Initial commit

Author: BodoKirsch

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+dev_history.R
+^dev$
+$run_dev.*
+^LICENSE\.md$

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

BIC-megaplot.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes

CODEOWNERS

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+# @BodoKirsch and @stjeske will be requested for
+# review when someone opens a pull request.
+*       @BodoKirsch @stjeske

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies
+when an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [INSERT CONTACT
+METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/
+code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://
+www.contributor-covenant.org/translations.

CONTRIBUTING.md

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+# Contribution Guidelines
+
+## Pull requests are always welcome
+
+We're trying very hard to keep our systems simple, lean and focused. We don't want them to be everything for everybody. This means that we might decide
+against incorporating a new request.
+
+
+## Create issues...
+
+Any significant change should be documented as a GitHub issue before anybody starts working on it.
+
+
+### ...but check for existing issues first!
+
+Please take a moment to check that an issue doesn't already exist documenting your request. If it does, it never hurts to add a quick "+1" or "I need this too". This will help prioritize the most common requests.
+
+
+## Conventions
+
+Fork the repository and make changes on your fork on a branch:
+
+1. Create the right type of issue (defect, enhancement, test, etc)
+2. Name the branch N-something where N is the number of the issue.
+
+Note that the maintainers work on branches in this repository.
+
+Work hard to ensure your pull request is valid. This includes code quality, clear naming, and including unit tests. Please read the Code Of Conduct at the bottom of this file.
+
+Pull request descriptions should be as clear as possible and include a reference to all the issues that they address. In GitHub, you can reference an
+issue by adding a line to your commit description that follows the format:
+
+  `Fixes #N`
+
+where N is the issue number.
+
+
+## Merge approval
+
+Repository maintainers will review the pull request and make sure it provides the appropriate level of code quality & correctness. 
+
+
+
+## How are decisions made?
+
+Short answer: with pull requests to this repository.
+
+All decisions, big and small, follow the same 3 steps:
+
+1. Open a pull request. Anyone can do this.
+
+2. Discuss the pull request. Anyone can do this.
+
+3. Accept or refuse a pull request. The relevant maintainers do this (see below "Who decides what?")
+
+   1. Accepting pull requests
+
+      1. If the pull request appears to be ready to merge, approve it.
+
+      2. If the pull request has some small problems that need to be changed, make a comment addressing the issues.
+
+      3. If the changes needed to a PR are small, you can add a "LGTM once the following comments are addressed..." this will reduce needless back and forth.
+
+      4. If the PR only needs a few changes before being merged, any MAINTAINER can make a replacement PR that incorporates the existing commits and fixes the problems before a fast track merge.
+
+   2. Closing pull requests
+
+      1. If a PR appears to be abandoned, after having attempted to contact the original contributor, then a replacement PR may be made. Once the replacement PR is made, any contributor may close the original one.
+
+      2. If you are not sure if the pull request implements a good feature or you do not understand the purpose of the PR, ask the contributor to provide more documentation. If the contributor is not able to adequately explain the purpose of the PR, the PR may be closed by any MAINTAINER.
+
+      3. If a MAINTAINER feels that the pull request is sufficiently architecturally flawed, or if the pull request needs significantly more design discussion before being considered, the MAINTAINER should close the pull request with a short explanation of what discussion still needs to be had. It is important not to leave such pull requests open, as this will waste both the MAINTAINER's time and the contributor's time. It is not good to string a contributor on for weeks or months, having them make many changes to a PR that will eventually be rejected.
+
+
+## Who decides what?
+
+All decisions are pull requests, and the relevant maintainers make decisions by accepting or refusing pull requests. Review and acceptance by anyone is
+denoted by adding a comment in the pull request: `LGTM`. However, only currently listed `MAINTAINERS` are counted towards the required majority.
+
+The maintainers will be listed in the MAINTAINER file, all these people will be in the employment of Bayer.
+
+
+## I'm a maintainer, should I make pull requests too?
+
+Yes. Nobody should ever push to master directly. All changes should be made through a pull request.
+
+## Code Of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant, version 1.0.0, available at https://www.contributor-covenant.org/version/1/0/0/code-of-conduct.html

DESCRIPTION

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+Package: megaplots
+Title: A 'shiny' Application for Pattern Detection
+Version: 1.1.2
+Authors@R: c(
+    person("Madhurima", "Majumder", role = "aut"),
+    person("Susanne", "Lippert", role = "aut"),
+    person("Bastian", "Becker", role = "aut"),
+    person("Steffen", "Jeske", , "[email protected]", role = c("cre", "aut")),
+    person("Svenja", "Jedhoff", role = "aut"),
+    person("Silke", "Janitza", role = "aut"),
+    person("Hermann", "Kulmann", role = "aut")
+  )
+Description: Depicts individual study courses per day.  Pre-specified
+    events on certain days, for example drug intake, efficacy, or safety
+    events, are indicated by different symbols.  The detection of patterns
+    in the data or the temporal connection of study procedures and outcome
+    events is supported by several functions, such as sorting, grouping,
+    and changing the complexity of the graphical display.
+License: GPL (>= 3)
+Depends: 
+    R (>= 3.5.0)
+Imports: 
+    colourpicker,
+    config,
+    dplyr,
+    DT,
+    golem,
+    graphics,
+    plyr,
+    RColorBrewer,
+    reshape2,
+    rlang,
+    seriation,
+    shiny,
+    shinycssloaders,
+    shinydashboard,
+    shinyjqui,
+    shinyjs,
+    shinyWidgets,
+    stats,
+    stringr,
+    magrittr,
+    tidyr,
+    TraMineR,
+    utils
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.2.3
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3