patent or covenant not to sue for patent +infringement). To “grant” such a patent license to a party means to make +such an agreement or commitment not to enforce a patent 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 anyone to copy, free of charge +and under the terms of this License, through a publicly available network server or +other readily accessible means, then you must either **(1)** cause the Corresponding +Source to be so available, or **(2)** arrange to deprive yourself of the benefit of the +patent license for this particular work, or **(3)** arrange, in a manner consistent with +the requirements of this License, to extend the patent license to downstream +recipients. “Knowingly relying” means you have actual knowledge that, but +for the patent license, your conveying the covered work in a country, or your +recipient's use of the covered work in a country, would infringe one or more +identifiable patents in that country that you have reason to believe are valid. + +If, pursuant to or in connection with a single transaction or arrangement, you +convey, or propagate by procuring conveyance of, a covered work, and grant a patent +license to some of the parties receiving the covered work authorizing them to use, +propagate, modify or convey a specific copy of the covered work, then the patent +license you grant is automatically extended to all recipients of the covered work and +works based on it. + +A patent license is “discriminatory” if it does not include within the +scope of its coverage, prohibits the exercise of, or is conditioned on the +non-exercise of one or more of the rights that are specifically granted under this +License. You may not convey a covered work if you are a party to an arrangement with +a third party that is in the business of distributing software, under which you make +payment to the third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties who would receive +the covered work from you, a discriminatory patent license **(a)** in connection with +copies of the covered work conveyed by you (or copies made from those copies), or **(b)** +primarily for and in connection with specific products or compilations that contain +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 limiting any implied +license or other defenses to infringement that may otherwise 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 or otherwise) +that contradict the conditions of this License, they do not excuse you from the +conditions of this License. If you cannot convey a covered work so as to satisfy +simultaneously your obligations under this License and any other pertinent +obligations, then as a consequence you may not convey it at all. For example, if you +agree to terms that obligate you to collect a royalty for further conveying from +those to whom you convey the Program, the only way you could satisfy both those terms +and this License 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 have permission to link or +combine any covered work with a work licensed under version 3 of the GNU Affero +General Public License into a single combined work, and to convey the resulting work. +The terms of this License 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 the combination as such. + +### 14. Revised Versions of this License + +The Free Software Foundation may publish revised and/or new versions of the GNU +General Public License from time to time. Such new versions will be similar in spirit +to the present version, but may differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program specifies that +a certain numbered version of the GNU General Public License “or any later +version” applies to it, you have the option of following the terms and +conditions either of that numbered version or of any later version published by the +Free Software Foundation. If the Program does not specify a version number of the GNU +General Public License, you may choose any version ever published by the Free +Software Foundation. + +If the Program specifies that a proxy can decide which future versions of the GNU +General Public License can be used, that proxy's public statement of acceptance of a +version permanently authorizes you to choose that version for the Program. + +Later license versions may give you additional or different permissions. However, no +additional obligations are imposed on any author or copyright holder as a result of +your choosing to follow a later version. + +### 15. Disclaimer of Warranty + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. +EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER +EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE +QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +### 16. Limitation of Liability + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY +COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS +PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, +INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE +PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE +OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES 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 OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16 + +If the disclaimer of warranty and limitation of liability provided above cannot be +given local legal effect according to their terms, reviewing courts shall apply local +law that most closely approximates an absolute waiver of all civil liability in +connection with the Program, unless a warranty or assumption of liability accompanies +a copy 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 greatest possible use to +the public, the best way to achieve this is to make it free software which everyone +can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest to attach them +to the start of each source file to most effectively state the exclusion of warranty; +and each file should have at least the “copyright” line and a pointer to +where the full notice is found. + + + Copyright (C) 2021 Alexandre Gouy + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short notice like this +when it starts in an interactive mode: + + straf Copyright (C) 2021 Alexandre Gouy + This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type 'show c' for details. + +The hypothetical commands `show w` and `show c` should show the appropriate parts of +the General Public License. Of course, your program's commands might 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 +<>. + +The GNU General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may consider it +more useful to permit linking proprietary applications with the library. If this is +what you want to do, use the GNU Lesser General Public License instead of this +License. But first, please read +<>. diff --git a/NAMESPACE b/NAMESPACE index d074ff7..6d70b1c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,17 +1,48 @@ # Generated by roxygen2: do not edit by hand -import(ade4) -import(adegenet) -import(car) -import(colourpicker) +export(runStraf) import(dplyr) import(ggplot2) -import(ggrepel) -import(hierfstat) -import(openxlsx) -import(pegas) -import(plotly) -import(reshape2) -import(shiny) -import(shinyWidgets) -import(tidyr) +import(shiny, except = c(dataTableOutput, renderDataTable)) +importClassesFrom(adegenet,genind) +importFrom(DT,dataTableOutput) +importFrom(DT,datatable) +importFrom(DT,renderDataTable) +importFrom(ade4,dudi.pca) +importFrom(adegenet,"pop<-") +importFrom(adegenet,as.genind) +importFrom(adegenet,df2genind) +importFrom(adegenet,dist.genpop) +importFrom(adegenet,funky) +importFrom(adegenet,genind2genpop) +importFrom(adegenet,loadingplot) +importFrom(adegenet,locNames) +importFrom(adegenet,makefreq) +importFrom(adegenet,pop) +importFrom(adegenet,transp) +importFrom(colourpicker,colourInput) +importFrom(ggrepel,geom_text_repel) +importFrom(graphics,abline) +importFrom(graphics,axis) +importFrom(graphics,barplot) +importFrom(graphics,hist) +importFrom(graphics,image) +importFrom(graphics,legend) +importFrom(graphics,par) +importFrom(hierfstat,genind2hierfstat) +importFrom(hierfstat,pairwise.WCfst) +importFrom(openxlsx,write.xlsx) +importFrom(pegas,genind2loci) +importFrom(reshape2,acast) +importFrom(shinyWidgets,awesomeCheckbox) +importFrom(shinyWidgets,pickerInput) +importFrom(stats,as.dist) +importFrom(stats,cmdscale) +importFrom(stats,cov) +importFrom(stats,frequency) +importFrom(stats,ks.test) +importFrom(stats,qqplot) +importFrom(stats,qunif) +importFrom(tidyr,gather) +importFrom(utils,read.table) +importFrom(utils,write.table) diff --git a/R/doc_tabs.R b/R/doc_tabs.R index 9d5ae16..a8cc09b 100644 --- a/R/doc_tabs.R +++ b/R/doc_tabs.R @@ -1,4 +1,3 @@ -### documentation tab documentation_tab <- function() { tabPanel( "Documentation", @@ -10,7 +9,6 @@ documentation_tab <- function() { ) } - about_tab <- function() { tabPanel( "About STRAF", diff --git a/R/helpers.R b/R/helpers.R index a315415..ea67608 100644 --- a/R/helpers.R +++ b/R/helpers.R @@ -1,7 +1,8 @@ ### straf helpers # EXTERNAL FUNCTIONS ----------------------------------------------------------- - ### convert input to genind object +#' @importFrom adegenet as.genind df2genind pop<- locNames +#' @importClassesFrom adegenet genind createGenind <- function(Ifile, Imicrovariants, Incode, Iploidy) { if(Imicrovariants == 2) { @@ -11,7 +12,7 @@ createGenind <- function(Ifile, Imicrovariants, Incode, Iploidy) { mat <- matrix(unlist(mat), nrow = length(mat), ncol = length(mat[[1]]), byrow = TRUE) - mat[mat == "0"] <- NA ### + mat[mat == "0"] <- NA colnames(mat) <- mat[1,] rownames(mat) <- mat[,1] @@ -19,26 +20,26 @@ createGenind <- function(Ifile, Imicrovariants, Incode, Iploidy) { loci <- unique(colnames(mat[,-1:-2])) freqTAB <- NULL mat2 <- mat - mat2 <- sub("[.]","-",mat2) + mat2 <- sub("[.]", "-", mat2) for(i in 1:length(loci)){ ids <- which(colnames(mat)==loci[i]) alleles <- unique(c(mat[,ids])) alleles <- sub("[.]","-",alleles) - alleles <- alleles[!is.na(alleles)] ### + alleles <- alleles[!is.na(alleles)] nameCol <- paste(loci[i],".",alleles,sep = "") - newmat <- matrix(NA,ncol = length(nameCol),nrow = dim(mat)[1]) + newmat <- matrix(NA, ncol = length(nameCol), nrow = dim(mat)[1]) for(ii in 1:length(alleles)){ - newmat[,ii] <- apply(mat2[,ids]==alleles[ii],1,sum) + newmat[, ii] <- apply(mat2[, ids] == alleles[ii], 1, sum) colnames(newmat) <- nameCol } freqTAB <- cbind(freqTAB,newmat) } - rownames(freqTAB) <- mat[,1] - colnames(freqTAB) <- sub(" ","",colnames(freqTAB)) + rownames(freqTAB) <- mat[, 1] + colnames(freqTAB) <- sub(" ", "", colnames(freqTAB)) dat2 <- as.genind(tab = freqTAB) - pop(dat2) <- mat[,"pop"] + pop(dat2) <- mat[, "pop"] } else { dat <- read.table(Ifile$datapath, header = TRUE, @@ -59,7 +60,6 @@ createGenind <- function(Ifile, Imicrovariants, Incode, Iploidy) { } } - dat2 <- df2genind(dat[, -1:-2],ncode = switch( Incode, "2" = 2, "3" = 3), ploidy = switch( Iploidy, Diploid = 2, Haploid = 1)) @@ -73,20 +73,14 @@ createGenind <- function(Ifile, Imicrovariants, Incode, Iploidy) { # input: genind object # output: a list of allele frequencies tables getFreqAllPop <- function(data) { - freq <- list() freq$all <- getFreqFromGenind(data) - for(popu in unique(data$pop)) { - freq <- c(freq, x = NA) mat <- getFreqFromGenind(data[data@pop == popu, ]) freq$x <- mat - names(freq)[length(freq)] <- popu - } - return(freq) } @@ -95,12 +89,8 @@ getFreqAllPop <- function(data) { # input: genind object # output: an allele frequencies tables getFreqFromGenind <- function(data) { - freq <- apply(data@tab, 2, sum, na.rm = TRUE) - nam <- strsplit( - names(freq), - split = "[.]" - ) + nam <- strsplit(names(freq), split = "[.]") loc <- as.factor(unlist( lapply(nam, function(x) x[1]) )) @@ -132,138 +122,11 @@ getFreqFromGenind <- function(data) { } -## getIndicesAllPop -## returns indices for each population -# input: genind object -# output: a list of indices tables -getIndicesAllPop <- function(data, hw = FALSE, hwperm = 1000, ploidy = "Diploid") { - ind <- list() - ind$all <- getIndicesFromGenind(data, hw, hwperm, ploidy) - for(popu in unique(data$pop)) { - ind <- c(ind, x = NA) - mat <- getIndicesFromGenind(data[data@pop == popu, ], hw, hwperm, ploidy) - ind$x <- mat - names(ind)[length(ind)] <- popu - } - return(ind) -} - -## getIndicesFromGenind -## returns indices for a given population -# input: genind object -# output: an indices table -getIndicesFromGenind <- function(data, - hw = FALSE, - hwperm = 1000, - ploidy = "Diploid") { - - freq <- apply(data@tab, 2, sum, na.rm = TRUE) - - nam <- strsplit( - names(freq), - split="[.]" - ) - - loc <- as.factor(unlist( - lapply(nam, function(x) x[1]) - )) - - alle <- as.numeric(unlist( - lapply(nam, function(x) sub("-", ".", x[2])) - )) - DAT <- data.frame(freq, loc, alle) - N <- tapply(DAT$freq, DAT$loc, sum) - DAT$frequency <- DAT$freq / N[DAT$loc] - - PIC <- NULL - for(i in unique(loc)) { - - #FR <- c(DAT$frequency[names(DAT$frequency) == i]) - FR <- c(DAT$frequency[DAT$loc == i]) - - xu <- outer(FR, FR, "fu") - som <- sum(xu[lower.tri(xu)]) - PIC[i] <- 1 - sum(FR ^ 2) - som - - } - Nall <- tapply( - DAT[DAT$freq>0, ]$freq, - DAT[DAT$freq>0, ]$loc, - length - ) - - GD <- tapply( - DAT$frequency, - DAT$loc, - function(x) 1 - sum(x ^ 2) - ) - - GD <- GD * N / (N - 1) - PIC <- PIC[names(GD)] - D2 <- genind2loci(data) - sumloc <- summary(D2)[names(GD)] - PM1 <- lapply(sumloc, function(x) { - sum((x$genotype / sum(x$genotype)) ^ 2) - }) - - PM <- unlist(PM1) - - DF <- data.frame( - locus = names(GD), - N = N, - Nall = Nall, - GD = GD, - PIC = PIC, - PM = PM, - PD = 1 - PM - ) - - if(ploidy == "Diploid") { - DF$Hobs <- adegenet::summary(data)$Hobs[names(GD)] - DF$PE <- (DF$Hobs ^ 2) * (1 - 2 * (DF$Hobs) * ((1 - DF$Hobs) ^ 2)) - DF$TPI <- 1 / (2 * (1 - DF$Hobs)) - } - - - if(length(unique(data@pop)) > 1 & length(locNames(data)) > 1) { - basicstat <- basic.stats( - data, - diploid = switch(ploidy, Diploid = TRUE, Haploid = FALSE), - digits = 4 - )$perloc - rownames(basicstat) <- as.character(unique(data@loc.fac)) - Fst <- wc( - data, - diploid = switch(ploidy, Diploid = TRUE, Haploid = FALSE) - )$per.loc$FST - names(Fst) <- as.character(unique(data@loc.fac)) - - DF$Fst <- Fst[names(GD)] - # DF$Fst <- basicstat[names(GD), "Fst"] - DF$Ht <- basicstat[names(GD), "Ht"] - DF$Fis <- basicstat[names(GD), "Fis"] - - } - - if(ploidy == "Diploid" & hw) { - withProgress(message = 'Performing HW test...', value = 0, { - DF$pHW <- hw.test(data, B = hwperm)[names(GD), 4] - }) - } - - return(DF) -} - - -fu <- function(a, b){ - 2 * (a ^ 2) * (b ^ 2) -} - plotPCA <- function(pca, popus, coul, axis) { - var1 <- round(100*(pca$eig/sum(pca$eig))[axis[1]], 2) - var2 <- round(100*(pca$eig/sum(pca$eig))[axis[2]], 2) + var1 <- round(100 * (pca$eig / sum(pca$eig))[axis[1]], 2) + var2 <- round(100 * (pca$eig / sum(pca$eig))[axis[2]], 2) plot(pca$li[, axis[1]], pca$li[, axis[2]], @@ -279,7 +142,7 @@ plotPCA <- function(pca, popus, coul, axis) { ) sapply(unique(popus), function(x) { - ellipse( + car::ellipse( c(mean(pca$li[popus %in% x, axis[1]]), mean(pca$li[popus %in% x, axis[2]])), cov(pca$li[, axis[1:2]]), 0.95, @@ -309,208 +172,3 @@ plotPCA <- function(pca, popus, coul, axis) { })) } - -straf2genepop <- function(f.name, ploidy = 2) { - df <- readLines(f.name) - - spt <- do.call("rbind", strsplit(df, "\t")) - colnames(spt) <- spt[1, ] - df <- as.data.frame(spt[-1, ]) - - df_tmp <- lapply(df[, -1:-2], function(x) gsub("[.]", "", x)) - - # add leading zeros - df_tmp2 <- lapply(df_tmp, function(x) { - x[nchar(x) == 1] <- paste0(x[nchar(x) == 1], "00") - x[nchar(x) == 2] <- paste0(x[nchar(x) == 2], "0") - if(any(nchar(x) != 3)) stop("Error while converting allele labels.") - return(x) - }) - - # concatenate - idx <- seq_len(length(df_tmp2)) - - if(ploidy == 2) { - ids <- idx %% 2 - - df_out <- list() - for(i in idx[as.logical(ids)]) { - nm <- names(df_tmp2[i]) - nm <- gsub(" ", "", nm) - df_out[[nm]] <- paste0(df_tmp2[[i]], df_tmp2[[i + 1]]) - } - } else if (ploidy == 1) { - df_out <- list() - for(i in idx) { - nm <- names(df_tmp2[i]) - nm <- gsub(" ", "", nm) - df_out[[nm]] <- df_tmp2[[i]] - } - } - - df_out <- as.data.frame(df_out) - - first.line <- "STRAF-generated GENEPOP input file." - loci <- colnames(df_out) - - str_out <- apply(df_out, 1, paste0, collapse = "\t") - - ## get pops - populations <- unique(df$pop) - vec_out <- c() - for(i in populations) { - idx <- df$pop %in% i - vec_out <- c( - vec_out, - "Pop", - paste(df[idx, ]$ind, str_out[idx], sep = "\t,\t") - ) - } - - ## write file - output <- c(first.line, loci, vec_out) - output <- paste(output, "\n", collapse = "") - - return(output) -} - - -straf2familias <- function(f.name) { - - df <- readLines(f.name) - - spt <- do.call("rbind", strsplit(df, "\t")) - colnames(spt) <- spt[1, ] - df <- as.data.frame(spt[-1, ]) - - df_tmp <- df[, -1:-2] - - # add leading zeros - # concatenate - idx <- seq_len(length(df_tmp)) - ids <- as.logical(idx %% 2) - - df_out <- list() - for(i in idx[ids]) { - nm <- names(df_tmp[i]) - nm <- gsub(" ", "", nm) - df_out[[nm]] <- c(df_tmp[[i]], df_tmp[[i + 1]]) - } - - - tbs <- lapply(df_out, table) - prop.tb <- lapply(tbs, prop.table) - - str.list <- lapply(prop.tb, function(x) { - vec <- x - str_loc <- paste0(names(vec), "\t", unname(vec), collapse = "\n") - return(str_loc) - }) - - output <- paste(names(prop.tb), str.list, sep = "\n") - out <- paste(output, collapse = "\n\n") - out <- paste0(out, "\n") - return(out) -} - -straf2arlequin <- function(f.name) { - df <- readLines(f.name) - - spt <- do.call("rbind", strsplit(df, "\t")) - colnames(spt) <- spt[1, ] - df <- as.data.frame(spt[-1, ]) - - df_tmp2 <- list() - - for(i in seq_len(ncol(df[, -1:-2]))) { - x <- df[, -1:-2][, i] - if(i %% 2 != 0) { - x2 <- df[, -1:-2][, i + 1] - dot_idx <- grep("[.]", x) - dot_idx2 <- grep("[.]", x2) - if(length(dot_idx) > 0 | length(dot_idx2) > 0) { - x <- gsub("[.]", "", x) - x[-dot_idx] <- paste0(x[-dot_idx], "0") - x2 <- gsub("[.]", "", x2) - x2[-dot_idx2] <- paste0(x2[-dot_idx2], "0") - if(length(dot_idx) == 0) x <- paste0(x, "0") - if(length(dot_idx2) == 0) x2 <- paste0(x2, "0") - } - df_tmp2[[i]] <- x - df_tmp2[[i+1]] <- x2 - - } - - } - df_tmp2 <- as.data.frame(df_tmp2) - - # concatenate - idx <- seq_len(length(df_tmp2)) - ids <- as.logical(idx %% 2) - - out_str <- c() - for(pp in unique(df$pop)) { - df_pop <- df[df$pop == pp, ] - out_str <- c(out_str, paste0('SampleName="', pp, '"\nSampleSize=',nrow(df_pop),'\nSampleData={\n')) - - for(i in which(df$pop == pp)) { - samp_nm <- df[i, 1] - l1 <- paste0(c(samp_nm, "1", unname(unlist(df_tmp2[i, c(idx[ids])]))), collapse = "\t") - l2 <- paste0(c("", "", unname(unlist(df_tmp2[i, c(idx[!ids])]))), collapse = "\t") - out_str <- c(out_str, l1, l2) - } - out_str <- c(out_str, "}\n\n") - } - npop <- length(unique(df$pop)) - header <- paste0('[Profile]\nTitle="STRAF-generated Arlequin file."\nNbSamples=',npop,'\nDataType=MICROSAT\n -GenotypicData=1\nGameticPhase=0\nMissingData="?"\nLocusSeparator=WHITESPACE\n\n[Data]\n\n[[Samples]]\n\n') - - output <- c(header, out_str) - ## write file - output <- paste(output, "\n", collapse = "") - - return(output) -} - -freq_to_mds <- function(fname) { - ln <- readLines(fname) - ln2 <- lapply(ln, function(x) strsplit(x, ",")[[1]]) - ln3 <- lapply(ln2, function(x) { - if(sum(nchar(x[-1]) == 0) == length(x[-1])) return(x[1]) - else return(x) - }) - hd <- lengths(ln3) - names_idx <- which(hd == 1) - st_idx <- names_idx + 1 - en_idx <- names_idx - 1 - en_idx <- c(en_idx[-1], length(ln2)) - df <- lapply(seq_along(names_idx), function(i) { - loc_id <- names_idx[i] - loc_name <- ln3[[loc_id]] - if(en_idx[i] - st_idx[i] > 1) { - mat <- do.call(rbind, ln2[st_idx[i]:en_idx[i]]) - colnames(mat) <- mat[1, ] - mat[mat == ""] <- "0" - df <- as.data.frame(mat[-1:-2, ]) - colnames(df) <- gsub(pattern = " ", replacement = "_", colnames(df)) - colnames(df) <- gsub(pattern = "\"", replacement = "", colnames(df)) - - df_long <- gather(df, location, frequency, -Allele, factor_key=TRUE) - df_long$locus <- loc_name - return(df_long) - - } else { - return(NULL) - } - }) - df_l <- do.call(rbind, df) - df_l$frequency <- as.numeric(df_l$frequency) - df_l$location <- as.character(df_l$location) - tt <- reshape2::acast(df_l, location ~ locus + Allele, value.var = 'frequency', fun.aggregate = mean, fill = -1) - ct <- rownames(tt) - tt <- tt %>% as_tibble() - df_f <- tt %>% as_tibble() %>% mutate_all(~ifelse(.x == -1, NA, .x)) #mean(.x[.x != -1], na.rm = TRUE) - matt <- (as.matrix(df_f)) - rownames(matt) <- ct - return(matt) -} diff --git a/R/module_data.R b/R/module_data.R index 9dc3c5d..a96e92a 100644 --- a/R/module_data.R +++ b/R/module_data.R @@ -1,4 +1,7 @@ ### Input data module +#' @importFrom shinyWidgets awesomeCheckbox +#' @importFrom DT dataTableOutput renderDataTable datatable +#' @importFrom openxlsx write.xlsx data_UI <- function(id) { ns <- NS(id) tabPanel( @@ -8,7 +11,7 @@ data_UI <- function(id) { tags$hr(), h3("Allele frequencies per locus"), - awesomeCheckbox( + shinyWidgets::awesomeCheckbox( ns('displayAlleleFreq'), 'Plot the distribution of allele frequencies', FALSE ), @@ -19,7 +22,7 @@ data_UI <- function(id) { ), tags$hr(), - awesomeCheckbox( + shinyWidgets::awesomeCheckbox( ns('displayAlleleTable'), 'Display a table of allele frequencies', FALSE @@ -81,7 +84,7 @@ data_Server <- function(id, getgenind, getData, barplotcolor, transparency, widt DAT$freq[DAT$loc == i], names.arg = DAT$alle[DAT$loc == i], main = i, - col = transp(barplotcolor(), transparency()), + col = adegenet::transp(barplotcolor(), transparency()), border = 0 ) } diff --git a/R/module_file_conversion.R b/R/module_file_conversion.R index 9a9826f..907925c 100644 --- a/R/module_file_conversion.R +++ b/R/module_file_conversion.R @@ -51,4 +51,214 @@ file_conv_Server <- function(id, fpath, ploidy) { } ) } - )} \ No newline at end of file + )} + + + + +straf2genepop <- function(f.name, ploidy = 2) { + df <- readLines(f.name) + + spt <- do.call("rbind", strsplit(df, "\t")) + colnames(spt) <- spt[1, ] + df <- as.data.frame(spt[-1, ]) + + df_tmp <- lapply(df[, -1:-2], function(x) gsub("[.]", "", x)) + + # add leading zeros + df_tmp2 <- lapply(df_tmp, function(x) { + x[nchar(x) == 1] <- paste0(x[nchar(x) == 1], "00") + x[nchar(x) == 2] <- paste0(x[nchar(x) == 2], "0") + if(any(nchar(x) != 3)) stop("Error while converting allele labels.") + return(x) + }) + + # concatenate + idx <- seq_len(length(df_tmp2)) + + if(ploidy == 2) { + ids <- idx %% 2 + + df_out <- list() + for(i in idx[as.logical(ids)]) { + nm <- names(df_tmp2[i]) + nm <- gsub(" ", "", nm) + df_out[[nm]] <- paste0(df_tmp2[[i]], df_tmp2[[i + 1]]) + } + } else if (ploidy == 1) { + df_out <- list() + for(i in idx) { + nm <- names(df_tmp2[i]) + nm <- gsub(" ", "", nm) + df_out[[nm]] <- df_tmp2[[i]] + } + } + + df_out <- as.data.frame(df_out) + + first.line <- "STRAF-generated GENEPOP input file." + loci <- colnames(df_out) + + str_out <- apply(df_out, 1, paste0, collapse = "\t") + + ## get pops + populations <- unique(df$pop) + vec_out <- c() + for(i in populations) { + idx <- df$pop %in% i + vec_out <- c( + vec_out, + "Pop", + paste(df[idx, ]$ind, str_out[idx], sep = "\t,\t") + ) + } + + ## write file + output <- c(first.line, loci, vec_out) + output <- paste(output, "\n", collapse = "") + + return(output) +} + + +straf2familias <- function(f.name) { + + df <- readLines(f.name) + + spt <- do.call("rbind", strsplit(df, "\t")) + colnames(spt) <- spt[1, ] + df <- as.data.frame(spt[-1, ]) + + df_tmp <- df[, -1:-2] + + # add leading zeros + # concatenate + idx <- seq_len(length(df_tmp)) + ids <- as.logical(idx %% 2) + + df_out <- list() + for(i in idx[ids]) { + nm <- names(df_tmp[i]) + nm <- gsub(" ", "", nm) + df_out[[nm]] <- c(df_tmp[[i]], df_tmp[[i + 1]]) + } + + + tbs <- lapply(df_out, table) + prop.tb <- lapply(tbs, prop.table) + + str.list <- lapply(prop.tb, function(x) { + vec <- x + str_loc <- paste0(names(vec), "\t", unname(vec), collapse = "\n") + return(str_loc) + }) + + output <- paste(names(prop.tb), str.list, sep = "\n") + out <- paste(output, collapse = "\n\n") + out <- paste0(out, "\n") + return(out) +} + +straf2arlequin <- function(f.name) { + df <- readLines(f.name) + + spt <- do.call("rbind", strsplit(df, "\t")) + colnames(spt) <- spt[1, ] + df <- as.data.frame(spt[-1, ]) + + df_tmp2 <- list() + + for(i in seq_len(ncol(df[, -1:-2]))) { + x <- df[, -1:-2][, i] + if(i %% 2 != 0) { + x2 <- df[, -1:-2][, i + 1] + dot_idx <- grep("[.]", x) + dot_idx2 <- grep("[.]", x2) + if(length(dot_idx) > 0 | length(dot_idx2) > 0) { + x <- gsub("[.]", "", x) + x[-dot_idx] <- paste0(x[-dot_idx], "0") + x2 <- gsub("[.]", "", x2) + x2[-dot_idx2] <- paste0(x2[-dot_idx2], "0") + if(length(dot_idx) == 0) x <- paste0(x, "0") + if(length(dot_idx2) == 0) x2 <- paste0(x2, "0") + } + df_tmp2[[i]] <- x + df_tmp2[[i+1]] <- x2 + + } + + } + df_tmp2 <- as.data.frame(df_tmp2) + + # concatenate + idx <- seq_len(length(df_tmp2)) + ids <- as.logical(idx %% 2) + + out_str <- c() + for(pp in unique(df$pop)) { + df_pop <- df[df$pop == pp, ] + out_str <- c(out_str, paste0('SampleName="', pp, '"\nSampleSize=',nrow(df_pop),'\nSampleData={\n')) + + for(i in which(df$pop == pp)) { + samp_nm <- df[i, 1] + l1 <- paste0(c(samp_nm, "1", unname(unlist(df_tmp2[i, c(idx[ids])]))), collapse = "\t") + l2 <- paste0(c("", "", unname(unlist(df_tmp2[i, c(idx[!ids])]))), collapse = "\t") + out_str <- c(out_str, l1, l2) + } + out_str <- c(out_str, "}\n\n") + } + npop <- length(unique(df$pop)) + header <- paste0('[Profile]\nTitle="STRAF-generated Arlequin file."\nNbSamples=',npop,'\nDataType=MICROSAT\n +GenotypicData=1\nGameticPhase=0\nMissingData="?"\nLocusSeparator=WHITESPACE\n\n[Data]\n\n[[Samples]]\n\n') + + output <- c(header, out_str) + ## write file + output <- paste(output, "\n", collapse = "") + + return(output) +} + +#' @importFrom reshape2 acast +#' @importFrom tidyr gather +freq_to_mds <- function(fname) { + ln <- readLines(fname) + ln2 <- lapply(ln, function(x) strsplit(x, ",")[[1]]) + ln3 <- lapply(ln2, function(x) { + if(sum(nchar(x[-1]) == 0) == length(x[-1])) return(x[1]) + else return(x) + }) + hd <- lengths(ln3) + names_idx <- which(hd == 1) + st_idx <- names_idx + 1 + en_idx <- names_idx - 1 + en_idx <- c(en_idx[-1], length(ln2)) + df <- lapply(seq_along(names_idx), function(i) { + loc_id <- names_idx[i] + loc_name <- ln3[[loc_id]] + if(en_idx[i] - st_idx[i] > 1) { + mat <- do.call(rbind, ln2[st_idx[i]:en_idx[i]]) + colnames(mat) <- mat[1, ] + mat[mat == ""] <- "0" + df <- as.data.frame(mat[-1:-2, ]) + colnames(df) <- gsub(pattern = " ", replacement = "_", colnames(df)) + colnames(df) <- gsub(pattern = "\"", replacement = "", colnames(df)) + Allele <- NA + df_long <- tidyr::gather(df, location, frequency, -Allele, factor_key=TRUE) + df_long$locus <- loc_name + return(df_long) + + } else { + return(NULL) + } + }) + df_l <- do.call(rbind, df) + df_l$frequency <- as.numeric(df_l$frequency) + df_l$location <- as.character(df_l$location) + tt <- reshape2::acast(df_l, location ~ locus + Allele, value.var = 'frequency', fun.aggregate = mean, fill = -1) + ct <- rownames(tt) + tt <- tt %>% as_tibble() + df_f <- tt %>% as_tibble() %>% mutate_all(~ifelse(.x == -1, NA, .x)) #mean(.x[.x != -1], na.rm = TRUE) + matt <- (as.matrix(df_f)) + rownames(matt) <- ct + return(matt) +} diff --git a/R/module_for_popgen.R b/R/module_for_popgen.R index ffec30a..639d895 100644 --- a/R/module_for_popgen.R +++ b/R/module_for_popgen.R @@ -1,4 +1,5 @@ ### Module +#' @importFrom shinyWidgets awesomeCheckbox for_UI <- function(id) { ns <- NS(id) tabPanel( @@ -122,7 +123,8 @@ popgen_UI <- function(id) { tags$hr() ) } -for_popgen_Server <- function(id, getgenind, popnames, ploidy) { +#' @importFrom hierfstat pairwise.WCfst genind2hierfstat +for_popgen_Server <- function(id, getgenind, popnames, ploidy, barplotcolor, transparency, cexaxis) { moduleServer( id, function(input, output, session) { @@ -172,7 +174,7 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { if(is.null(input$selectPop2)) taB <- reacIndices()[[1]] else taB <- reacIndices()[[input$selectPop2]] write.table( - taB[, ! colnames(taB) %in% c("Ht", "Fis", "Fst")], + taB[, !colnames(taB) %in% c("Ht", "Fis", "Fst")], file, sep = "\t", row.names = FALSE ) } @@ -244,7 +246,7 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { }) # plot in the reactive UI - output$plotIndices <- renderPlotly({ + output$plotIndices <- plotly::renderPlotly({ if(is.null(input$selectPop2)) return(NULL) else taB <- reacIndices()[[input$selectPop2]] @@ -254,7 +256,7 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { if(is.null(input$plotIndicesFOR)) return(NULL) - fig <- plot_ly( + fig <- plotly::plot_ly( x = dat[, input$plotIndicesFOR], y = dat[, "locus"], name = "bp_for", @@ -264,8 +266,8 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { "\nValue: ", round(dat[, input$plotIndicesFOR], 4) ), hoverinfo = 'text', - marker = list(color = transp(input$barplotcolor, input$transparency)) - ) %>% layout( + marker = list(color = adegenet::transp(barplotcolor(), transparency())) + ) %>% plotly::layout( xaxis = list(title = input$plotIndicesFOR, zeroline = FALSE), yaxis = list(title = "Locus") ) @@ -274,7 +276,7 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { }) output$plotFOR <- renderUI({ - plotlyOutput(ns('plotIndices')) + plotly::plotlyOutput(ns('plotIndices')) }) output$plotIndicesPopgen <- renderPlot({ @@ -293,10 +295,10 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { names.arg = datpl[, "locus"], horiz = TRUE, las = 1, - col = transp(input$barplotcolor, input$transparency), - border = as.numeric(input$borderbarplot), - cex.axis = input$cexaxis, - cex.names = input$cexaxis, + col = transp(barplotcolor(), transparency()), + border = 0, + cex.axis = cexaxis(), + cex.names = cexaxis(), xlab = input$plotIndicesPG ) }) @@ -314,7 +316,7 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { if (length(unique(dat2@pop)) == 1) stop("Multiple populations are required to perform this analysis") - matFST <- pairwise.WCfst(genind2hierfstat(dat2)) + matFST <- hierfstat::pairwise.WCfst(hierfstat::genind2hierfstat(dat2)) matFST[lower.tri(matFST)] <- NA matFST }) @@ -361,9 +363,9 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { for(i in 1:nloc){ for(ii in 1:nloc){ if(i30) + return(length(M) > 30) }) outputOptions(output, 'LD30', suspendWhenHidden=FALSE) @@ -398,15 +400,9 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { M <- -log10(reacLDtable()) M[lower.tri(M)] <- NA - col <- redpal(100) + col <- adegenet::redpal(100) - image( - M, - col = col, - frame = F, - xaxt = "n", - yaxt = "n" - ) + image(M, col = col, frame = F, xaxt = "n", yaxt = "n") axis( 2, at = seq(0, 1, length.out = ncol(M)), @@ -424,9 +420,7 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { }) - output$plotLD2 <- renderUI({ - plotOutput(ns('plotLD')) - }) + output$plotLD2 <- renderUI({plotOutput(ns('plotLD'))}) #plot p-values distribution output$plotLDpval <- renderPlot({ @@ -488,4 +482,126 @@ for_popgen_Server <- function(id, getgenind, popnames, ploidy) { ) } ) -} \ No newline at end of file +} + + +## getIndicesAllPop +## returns indices for each population +# input: genind object +# output: a list of indices tables +getIndicesAllPop <- function(data, hw = FALSE, hwperm = 1000, ploidy = "Diploid") { + ind <- list() + ind$all <- getIndicesFromGenind(data, hw, hwperm, ploidy) + for(popu in unique(data$pop)) { + ind <- c(ind, x = NA) + mat <- getIndicesFromGenind(data[data@pop == popu, ], hw, hwperm, ploidy) + ind$x <- mat + names(ind)[length(ind)] <- popu + } + return(ind) +} + +## getIndicesFromGenind +## returns indices for a given population +# input: genind object +# output: an indices table +#' @importFrom pegas genind2loci +getIndicesFromGenind <- function(data, + hw = FALSE, + hwperm = 1000, + ploidy = "Diploid") { + + freq <- apply(data@tab, 2, sum, na.rm = TRUE) + + nam <- strsplit( + names(freq), + split="[.]" + ) + + loc <- as.factor(unlist( + lapply(nam, function(x) x[1]) + )) + + alle <- as.numeric(unlist( + lapply(nam, function(x) sub("-", ".", x[2])) + )) + DAT <- data.frame(freq, loc, alle) + N <- tapply(DAT$freq, DAT$loc, sum) + DAT$frequency <- DAT$freq / N[DAT$loc] + + PIC <- NULL + for(i in unique(loc)) { + + #FR <- c(DAT$frequency[names(DAT$frequency) == i]) + FR <- c(DAT$frequency[DAT$loc == i]) + + xu <- outer(FR, FR, "fu") + som <- sum(xu[lower.tri(xu)]) + PIC[i] <- 1 - sum(FR ^ 2) - som + + } + Nall <- tapply( + DAT[DAT$freq > 0, ]$freq, + DAT[DAT$freq > 0, ]$loc, + length + ) + + GD <- tapply(DAT$frequency, DAT$loc, function(x) 1 - sum(x ^ 2)) + + GD <- GD * N / (N - 1) + PIC <- PIC[names(GD)] + D2 <- pegas::genind2loci(data) + sumloc <- summary(D2)[names(GD)] + PM1 <- lapply(sumloc, function(x) { + sum((x$genotype / sum(x$genotype)) ^ 2) + }) + + PM <- unlist(PM1) + + DF <- data.frame( + locus = names(GD), + N = N, + Nall = Nall, + GD = GD, + PIC = PIC, + PM = PM, + PD = 1 - PM + ) + + if(ploidy == "Diploid") { + DF$Hobs <- adegenet::summary(data)$Hobs[names(GD)] + DF$PE <- (DF$Hobs ^ 2) * (1 - 2 * (DF$Hobs) * ((1 - DF$Hobs) ^ 2)) + DF$TPI <- 1 / (2 * (1 - DF$Hobs)) + } + + + if(length(unique(data@pop)) > 1 & length(locNames(data)) > 1) { + basicstat <- hierfstat::basic.stats( + data, + diploid = switch(ploidy, Diploid = TRUE, Haploid = FALSE), + digits = 4 + )$perloc + rownames(basicstat) <- as.character(unique(data@loc.fac)) + Fst <- hierfstat::wc( + data, + diploid = switch(ploidy, Diploid = TRUE, Haploid = FALSE) + )$per.loc$FST + names(Fst) <- as.character(unique(data@loc.fac)) + + DF$Fst <- Fst[names(GD)] + # DF$Fst <- basicstat[names(GD), "Fst"] + DF$Ht <- basicstat[names(GD), "Ht"] + DF$Fis <- basicstat[names(GD), "Fis"] + + } + + if(ploidy == "Diploid" & hw) { + withProgress(message = 'Performing HW test...', value = 0, { + DF$pHW <- pegas::hw.test(data, B = hwperm)[names(GD), 4] + }) + } + return(DF) +} + + +fu <- function(a, b) {2 * (a ^ 2) * (b ^ 2)} diff --git a/R/module_pca_mds.R b/R/module_pca_mds.R index b0154d8..2fb6ef5 100644 --- a/R/module_pca_mds.R +++ b/R/module_pca_mds.R @@ -1,5 +1,5 @@ ### PCA and MDS module - +#' @importFrom shinyWidgets awesomeCheckbox pca_mds_UI <- function(id) { ns <- NS(id) tabPanel( @@ -45,7 +45,9 @@ pca_mds_UI <- function(id) { ) } - +#' @importFrom adegenet genind2genpop transp funky dist.genpop loadingplot makefreq pop +#' @importFrom ggrepel geom_text_repel +#' @importFrom ade4 dudi.pca pca_mds_Server <- function(id, getgenind) { moduleServer( id, @@ -100,8 +102,8 @@ pca_mds_Server <- function(id, getgenind) { dst <- dist.genpop(obj, method = 1) MDS <- cmdscale(dst) MDS <- data.frame(ax1 = MDS[, 1], ax2 = MDS[, 2], pop = rownames(MDS)) - - p <- ggplot(MDS, aes(x=ax1, y=ax2, color = pop, label = pop)) + + + p <- ggplot(MDS, aes(x = .data$ax1, y = .data$ax2, color = pop, label = pop)) + geom_point() + geom_text_repel() + labs( x = "MDS Axis 1", y = "MDS Axis 2", title = "MDS based on Nei's distance") + diff --git a/R/module_reference_mds.R b/R/module_reference_mds.R index 657a5c9..0154ad4 100644 --- a/R/module_reference_mds.R +++ b/R/module_reference_mds.R @@ -1,4 +1,5 @@ ## Reference population MDS module +#' @importFrom shinyWidgets awesomeCheckbox ref_mds_UI <- function(id) { ns <- NS(id) @@ -17,8 +18,7 @@ ref_mds_UI <- function(id) { ) } - - +#' @importFrom adegenet genind2genpop ref_mds_Server <- function(id, getgenind) { moduleServer( id, @@ -101,7 +101,7 @@ ref_mds_Server <- function(id, getgenind) { mds <- cmdscale(d) MDS <- data.frame(ax1 = mds[, 1], ax2 = mds[, 2], pop = rownames(mds)) - p <- ggplot(MDS, aes(x=ax1, y=ax2, color = pop, label = pop)) + + p <- ggplot(MDS, aes(x=.data$ax1, y=.data$ax2, color = pop, label = pop)) + geom_point() + geom_text_repel(max.overlaps = 50) + labs( x = "MDS Axis 1", y = "MDS Axis 2", title = "MDS based on Nei's distance") + diff --git a/R/runStraf.R b/R/runStraf.R index b910d7e..794ef2b 100644 --- a/R/runStraf.R +++ b/R/runStraf.R @@ -1,19 +1,17 @@ -#' @import shiny -#' @import colourpicker -#' @import plotly -#' @import shinyWidgets -#' @import ade4 -#' @import adegenet -#' @import pegas -#' @import hierfstat -#' @import car -#' @import openxlsx -#' @import reshape2 +#' Run the STRAF application +#' @description Main function to be called in order to start STRAF, +#' @return Runs the shiny application. +#' @examples +#' # runStraf() +#' +#' @export +#' +#' @rawNamespace import(shiny, except = c(dataTableOutput, renderDataTable)) #' @import dplyr -#' @import tidyr #' @import ggplot2 -#' @import ggrepel - +#' @importFrom graphics abline axis barplot hist image legend par +#' @importFrom stats as.dist cmdscale cov frequency ks.test qqplot qunif +#' @importFrom utils read.table write.table runStraf <- function() { options( warn = -1, diff --git a/R/sidebar.R b/R/sidebar.R index e950ae2..b91710d 100644 --- a/R/sidebar.R +++ b/R/sidebar.R @@ -1,4 +1,7 @@ -### Sidebar UI code +#' Generate the sidebar UI. +#' @noRd +#' @importFrom shinyWidgets awesomeCheckbox pickerInput +#' @importFrom colourpicker colourInput sidebarUI <- function() { sidebarPanel( width = 3, diff --git a/inst/application/server.R b/inst/application/server.R index 8955310..6a549a6 100644 --- a/inst/application/server.R +++ b/inst/application/server.R @@ -33,7 +33,7 @@ shinyServer(function(input, output) { if(length(unique(testGeno@pop)) > 1 & length(locNames(testGeno)) > 1) { testGeno3 <- try( - wc( + hierfstat::wc( testGeno, diploid = switch( input$ploidy, @@ -56,7 +56,7 @@ shinyServer(function(input, output) { output$checkInputFile <- renderText({ - if(is.null(input$file1)) { return("Please import a data set.") } + if(is.null(input$file1)) { return("Please import a data set.") } else { X <- read.table(input$file1$datapath, header = TRUE, @@ -83,7 +83,7 @@ shinyServer(function(input, output) { } testGeno3 <- try( - wc( + hierfstat::wc( testGeno, diploid = switch( input$ploidy, @@ -136,11 +136,12 @@ shinyServer(function(input, output) { ploidy <- reactive({input$ploidy}) barplotcolor <- reactive({input$barplotcolor}) transparency <- reactive({input$transparency}) + cexaxis <- reactive({input$cexaxis}) width <- reactive({input$width}) height <- reactive({input$height}) data_Server("data_ns", getgenind, getData, barplotcolor, transparency, width, height,popnames) - for_popgen_Server("for_popgen", getgenind, popnames, ploidy) + for_popgen_Server("for_popgen", getgenind, popnames, ploidy, barplotcolor, transparency, cexaxis) pca_mds_Server("pca_mds", getgenind) ref_mds_Server("ref_mds", getgenind) file_conv_Server("file_conv", reactive({input$file1$datapath}), reactive({input$ploidy})) diff --git a/man/runStraf.Rd b/man/runStraf.Rd new file mode 100644 index 0000000..f5b3195 --- /dev/null +++ b/man/runStraf.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/runStraf.R +\name{runStraf} +\alias{runStraf} +\title{Run the STRAF application} +\usage{ +runStraf() +} +\value{ +Runs the shiny application. +} +\description{ +Main function to be called in order to start STRAF, +} +\examples{ +# runStraf() + +} diff --git a/operator.json b/operator.json deleted file mode 100644 index 7f6ca2d..0000000 --- a/operator.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "name": "STRAF", - "description": "STRAF (STR Analysis for Forensics) in Tercen", - "tags": ["forensics", "genetics"], - "authors": ["tercen"], - "urls": ["https://github.com/agouy/straf"] -}