diff --git a/.Rbuildignore b/.Rbuildignore index 91114bf..31e3754 100755 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,4 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +^LICENSE\.md$ +^\.github$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..74d8c97 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,49 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true diff --git a/DESCRIPTION b/DESCRIPTION index a71e4f6..3977556 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,27 +1,27 @@ -Package: SRSim Type: Package +Package: SRSim Title: Spontaneous Reporting Simulator (SRSim) Version: 0.1 -Date: 2018-01-18 Author: Louis Dijkstra [aut, cre], Marco Garling [ctb] Maintainer: Louis Dijkstra -Description: A package for simulating spontaneous reporting - data as used in the field of pharmacovigilance. +Description: A package for simulating spontaneous reporting data as used + in the field of pharmacovigilance. +License: GPL (>= 3) +URL: https://github.com/bips-hb/srsim +BugReports: https://github.com/bips-hb/srsim/issues Depends: - R (>= 3.2.3), - Rcpp, - RcppArmadillo, - RcppProgress, - dplyr, - tidyr, - mvtnorm, - corpcor, - pcalg, - Rgraphviz -LinkingTo: Rcpp, RcppArmadillo, RcppProgress -License: GPL-3 + R (>= 3.2.3) +Imports: + corpcor, + igraph, + Rcpp, + RcppArmadillo, + tibble +LinkingTo: + Rcpp, + RcppArmadillo, + RcppProgress Encoding: UTF-8 LazyData: true -RoxygenNote: 6.0.1 -URL: https://github.com/bips-hb/srsim -BugReports: https://github.com/bips-hb/srsim/issues +RoxygenNote: 7.3.1 +Roxygen: list(markdown = TRUE) diff --git a/LICENSE b/LICENSE deleted file mode 100755 index e72bfdd..0000000 --- a/LICENSE +++ /dev/null @@ -1,674 +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. 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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) - - 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: - - Copyright (C) - 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 -. \ No newline at end of file diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..175443c --- /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) + + 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: + + Copyright (C) + 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 784167a..dfb07eb 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,6 +8,11 @@ export(validReport) import(Rcpp) import(RcppArmadillo) import(corpcor) -import(dplyr) -import(tidyr) +importFrom(stats,optim) +importFrom(stats,rbeta) +importFrom(stats,rnorm) +importFrom(tibble,as_tibble) +importFrom(tibble,tibble) +importFrom(utils,setTxtProgressBar) +importFrom(utils,txtProgressBar) useDynLib(SRSim) diff --git a/R/SRSim-package.R b/R/SRSim-package.R new file mode 100644 index 0000000..3ea0351 --- /dev/null +++ b/R/SRSim-package.R @@ -0,0 +1,14 @@ +#' @author Louis Dijkstra & Marco Garling +#' @useDynLib SRSim +#' @keywords internal +"_PACKAGE" + +## usethis namespace: start +#' @import corpcor +#' @import Rcpp +#' @import RcppArmadillo +#' @importFrom stats optim rbeta rnorm +#' @importFrom tibble tibble as_tibble +#' @importFrom utils setTxtProgressBar txtProgressBar +## usethis namespace: end +NULL diff --git a/R/convert2Tables.R b/R/convert2Tables.R index 32491d1..379b2f1 100644 --- a/R/convert2Tables.R +++ b/R/convert2Tables.R @@ -1,37 +1,37 @@ #' Create 2 x 2 Tables from DAG based SR data #' #' Creates a data frame with all 2 x 2 contigency tables given a simulated data -#' set from \code{simulateSRS}. The tables are organized +#' set from `simulateSRS`. The tables are organized #' as follows: #' \tabular{lccc}{ -#' \tab event \eqn{j} \tab not event \eqn{j} \tab \emph{total}\cr -#' drug \eqn{i} \tab \code{a} \tab \code{c} \tab \code{a} + \code{c}\cr -#' not drug \eqn{i} \tab \code{b} \tab \code{d} \tab \code{b} + \code{d}\cr -#' \emph{total} \tab \code{a} + \code{b} \tab \code{c} + \code{d} \tab \code{n_reports} +#' \tab event \eqn{j} \tab not event \eqn{j} \tab *total*\cr +#' drug \eqn{i} \tab `a` \tab `c` \tab `a` + `c`\cr +#' not drug \eqn{i} \tab `b` \tab `d` \tab `b` + `d`\cr +#' *total* \tab `a` + `b` \tab `c` + `d` \tab `n_reports` #' } #' -#' @param sr The output generated by the \code{\link{simulateSRS}} function +#' @param sr The output generated by the [simulateSRS()] function #' #' @return A data frame where each row represents a 2 x 2 table. The columns represent: -#' \item{\code{drug_id}}{The ID of the drug} -#' \item{\code{event_id}}{The ID of the event} -#' \item{\code{prob_drug}}{The marginal probability of that drug} -#' \item{\code{prob_event}}{The marginal probability of that event} -#' \item{\code{or}}{The increase of the odds ratio when the drug is on the report} -#' \item{\code{associated}}{\code{TRUE} is there is a non-zero correlation, \code{FALSE} otherwise} -#' \item{\code{a}}{Number of times the drug and event appeared together in a report} -#' \item{\code{b}}{Number of times the event appeared without the drug in a report} -#' \item{\code{c}}{Number of times the drug appeared without the event in a report} -#' \item{\code{d}}{Number of times the drug and event both did not appear in a report} +#' \item{`drug_id`}{The ID of the drug} +#' \item{`event_id`}{The ID of the event} +#' \item{`prob_drug`}{The marginal probability of that drug} +#' \item{`prob_event`}{The marginal probability of that event} +#' \item{`or`}{The increase of the odds ratio when the drug is on the report} +#' \item{`associated`}{`TRUE` is there is a non-zero correlation, `FALSE` otherwise} +#' \item{`a`}{Number of times the drug and event appeared together in a report} +#' \item{`b`}{Number of times the event appeared without the drug in a report} +#' \item{`c`}{Number of times the drug appeared without the event in a report} +#' \item{`d`}{Number of times the drug and event both did not appear in a report} #' #' @examples -#' sr <- simulateSRS() -#' tables <- create2x2Tables(sr) +#' sr <- simulateSRS(verbose = FALSE) +#' tables <- convert2Tables(sr) #' -#' @seealso \code{\link{simulateSRS}} +#' @seealso [simulateSRS()] #' @export convert2Tables <- function(sr) { - return(dplyr::as_tibble( + tibble::as_tibble( create2x2TablesDAGRcpp( as.matrix(sr$sr), sr$prob_drugs, @@ -40,5 +40,5 @@ convert2Tables <- function(sr) { as.integer(sr$nodes$parent_id), sr$nodes$beta1 ) - )) -} \ No newline at end of file + ) +} diff --git a/R/f_beta0.R b/R/f_beta0.R index 839a7d2..efd6e85 100644 --- a/R/f_beta0.R +++ b/R/f_beta0.R @@ -1,6 +1,6 @@ #' Determining the Intercept #' -#' \code{f_beta0} is used by \code{\link{simulateSRS}} to find the appropriate +#' `f_beta0` is used by [simulateSRS()] to find the appropriate #' intercept for a logistic regression model. #' #' @param beta0 The intercept @@ -14,4 +14,4 @@ f_beta0 <- function(beta0, margprob, beta1, margprob_parent) { abs(margprob - (1 - margprob_parent)*(exp(beta0) / (1 + exp(beta0))) - margprob_parent*(exp(beta0 + beta1) / (1 + exp(beta0 + beta1)))) -} \ No newline at end of file +} diff --git a/R/generateDAG.R b/R/generateDAG.R index 748eba1..e8acd27 100644 --- a/R/generateDAG.R +++ b/R/generateDAG.R @@ -1,6 +1,6 @@ #' Directed Acyclic Graph for SR Data #' -#' \code{generateDAG} creates a directed acyclic graph used for generating +#' `generateDAG` creates a directed acyclic graph used for generating #' spontaneous reporting data #' #' @param n_drugs Number of drugs (Default: 10) @@ -8,9 +8,9 @@ #' @param n_innocent_bystanders Number of innocent bystanders (Default: 5) #' @param n_correlated_pairs Number of drug-event pairs that will be associated (Default: 2) #' -#' @return The DAG as an \code{igraph} object +#' @return The DAG as an `igraph` object #' -#' @seealso \code{\link{simulateSRS}} +#' @seealso [simulateSRS()] #' @export generateDAG <- function(n_drugs = 10, n_events = 10, @@ -44,4 +44,4 @@ generateDAG <- function(n_drugs = 10, DAG <- igraph::add.edges(DAG, edges) return(DAG) -} \ No newline at end of file +} diff --git a/R/simulateSRS.R b/R/simulateSRS.R index 153d60d..f750ece 100644 --- a/R/simulateSRS.R +++ b/R/simulateSRS.R @@ -1,31 +1,31 @@ #' Simulating a Spontaneous Reporting System #' -#' \code{simulateSRS} simulates a spontaneous reporting (SR) data set. The relationships between -#' the drugs and the adverse events (AEs) are specified by a directed acyclic graph (DAG), -#' see \code{\link{generateDAG}}. +#' `simulateSRS` simulates a spontaneous reporting (SR) data set. The relationships between +#' the drugs and the adverse events (AEs) are specified by a directed acyclic graph (DAG), +#' see [generateDAG()]. #' \cr\cr -#' Each report to a SRS contains two lists: +#' Each report to a SRS contains two lists: #' \enumerate{ -#' \item the drugs to which the patient was (thought to be) exposed to, and -#' \item the AEs that the patient experienced. +#' \item the drugs to which the patient was (thought to be) exposed to, and +#' \item the AEs that the patient experienced. #' } -#' We will represent each report as a binary vector. The first items represent whether -#' the patient was exposed to the drug (\code{1} if he/she was, and \code{0} otherwise). -#' The second part represents whether the patient experienced the event or not -#' (\code{1} if he/she did, and \code{0} otherwise). For example, if there are 3 drugs and -#' 4 events in total, a typical report could be -#' \deqn{0 1 0 1 1 0 0} -#' which represents that the patient was exposed to drug 2 (but not to drug 1 and 3), and +#' We will represent each report as a binary vector. The first items represent whether +#' the patient was exposed to the drug (`1` if he/she was, and `0` otherwise). +#' The second part represents whether the patient experienced the event or not +#' (`1` if he/she did, and `0` otherwise). For example, if there are 3 drugs and +#' 4 events in total, a typical report could be +#' \deqn{0 1 0 1 1 0 0} +#' which represents that the patient was exposed to drug 2 (but not to drug 1 and 3), and #' experienced event 1 and 2 (but not 3 and 4). The simulation results in a binary matrix -#' where each row is a report. +#' where each row is a report. #' \cr\cr -#' \strong{Valid Reports} Not any binary sequence is a valid report. Each report -#' should contain at least one drug and at least one event (otherwise it would -#' never been sent to the spontaneous reporitng sytem). +#' **Valid Reports** Not any binary sequence is a valid report. Each report +#' should contain at least one drug and at least one event (otherwise it would +#' never been sent to the spontaneous reporitng sytem). #' While generating reports, we make sure that this is indeed the case. When one does not -#' want to check the validity and wants to allow any binary sequence, one can set -#' \code{valid_reports} to \code{FALSE}. -#' +#' want to check the validity and wants to allow any binary sequence, one can set +#' `valid_reports` to `FALSE`. +#' #' @param n_reports Number of reports (Default: 100) #' @param n_drugs Number of drugs (Default: 10) #' @param n_events Number of adverse drug events (Default: 10) @@ -34,38 +34,38 @@ #' @param alpha_events Alpha parameter for the event marginal probabilities (Default: 1.0) #' @param beta_events Beta parameter for the event marginal probabilities (Default: 20.0) #' @param n_innocent_bystanders Number of innocent bystanders (Default: 5) -#' @param bystander_prob The conditional probability of the innocent bystander being one when +#' @param bystander_prob The conditional probability of the innocent bystander being one when #' the drug that is actually causing the AE is equal to 1. This parameter #' corresponds to \eqn{\gamma} in the paper (Default: .9) #' @param n_correlated_pairs Number of drug-AE pairs that are associated (Default: 2) #' @param theta Increase in odds-ratio when there is an edge going from a drug to an AE (Default: 2.0). -#' In case theta is a vector of length two, the odds ratio is drawn from a truncated -#' Normal distribution with mean \code{theta[1]} and variance \code{theta[2]} -#' @param valid_reports If \code{TRUE}, only valid reports (with at least one drug and at least one AE) -#' are accepted. (Default: \code{TRUE}) +#' In case theta is a vector of length two, the odds ratio is drawn from a truncated +#' Normal distribution with mean `theta[1]` and variance `theta[2]` +#' @param valid_reports If `TRUE`, only valid reports (with at least one drug and at least one AE) +#' are accepted. (Default: `TRUE`) #' @param seed The seed used by the RNG (Default: automatically set) -#' @param verbose Verbosity (Default: \code{TRUE}) +#' @param verbose Verbosity (Default: `TRUE`) #' -#' @return \item{sr}{A binary data frame with the simulated reports. The columns are -#' named \code{drug1}, \code{drug2} ..., \code{event1}, \code{event2}, ...} -#' \item{dag}{The directed acycled graph as an \code{igraph} object} +#' @return \item{sr}{A binary data frame with the simulated reports. The columns are +#' named `drug1`, `drug2` ..., `event1`, `event2`, ...} +#' \item{dag}{The directed acycled graph as an `igraph` object} #' \item{nodes}{A tibble with all the information on each node/variate: #' \itemize{ -#' \item{\code{label}}{ The label for each node/variate} -#' \item{\code{in_degree}}{ The number of edges pointing to the node} -#' \item{\code{id}}{ The ID of each node (simple integer)} -#' \item{\code{parent_id}}{ The ID of the parent node - if any. Otherwise equal to \code{-1}} -#' \item{\code{margprob}}{ The marginal probability of the node/variate} -#' \item{\code{beta0}}{ The intercept in the logistic regression model for that node} -#' \item{\code{beta1}}{ The regression coefficient in the logistic regression model for the parent} +#' \item{`label`}{ The label for each node/variate} +#' \item{`in_degree`}{ The number of edges pointing to the node} +#' \item{`id`}{ The ID of each node (simple integer)} +#' \item{`parent_id`}{ The ID of the parent node - if any. Otherwise equal to `-1`} +#' \item{`margprob`}{ The marginal probability of the node/variate} +#' \item{`beta0`}{ The intercept in the logistic regression model for that node} +#' \item{`beta1`}{ The regression coefficient in the logistic regression model for the parent} #' } #' } #' \item{prob_drugs}{A vector with marginal probabilities of the drugs} #' \item{prob_events}{A vector with marginal probabilities of the events} -#' #' -#' @seealso \code{\link{convert2Tables}}, -#' \code{\link{generateDAG}} +#' +#' @seealso [convert2Tables()], +#' [generateDAG()] #' @export simulateSRS <- function(n_reports = 100, n_drugs = 10, @@ -81,35 +81,38 @@ simulateSRS <- function(n_reports = 100, valid_reports = TRUE, seed = NULL, verbose = TRUE) { - + # set the seed --- if (!is.null(seed)) { set.seed(seed) } + # Silence global variable NOTE (could use globalVariables() if need be) + margprob <- NULL + n <- n_drugs + n_events - sr <- matrix(NA, nrow = n_reports, ncol = n) # matrix that will contain the reports - + sr <- matrix(NA, nrow = n_reports, ncol = n) # matrix that will contain the reports + beta <- log(theta) # coefficient for the logistic model given the desired OR, theta - + # generate the DAG --- - + if (verbose) { cat("Creating DAG...\n") } - - DAG <- SRSim::generateDAG( + + DAG <- generateDAG( n_drugs = n_drugs, n_events = n_events, n_innocent_bystanders = n_innocent_bystanders, n_correlated_pairs = n_correlated_pairs ) - + if (verbose) { cat("DONE Creating DAG...\n") } drug_labels <- sprintf("drug%d", 1:n_drugs) event_labels <- sprintf("event%d", 1:n_events) - + # a data frame that contains all the data for each node (or variate) - nodes <- dplyr::tibble( + nodes <- tibble::tibble( label = c(drug_labels, event_labels), in_degree = igraph::degree(DAG, mode = "in"), id = 1:n, @@ -120,46 +123,46 @@ simulateSRS <- function(n_reports = 100, ), beta0 = log(margprob / (1 - margprob)), beta1 = 0 - ) - + ) + # create a tibble with all the edges edgelist <- igraph::as_edgelist(DAG) - edges <- tibble( - from = edgelist[,1], + edges <- tibble::tibble( + from = edgelist[,1], to = edgelist[,2] ) - + # walk through the edges and add the information to the nodes tibble for (i in 1:nrow(edges)) { - from <- edges[i,]$from - to <- edges[i,]$to - + from <- edges[i,]$from + to <- edges[i,]$to + # add the parent to the nodes tibble nodes[nodes$id == to,]$parent_id <- from - + # add the appropriate beta value for this edge - if (to <= n_drugs) { # a drug + if (to <= n_drugs) { # a drug no_bystander_prob <- rbeta(1, alpha_drugs, beta_drugs) nodes[nodes$id == to,]$beta0 <- log(no_bystander_prob / (1 - no_bystander_prob)) nodes[nodes$id == to,]$beta1 <- log(bystander_prob / (1 - bystander_prob)) - log(no_bystander_prob / (1 - no_bystander_prob)) - + # recompute the marginal probability margprob_parent <- nodes[nodes$id == from, ]$margprob nodes[nodes$id == to, ]$margprob <- margprob_parent*bystander_prob + (1 - margprob_parent)*no_bystander_prob } else { # an event - # determine beta1 - if (length(theta) == 1) { + # determine beta1 + if (length(theta) == 1) { nodes[nodes$id == to,]$beta1 <- log(theta) } else { - nodes[nodes$id == to,]$beta1 <- log(max(1, rnorm(1, theta[1], theta[2]))) + nodes[nodes$id == to,]$beta1 <- log(max(1, rnorm(1, theta[1], theta[2]))) } } } - + # determine the beta0's (the intercepts) for the events for (i in (n_drugs + 1):n) { node <- nodes[i,] @@ -179,16 +182,16 @@ simulateSRS <- function(n_reports = 100, nodes[i, ]$beta0 <- res$par } } - - nodes$in_degree <- as.integer(nodes$in_degree) - nodes$parent_id <- as.integer(nodes$parent_id) - # generating the actual reports - if (verbose) { + nodes$in_degree <- as.integer(nodes$in_degree) + nodes$parent_id <- as.integer(nodes$parent_id) + + # generating the actual reports + if (verbose) { pb <- txtProgressBar(min = 0, max = n_reports, initial = 0, char = "=", style = 3, file = "") } - + n_reports_generated <- 0 while (n_reports_generated <= n_reports) { report <- @@ -200,9 +203,9 @@ simulateSRS <- function(n_reports = 100, nodes$beta1, nodes$parent_id ) - + if (valid_reports) { - # check whether the report is valid + # check whether the report is valid if (validReport(t(matrix(report == 1)), n_drugs, n_events)) { sr[n_reports_generated,] <- report n_reports_generated <- n_reports_generated + 1 @@ -211,13 +214,13 @@ simulateSRS <- function(n_reports = 100, sr[n_reports_generated,] <- report n_reports_generated <- n_reports_generated + 1 } - + if (verbose) { setTxtProgressBar(pb, n_reports_generated) } } - - sr <- as_tibble(sr) + colnames(sr) <- c(sprintf("drug%d", 1:n_drugs), sprintf("event%d", 1:n_events)) - + sr <- tibble::as_tibble(sr) + return( list( sr = sr, diff --git a/R/zzz.R b/R/zzz.R deleted file mode 100644 index 0ca9a8b..0000000 --- a/R/zzz.R +++ /dev/null @@ -1,12 +0,0 @@ -#' SRSim -#' -#' A package for simulating data from spontaneous reporting systems (SRSs). -#' Spontaneous reporting systems are used to -#' -#' @docType package -#' @author Louis Dijkstra & Marco Garling -#' @import Rcpp RcppArmadillo dplyr tidyr corpcor -#' @useDynLib SRSim -#' @name SRSim -NULL - diff --git a/README.md b/README.md index 266c1f7..3df2d8d 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ # Simulating Spontaneous Reporting Systems (SRSim) + +[![R-CMD-check](https://github.com/bips-hb/srsim/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bips-hb/srsim/actions/workflows/R-CMD-check.yaml) + + Spontaneous reporting systems are used in the field of pharmacovigilance to detect (previously unknown) associations between drugs and adverse events (AEs). This `R` package allows for simulating large spontaneous reporting data sets. See https://srs.bips.eu/ for an example on how this simulator could be used. ### Installation diff --git a/man/SRSim-package.Rd b/man/SRSim-package.Rd new file mode 100644 index 0000000..f11dc00 --- /dev/null +++ b/man/SRSim-package.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/SRSim-package.R +\docType{package} +\name{SRSim-package} +\alias{SRSim} +\alias{SRSim-package} +\title{SRSim: Spontaneous Reporting Simulator (SRSim)} +\description{ +A package for simulating spontaneous reporting data as used in the field of pharmacovigilance. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/bips-hb/srsim} + \item Report bugs at \url{https://github.com/bips-hb/srsim/issues} +} + +} +\author{ +Louis Dijkstra & Marco Garling +} +\keyword{internal} diff --git a/man/SRSim.Rd b/man/SRSim.Rd deleted file mode 100644 index f8d1f48..0000000 --- a/man/SRSim.Rd +++ /dev/null @@ -1,14 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/zzz.R -\docType{package} -\name{SRSim} -\alias{SRSim} -\alias{SRSim-package} -\title{SRSim} -\description{ -A package for simulating data from spontaneous reporting systems (SRSs). -Spontaneous reporting systems are used to -} -\author{ -Louis Dijkstra & Marco Garling -} diff --git a/man/convert2Tables.Rd b/man/convert2Tables.Rd index a498df9..dfa86b1 100644 --- a/man/convert2Tables.Rd +++ b/man/convert2Tables.Rd @@ -7,37 +7,37 @@ convert2Tables(sr) } \arguments{ -\item{sr}{The output generated by the \code{\link{simulateSRS}} function} +\item{sr}{The output generated by the \code{\link[=simulateSRS]{simulateSRS()}} function} } \value{ A data frame where each row represents a 2 x 2 table. The columns represent: - \item{\code{drug_id}}{The ID of the drug} - \item{\code{event_id}}{The ID of the event} - \item{\code{prob_drug}}{The marginal probability of that drug} - \item{\code{prob_event}}{The marginal probability of that event} - \item{\code{or}}{The increase of the odds ratio when the drug is on the report} - \item{\code{associated}}{\code{TRUE} is there is a non-zero correlation, \code{FALSE} otherwise} - \item{\code{a}}{Number of times the drug and event appeared together in a report} - \item{\code{b}}{Number of times the event appeared without the drug in a report} - \item{\code{c}}{Number of times the drug appeared without the event in a report} - \item{\code{d}}{Number of times the drug and event both did not appear in a report} +\item{\code{drug_id}}{The ID of the drug} +\item{\code{event_id}}{The ID of the event} +\item{\code{prob_drug}}{The marginal probability of that drug} +\item{\code{prob_event}}{The marginal probability of that event} +\item{\code{or}}{The increase of the odds ratio when the drug is on the report} +\item{\code{associated}}{\code{TRUE} is there is a non-zero correlation, \code{FALSE} otherwise} +\item{\code{a}}{Number of times the drug and event appeared together in a report} +\item{\code{b}}{Number of times the event appeared without the drug in a report} +\item{\code{c}}{Number of times the drug appeared without the event in a report} +\item{\code{d}}{Number of times the drug and event both did not appear in a report} } \description{ Creates a data frame with all 2 x 2 contigency tables given a simulated data set from \code{simulateSRS}. The tables are organized as follows: \tabular{lccc}{ - \tab event \eqn{j} \tab not event \eqn{j} \tab \emph{total}\cr - drug \eqn{i} \tab \code{a} \tab \code{c} \tab \code{a} + \code{c}\cr - not drug \eqn{i} \tab \code{b} \tab \code{d} \tab \code{b} + \code{d}\cr - \emph{total} \tab \code{a} + \code{b} \tab \code{c} + \code{d} \tab \code{n_reports} +\tab event \eqn{j} \tab not event \eqn{j} \tab \emph{total}\cr +drug \eqn{i} \tab \code{a} \tab \code{c} \tab \code{a} + \code{c}\cr +not drug \eqn{i} \tab \code{b} \tab \code{d} \tab \code{b} + \code{d}\cr +\emph{total} \tab \code{a} + \code{b} \tab \code{c} + \code{d} \tab \code{n_reports} } } \examples{ -sr <- simulateSRS() -tables <- create2x2Tables(sr) +sr <- simulateSRS(verbose = FALSE) +tables <- convert2Tables(sr) } \seealso{ -\code{\link{simulateSRS}} +\code{\link[=simulateSRS]{simulateSRS()}} } diff --git a/man/create2x2TablesDAGRcpp.Rd b/man/create2x2TablesDAGRcpp.Rd index 5e941d5..048895c 100644 --- a/man/create2x2TablesDAGRcpp.Rd +++ b/man/create2x2TablesDAGRcpp.Rd @@ -4,8 +4,14 @@ \alias{create2x2TablesDAGRcpp} \title{Create 2 x 2 Tables} \usage{ -create2x2TablesDAGRcpp(reports, prob_drugs, prob_events, n_parents, parent_id, - beta1) +create2x2TablesDAGRcpp( + reports, + prob_drugs, + prob_events, + n_parents, + parent_id, + beta1 +) } \arguments{ \item{reports}{A binary matrix. Each row is a report} @@ -22,11 +28,11 @@ create2x2TablesDAGRcpp(reports, prob_drugs, prob_events, n_parents, parent_id, } \value{ A dataframe. A description of the columns can be found in the commentary - for the function \code{\link{convert2Tables}} +for the function \code{\link{convert2Tables}} } \description{ -Creates a data frame containing all 2 x 2 contingency tables -from the results generated by \code{\link{simulateSRS}}. +Creates a data frame containing all 2 x 2 contingency tables +from the results generated by \code{\link{simulateSRS}}. See the R wrapper function \code{\link{convert2Tables}} for more information. } diff --git a/man/f_beta0.Rd b/man/f_beta0.Rd index fde998a..9ac0ce7 100644 --- a/man/f_beta0.Rd +++ b/man/f_beta0.Rd @@ -16,10 +16,10 @@ f_beta0(beta0, margprob, beta1, margprob_parent) \item{margprob_parent}{The marginal probability of the parent} } \value{ -The absolute difference between the desired marginal probability - and the current marginal probability +The absolute difference between the desired marginal probability +and the current marginal probability } \description{ -\code{f_beta0} is used by \code{\link{simulateSRS}} to find the appropriate +\code{f_beta0} is used by \code{\link[=simulateSRS]{simulateSRS()}} to find the appropriate intercept for a logistic regression model. } diff --git a/man/generateDAG.Rd b/man/generateDAG.Rd index 9b71b79..9fc5df0 100644 --- a/man/generateDAG.Rd +++ b/man/generateDAG.Rd @@ -4,8 +4,12 @@ \alias{generateDAG} \title{Directed Acyclic Graph for SR Data} \usage{ -generateDAG(n_drugs = 10, n_events = 10, n_innocent_bystanders = 5, - n_correlated_pairs = 2) +generateDAG( + n_drugs = 10, + n_events = 10, + n_innocent_bystanders = 5, + n_correlated_pairs = 2 +) } \arguments{ \item{n_drugs}{Number of drugs (Default: 10)} @@ -24,5 +28,5 @@ The DAG as an \code{igraph} object spontaneous reporting data } \seealso{ -\code{\link{simulateSRS}} +\code{\link[=simulateSRS]{simulateSRS()}} } diff --git a/man/simulateReport.Rd b/man/simulateReport.Rd index 1f96c1a..7b5f204 100644 --- a/man/simulateReport.Rd +++ b/man/simulateReport.Rd @@ -23,7 +23,7 @@ simulateReport(n_drugs, n_events, n_parents, beta0, beta1, parent_id) A binary vector } \description{ -Returns a single report for a spontaneous reporting system. -Note that this function does not check whether the report is +Returns a single report for a spontaneous reporting system. +Note that this function does not check whether the report is 'valid', see \code{\link{validReport}} } diff --git a/man/simulateSRS.Rd b/man/simulateSRS.Rd index 679151c..a96a506 100644 --- a/man/simulateSRS.Rd +++ b/man/simulateSRS.Rd @@ -4,10 +4,22 @@ \alias{simulateSRS} \title{Simulating a Spontaneous Reporting System} \usage{ -simulateSRS(n_reports = 100, n_drugs = 10, n_events = 10, - alpha_drugs = 1, beta_drugs = 20, alpha_events = 1, beta_events = 20, - n_innocent_bystanders = 5, bystander_prob = 0.9, n_correlated_pairs = 2, - theta = 2, valid_reports = TRUE, seed = NULL, verbose = TRUE) +simulateSRS( + n_reports = 100, + n_drugs = 10, + n_events = 10, + alpha_drugs = 1, + beta_drugs = 20, + alpha_events = 1, + beta_events = 20, + n_innocent_bystanders = 5, + bystander_prob = 0.9, + n_correlated_pairs = 2, + theta = 2, + valid_reports = TRUE, + seed = NULL, + verbose = TRUE +) } \arguments{ \item{n_reports}{Number of reports (Default: 100)} @@ -26,17 +38,17 @@ simulateSRS(n_reports = 100, n_drugs = 10, n_events = 10, \item{n_innocent_bystanders}{Number of innocent bystanders (Default: 5)} -\item{bystander_prob}{The conditional probability of the innocent bystander being one when +\item{bystander_prob}{The conditional probability of the innocent bystander being one when the drug that is actually causing the AE is equal to 1. This parameter corresponds to \eqn{\gamma} in the paper (Default: .9)} \item{n_correlated_pairs}{Number of drug-AE pairs that are associated (Default: 2)} \item{theta}{Increase in odds-ratio when there is an edge going from a drug to an AE (Default: 2.0). -In case theta is a vector of length two, the odds ratio is drawn from a truncated +In case theta is a vector of length two, the odds ratio is drawn from a truncated Normal distribution with mean \code{theta[1]} and variance \code{theta[2]}} -\item{valid_reports}{If \code{TRUE}, only valid reports (with at least one drug and at least one AE) +\item{valid_reports}{If \code{TRUE}, only valid reports (with at least one drug and at least one AE) are accepted. (Default: \code{TRUE})} \item{seed}{The seed used by the RNG (Default: automatically set)} @@ -44,51 +56,51 @@ are accepted. (Default: \code{TRUE})} \item{verbose}{Verbosity (Default: \code{TRUE})} } \value{ -\item{sr}{A binary data frame with the simulated reports. The columns are - named \code{drug1}, \code{drug2} ..., \code{event1}, \code{event2}, ...} - \item{dag}{The directed acycled graph as an \code{igraph} object} - \item{nodes}{A tibble with all the information on each node/variate: - \itemize{ - \item{\code{label}}{ The label for each node/variate} - \item{\code{in_degree}}{ The number of edges pointing to the node} - \item{\code{id}}{ The ID of each node (simple integer)} - \item{\code{parent_id}}{ The ID of the parent node - if any. Otherwise equal to \code{-1}} - \item{\code{margprob}}{ The marginal probability of the node/variate} - \item{\code{beta0}}{ The intercept in the logistic regression model for that node} - \item{\code{beta1}}{ The regression coefficient in the logistic regression model for the parent} - } - } - \item{prob_drugs}{A vector with marginal probabilities of the drugs} - \item{prob_events}{A vector with marginal probabilities of the events} +\item{sr}{A binary data frame with the simulated reports. The columns are +named \code{drug1}, \code{drug2} ..., \code{event1}, \code{event2}, ...} +\item{dag}{The directed acycled graph as an \code{igraph} object} +\item{nodes}{A tibble with all the information on each node/variate: +\itemize{ +\item{\code{label}}{ The label for each node/variate} +\item{\code{in_degree}}{ The number of edges pointing to the node} +\item{\code{id}}{ The ID of each node (simple integer)} +\item{\code{parent_id}}{ The ID of the parent node - if any. Otherwise equal to \code{-1}} +\item{\code{margprob}}{ The marginal probability of the node/variate} +\item{\code{beta0}}{ The intercept in the logistic regression model for that node} +\item{\code{beta1}}{ The regression coefficient in the logistic regression model for the parent} +} +} +\item{prob_drugs}{A vector with marginal probabilities of the drugs} +\item{prob_events}{A vector with marginal probabilities of the events} } \description{ \code{simulateSRS} simulates a spontaneous reporting (SR) data set. The relationships between -the drugs and the adverse events (AEs) are specified by a directed acyclic graph (DAG), -see \code{\link{generateDAG}}. +the drugs and the adverse events (AEs) are specified by a directed acyclic graph (DAG), +see \code{\link[=generateDAG]{generateDAG()}}. \cr\cr -Each report to a SRS contains two lists: +Each report to a SRS contains two lists: \enumerate{ - \item the drugs to which the patient was (thought to be) exposed to, and - \item the AEs that the patient experienced. +\item the drugs to which the patient was (thought to be) exposed to, and +\item the AEs that the patient experienced. } -We will represent each report as a binary vector. The first items represent whether -the patient was exposed to the drug (\code{1} if he/she was, and \code{0} otherwise). -The second part represents whether the patient experienced the event or not -(\code{1} if he/she did, and \code{0} otherwise). For example, if there are 3 drugs and -4 events in total, a typical report could be -\deqn{0 1 0 1 1 0 0} -which represents that the patient was exposed to drug 2 (but not to drug 1 and 3), and +We will represent each report as a binary vector. The first items represent whether +the patient was exposed to the drug (\code{1} if he/she was, and \code{0} otherwise). +The second part represents whether the patient experienced the event or not +(\code{1} if he/she did, and \code{0} otherwise). For example, if there are 3 drugs and +4 events in total, a typical report could be +\deqn{0 1 0 1 1 0 0} +which represents that the patient was exposed to drug 2 (but not to drug 1 and 3), and experienced event 1 and 2 (but not 3 and 4). The simulation results in a binary matrix -where each row is a report. +where each row is a report. \cr\cr -\strong{Valid Reports} Not any binary sequence is a valid report. Each report -should contain at least one drug and at least one event (otherwise it would -never been sent to the spontaneous reporitng sytem). +\strong{Valid Reports} Not any binary sequence is a valid report. Each report +should contain at least one drug and at least one event (otherwise it would +never been sent to the spontaneous reporitng sytem). While generating reports, we make sure that this is indeed the case. When one does not -want to check the validity and wants to allow any binary sequence, one can set +want to check the validity and wants to allow any binary sequence, one can set \code{valid_reports} to \code{FALSE}. } \seealso{ -\code{\link{convert2Tables}}, - \code{\link{generateDAG}} +\code{\link[=convert2Tables]{convert2Tables()}}, +\code{\link[=generateDAG]{generateDAG()}} } diff --git a/man/validReport.Rd b/man/validReport.Rd index fac4732..cc4883c 100644 --- a/man/validReport.Rd +++ b/man/validReport.Rd @@ -18,6 +18,6 @@ validReport(report, n_drugs, n_events) } \description{ Checks whether the given report is 'valid'. A report should contain at least -one drug and at least one event (otherwise it would never been sent to the +one drug and at least one event (otherwise it would never been sent to the spontaneous reporitng sytem anyway). } diff --git a/src/Makevars b/src/Makevars deleted file mode 100644 index 814bae0..0000000 --- a/src/Makevars +++ /dev/null @@ -1,15 +0,0 @@ - -## With R 3.1.0 or later, you can uncomment the following line to tell R to -## enable compilation with C++11 (where available) -## -## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider -## availability of the package we do not yet enforce this here. It is however -## recommended for client packages to set it. -## -## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP -## support within Armadillo prefers / requires it -CXX_STD = CXX11 - -#PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -#PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -#PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) diff --git a/src/Makevars.win b/src/Makevars.win deleted file mode 100644 index 814bae0..0000000 --- a/src/Makevars.win +++ /dev/null @@ -1,15 +0,0 @@ - -## With R 3.1.0 or later, you can uncomment the following line to tell R to -## enable compilation with C++11 (where available) -## -## Also, OpenMP support in Armadillo prefers C++11 support. However, for wider -## availability of the package we do not yet enforce this here. It is however -## recommended for client packages to set it. -## -## And with R 3.4.0, and RcppArmadillo 0.7.960.*, we turn C++11 on as OpenMP -## support within Armadillo prefers / requires it -CXX_STD = CXX11 - -#PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) -#PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) -#PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index fe9b5f6..63f00f1 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -6,6 +6,11 @@ using namespace Rcpp; +#ifdef RCPP_USE_GLOBAL_ROSTREAM +Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get(); +Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(); +#endif + // validReport bool validReport(Rcpp::LogicalMatrix report, int n_drugs, int n_events); RcppExport SEXP _SRSim_validReport(SEXP reportSEXP, SEXP n_drugsSEXP, SEXP n_eventsSEXP) {