From 9430dd13a25dc9a761ffbde3770a6a76b3e04555 Mon Sep 17 00:00:00 2001 From: Shu Fai Cheung Date: Sat, 1 Jun 2024 19:33:51 +0800 Subject: [PATCH 1/2] Initial commit --- .Rbuildignore | 4 + .github/.gitignore | 1 + .github/workflows/R-CMD-check.yaml | 55 ++ .gitignore | 98 +- .lintr | 3 + DESCRIPTION | 22 + LICENSE | 1348 ++++++++++++++-------------- LICENSE.md | 595 ++++++++++++ NAMESPACE | 2 + NEWS.md | 3 + README.md | 42 +- tests/testthat.R | 12 + 12 files changed, 1460 insertions(+), 725 deletions(-) create mode 100644 .Rbuildignore create mode 100644 .github/.gitignore create mode 100644 .github/workflows/R-CMD-check.yaml create mode 100644 .lintr create mode 100644 DESCRIPTION create mode 100644 LICENSE.md create mode 100644 NAMESPACE create mode 100644 NEWS.md create mode 100644 tests/testthat.R diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..5bbb26f --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,4 @@ +^LICENSE\.md$ +^\.github$ +^LICENSE +^\.lintr \ No newline at end of file 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..5b8da6c --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,55 @@ +# 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 + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.special }} + + 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'} + - {os: ubuntu-latest, r: 'release', nosuggests: true, special: "No Suggests"} + + env: + _R_CHECK_DEPENDS_ONLY_: ${{ matrix.config.nosuggests }} + _R_CHECK_DEPENDS_ONLY_VIGNETTES_: false + 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, any::XML + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.gitignore b/.gitignore index e75435c..5de9431 100644 --- a/.gitignore +++ b/.gitignore @@ -1,49 +1,49 @@ -# History files -.Rhistory -.Rapp.history - -# Session Data files -.RData -.RDataTmp - -# User-specific files -.Ruserdata - -# Example code in package build process -*-Ex.R - -# Output files from R CMD build -/*.tar.gz - -# Output files from R CMD check -/*.Rcheck/ - -# RStudio files -.Rproj.user/ - -# produced vignettes -vignettes/*.html -vignettes/*.pdf - -# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 -.httr-oauth - -# knitr and R markdown default cache directories -*_cache/ -/cache/ - -# Temporary files created by R markdown -*.utf8.md -*.knit.md - -# R Environment Variables -.Renviron - -# pkgdown site -docs/ - -# translation temp files -po/*~ - -# RStudio Connect folder -rsconnect/ +# History files +.Rhistory +.Rapp.history + +# Session Data files +.RData +.RDataTmp + +# User-specific files +.Ruserdata + +# Example code in package build process +*-Ex.R + +# Output files from R CMD build +/*.tar.gz + +# Output files from R CMD check +/*.Rcheck/ + +# RStudio files +.Rproj.user/ + +# produced vignettes +vignettes/*.html +vignettes/*.pdf + +# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 +.httr-oauth + +# knitr and R markdown default cache directories +*_cache/ +/cache/ + +# Temporary files created by R markdown +*.utf8.md +*.knit.md + +# R Environment Variables +.Renviron + +# pkgdown site +docs/ + +# translation temp files +po/*~ + +# RStudio Connect folder +rsconnect/ diff --git a/.lintr b/.lintr new file mode 100644 index 0000000..331fd9a --- /dev/null +++ b/.lintr @@ -0,0 +1,3 @@ +linters: linters_with_defaults( + indentation_linter = NULL + ) diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..9b29217 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,22 @@ +Package: betaselectr +Title: Selective Standardization in Structural Equation Models +Version: 0.0.0.9000 +Authors@R: + c(person(given = "Shu Fai", + family = "Cheung", + role = c("aut", "cre"), + email = "shufai.cheung@gmail.com", + comment = c(ORCID = "0000-0002-9871-9448"))) +Description: It computes Beta_Select, standardization in + structural equation models with only selected variables + standardized. It supports models with moderation, as well + as regression models. It can form confidence intervals + that takes into account the standardization appropriately. +License: GPL (>= 3) +Encoding: UTF-8 +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.1 +Suggests: + testthat (>= 3.0.0) +Config/testthat/edition: 3 +Config/testthat/parallel: true diff --git a/LICENSE b/LICENSE index f288702..3877ae0 100644 --- a/LICENSE +++ b/LICENSE @@ -1,674 +1,674 @@ - 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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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/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..2e4c51a --- /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. 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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. 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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 new file mode 100644 index 0000000..50b77c0 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,2 @@ +# Generated by roxygen2: do not edit by hand + diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..1ae01d0 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,3 @@ +# betaselectr 0.0.0.9000 + +Initial commit. diff --git a/README.md b/README.md index 62108eb..0555efa 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,40 @@ -# betaselectr -Do selective standardization in structural equation models and regression models + + +[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) +[![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) +[![Code size](https://img.shields.io/github/languages/code-size/sfcheung/betaselectr.svg)](https://github.com/sfcheung/betaselectr) +[![Last Commit at Main](https://img.shields.io/github/last-commit/sfcheung/betaselectr.svg)](https://github.com/sfcheung/betaselectr/commits/main) +[![R-CMD-check](https://github.com/sfcheung/betaselectr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sfcheung/betaselectr/actions/workflows/R-CMD-check.yaml) + + +**IMPORTANT**: It is a work-in-progress. +Not ready for use. + +# betaselectr: Do selective standardization in structural equation models and regression models + +(Version 0.0.0.9000, updated on 2024-06-01, [release history](https://sfcheung.github.io/betaselectr/news/index.html)) + +It computes Beta_Select, standardization +in structural equation models with only +selected variables standardized. It +supports models with moderation, as well +as regression models. It can form +confidence intervals that takes into +account the standardization +appropriately. + +For more information on this package, +please visit its GitHub page: + +https://sfcheung.github.io/betaselectr/ + +# Installation + +**DO NOT INSTALL**: It is a +work-in-progress. Not ready for use. + +# Issues + +If you have any suggestions and found +any bugs, please feel feel to open a +GitHub issue. Thanks. diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..18be1c3 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(betaselectr) + +test_check("betaselectr") From 19901066187b816910e88cb1198c7014573deb85 Mon Sep 17 00:00:00 2001 From: Shu Fai Cheung Date: Sat, 1 Jun 2024 19:40:24 +0800 Subject: [PATCH 2/2] Create test-holder.R --- tests/testthat/test-holder.R | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 tests/testthat/test-holder.R diff --git a/tests/testthat/test-holder.R b/tests/testthat/test-holder.R new file mode 100644 index 0000000..615ee4c --- /dev/null +++ b/tests/testthat/test-holder.R @@ -0,0 +1,3 @@ +test_that("multiplication works", { + expect_equal(2 * 2, 4) +})