enforce factor labels in vignette; add CoC

.Rbuildignore

@@ -9,3 +9,5 @@
 ^joss-review-notes\.md$
 ^reviewer-response\.md$
 ^cran-comments\.md$
+^CONTRIBUTING\.md$
+^CODE_OF_CONDUCT\.md$

.travis.yml

@@ -1,10 +1,7 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
 # Use default Ubuntu
-sudo: required
-
 language: R
-sudo: true
 cache: packages
 warnings_are_errors: true
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+Code of Conduct
+====================================
+
+This code of conduct applies to participation in this GitHub repository.
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project contributors are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project contributors 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, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This code of conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project contributors.
+
+## Enforcement
+
+If a contributor engages in harassing behaviour, the repository contributors may take any action they deem appropriate, including warning the offender or expelling them from online forums, online project resources, face-to-face meetings, or any other project-related activity or resource.
+
+If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact a member of the project team immediately.  Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team.  All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances.  The project team is obligated to maintain confidentiality with regard to the reporter of an incident.  Further details of specific enforcement policies may be posted separately.
+
+## Attribution
+
+This Code of Conduct was borrowed from [Combine-Org](https://github.com/combine-org/Community-guidelines/blob/master/CODE_OF_CONDUCT.md) which was adapted from Portions of this Code of Conduct were adapted from Electron's [Contributor Covenant Code of Conduct](https://github.com/electron/electron/blob/master/CODE_OF_CONDUCT.md), which itself was adapted from the [Contributor Covenant](http://contributor-covenant.org/version/1/4), version 1.4.

CONTRIBUTING.md

@@ -0,0 +1,39 @@
+# Guidelines for contributing to this project
+
+Any constructive contributions – bug reports, pull requests (code or documentation), suggestions for improvements, and more – are welcome.
+
+## Discussions
+
+Discussion is welcome by creating a new issue [in this repository](https://github.com/trashbirdecology/bbsassistant/issues).
+
+## Conduct
+
+Everyone is asked to read and respect the [code of conduct](https://github.com/trashbirdecology/bbsassistant/CODE_OF_CONDUCT.md) before participating directly in this project.
+
+## How to contribute text, edits, and other materials
+
+### Using GitHub (doesn't require knowing Git)
+
+1. Fork the repository
+1. Click the link for one of the files
+1. Click the **Edit** button, then make some edits
+1. Add a commit summary and (optionally) an extended description
+1. Click the **Commit Changes** button
+1. Create a pull request by clicking the **Pull Request** button at the top of the main page of your copy of the repository
+
+### Using Git
+
+1. Fork the repository, for example to https://github.com/YOUR-GITHUB-ACCOUNT/bbsassistant
+1. Clone your fork locally
+1. Create a branch to hold your changes (`git checkout -b my-changes`)
+1. Commit the changes you've made (`git commit -am "Some descriptive text around what you've added"`)
+1. Push your branch to GitHub (`git push origin my-changes`)
+1. Create a pull request, for example at https://github.com/YOUR-GITHUB-ACCOUNT/bbsassistant/pull/new/master
+
+## License
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)
+
+## Acknowledgments
+
+This file was adapted from which was adapted from [Combine-Org](https://raw.githubusercontent.com/combine-org/Community-guidelines/master/CONTRIBUTING.md) the [code4lib anti-harassment policy repository](https://github.com/code4lib/code-of-conduct) on GitHub.  Their content is licensed under CC0.  Subsequent modifications were made by COMBINE members as indicated in the GitHub commit history.

vignettes/using_rucrdtw.Rmd

@@ -123,9 +123,14 @@ benchmarks <- rbenchmark::benchmark(
   ucrdtw_5000 = ucrdtw_vv(rwalk, query, 0.05),
   replications = 5)
 
+#ensure benchmark test column is of type factor for compatibility with r-devel
+benchmarks$test <- as.factor(benchmarks$test)
+
 colors <- rep(c("#33a02c","#1f78b4"), each=3)
-plot(log10(benchmarks$elapsed*200) ~ benchmarks$test, cex.axis=0.7, las = 2, yaxt = "n", xlab = "", ylab = "execution time [ms]", ylim = c(0,5), medcol = colors, staplecol=colors, boxcol=colors)
-axis(2, at = c(0:4), labels = 10^(0:4), cex.axis = 0.7)
+
+#plot with log1p transformed axes, as some execution times may be numerically zero
+plot(log1p(benchmarks$elapsed*200) ~ benchmarks$test, cex.axis=0.7, las = 2, yaxt = "n", xlab = "", ylab = "execution time [ms]", ylim = c(0,10), medcol = colors, staplecol=colors, boxcol=colors)
+axis(2, at = log1p(c(1,10,100,1000,10000)), labels = c(1,10,100,1000,10000), cex.axis = 0.7)
 legend("topright", legend = c("naive DTW", "UCR DTW"), fill = c("#33a02c","#1f78b4"), bty="n")
 }
 ```