Merge pull request #20 from inbo/rename

Rename package

.Rbuildignore

@@ -1,2 +1,11 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^README\.Rmd$
+^README-.*\.png$
+^\.travis\.yml$
+^appveyor\.yml$
+^docs$
+^_pkgdown\.yml$
+^CODE_OF_CONDUCT\.md$
+^CONTRIBUTING\.md$
+.github/

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,25 @@
+# Contributor 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 
+(http://contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

.github/CONTRIBUTING.md

@@ -0,0 +1,84 @@
+# Contributing to uvabits
+
+First of all, thanks for considering contributing to uvabits! 👍 It's people like you that make it rewarding for us - the project maintainers - to work on uvabits. 😊
+
+uvabits is an open source project, maintained by people who care. We are not directly funded to do so.
+
+[repo]: https://github.com/inbo/uvabits
+[issues]: https://github.com/inbo/uvabits/issues
+[new_issue]: https://github.com/inbo/uvabits/issues/new
+[website]: https://inbo.github.io/uvabits
+[citation]: https://inbo.github.io/uvabits/authors.html
+[email]: mailto:peter.desmet@inbo.be
+
+## Code of conduct
+
+Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.
+
+## How you can contribute
+
+There are several ways you can contribute to this project. If you want to know more about why and how to contribute to open source projects like this one, see this [Open Source Guide](https://opensource.guide/how-to-contribute/).
+
+### Share the love ❤️
+
+Think uvabits is useful? Let others discover it, by telling them in person, via Twitter or a blog post.
+
+Using uvabits for a paper you are writing? Consider [citing it][citation].
+
+### Ask a question ⁉️
+
+Using uvabits and got stuck? Browse the [documentation][website] to see if you can find a solution. Still stuck? Post your question as an [issue on GitHub][new_issue]. While we cannot offer user support, we'll try to do our best to address it, as questions often lead to better documentation or the discovery of bugs.
+
+Want to ask a question in private? Contact the package maintainer by [email][email].
+
+### Propose an idea 💡
+
+Have an idea for a new uvabits feature? Take a look at the [documentation][website] and [issue list][issues] to see if it isn't included or suggested yet. If not, suggest your idea as an [issue on GitHub][new_issue]. While we can't promise to implement your idea, it helps to:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible.
+
+See below if you want to contribute code for your idea as well.
+
+### Report a bug 🐛
+
+Using uvabits and discovered a bug? That's annoying! Don't let others have the same experience and report it as an [issue on GitHub][new_issue] so we can fix it. A good bug report makes it easier for us to do so, so please include:
+
+* Your operating system name and version (e.g. Mac OS 10.13.6).
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Improve the documentation 📖
+
+Noticed a typo on the website? Think a function could use a better example? Good documentation makes all the difference, so your help to improve it is very welcome!
+
+#### The website
+
+[This website][website] is generated with [`pkgdown`](http://pkgdown.r-lib.org/). That means we don't have to write any html: content is pulled together from documentation in the code, vignettes, [Markdown](https://guides.github.com/features/mastering-markdown/) files, the package `DESCRIPTION` and `_pkgdown.yml` settings. If you know your way around `pkgdown`, you can [propose a file change](https://help.github.com/articles/editing-files-in-another-user-s-repository/) to improve documentation. If not, [report an issue][new_issue] and we can point you in the right direction.
+
+#### Function documentation
+
+Functions are described as comments near their code and translated to documentation using [`roxygen2`](https://klutometis.github.io/roxygen/). If you want to improve a function description:
+
+1. Go to `R/` directory in the [code repository][repo].
+2. Look for the file with the name of the function.
+3. [Propose a file change](https://help.github.com/articles/editing-files-in-another-user-s-repository/) to update the function documentation in the roxygen comments (starting with `#'`).
+
+### Contribute code 📝
+
+Care to fix bugs or implement new functionality for uvabits? Awesome! 👏 Have a look at the [issue list][issues] and leave a comment on the things you want to work on. See also the development guidelines below.
+
+## Development guidelines
+
+We try to follow the [GitHub flow](https://guides.github.com/introduction/flow/) for development.
+
+1. Fork [this repo][repo] and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/).
+2. If you have forked and cloned the project before and it has been a while since you worked on it, [pull changes from the original repo](https://help.github.com/articles/merging-an-upstream-repository-into-your-fork/) to your clone by using `git pull upstream master`.
+3. Open the RStudio project file (`.Rproj`).
+5. Make your changes:
+    * Write your code.
+    * Test your code (bonus points for adding unit tests).
+    * Document your code (see function documentation above).
+    * Do an `R CMD check` using `devtools::check()` and aim for 0 errors and warnings.
+5. Commit and push your changes.
+6. Submit a [pull request](https://guides.github.com/activities/forking/#making-a-pull-request).

.gitignore

@@ -1,10 +1,40 @@
-.Rproj.user
-*.Rproj
+# History files
 .Rhistory
+.Rapp.history
+
+# Session Data files
 .RData
-inst/doc
-UvaBitsWarehouse.Rproj
-*.Rproj
-instal*.R
-vignettes/performance-optimisation_cache
-draft/
+
+# 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/
+.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
+
+# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
+rsconnect/
+
+# Mac OS X
+.DS_Store

DESCRIPTION

@@ -1,28 +1,36 @@
-Package: BirdTrackingEtl
-Type: Package
-Title: Bird tracking ETL
-Version: 1.0
-Date: 2015-11-09
-Author: Bart Aelterman, <bart.aelterman@inbo.be>
-Maintainer: Bart Aelterman, <bart.aelterman@inbo.be>
-Description: Extract, Transform and Load procedures for cleaning, enriching
-	and loading bird tracking data into a query-optimized data store.
-	This package is only intended to work with data generated by the UvA-BiTS
-	(http://www.uva-bits.nl/) system and requires you to have set up a data store
-	in advance (only tested using SQLite)
-License: MIT (https://tldrlegal.com/license/mit-license)
-Encoding: UTF-8
-Depends: R (>= 3.2.0)
+Package: uvabits
+Title: Download Bird Tracking Data from UvA-BiTS
+Version: 0.1.0.9000
+Description: The uvabits package provides an R interface to the UvA-BiTS 
+    database (http://www.uva-bits.nl/), which stores bird movement data 
+    collected with UvA-BiTS GPS trackers. The package provides functionality to 
+    download data and metadata, calculate some metrics, and load the data into a 
+    query-optimized SQLite database for local analysis. It also allows to 
+    download the data in a format that can easily be uploaded to Movebank 
+    (https://www.movebank.org/), a free online database for animal tracking 
+    data.
+Authors@R: c(
+    person("Bart", "Aelterman", role = c("aut", "cre"), email = "bart.aelterman@inbo.be"),
+    person("Peter", "Desmet", role = "aut", email = "peter.desmet@inbo.be", comment = c(ORCID = "0000-0002-8442-8025")),
+    person("Stijn", "Van Hoey", role = "aut", email = "stijn.vanhoey@inbo.be", comment = c(ORCID = "0000-0001-6413-3185"))
+    )
+License: MIT + file LICENSE
+URL: https://github.com/inbo/uvabits, https://inbo.github.io/uvabits
+BugReports: https://github.com/inbo/uvabits/issues
+Depends:
+    R (>= 3.2.0)
 Imports: 
-	lubridate (== 1.5.6),
-	DBI (== 0.3.1),
-	data.table (== 1.9.6),
-	geosphere (== 1.3.13),
-	maptools (== 0.8.36),
-	sp (== 1.1.1),
-	raster (== 2.4.18)
-Suggests: testthat (== 1.0.1),
-    knitr (== 1.11),
-VignetteBuilder: knitr
+    data.table (>= 1.9.6),
+    DBI (>= 0.3.1),
+    geosphere (>= 1.3.13),
+    lubridate (>= 1.5.6),
+    maptools (>= 0.8.36),
+    raster (>= 2.4.18),
+    sp (>= 1.1.1)
+Suggests:
+    knitr (>= 1.11),
+    testthat (>= 1.0.1)
 LazyData: true
-URL: https://github.com/inbo/bird-tracking-etl
+Encoding: UTF-8
+VignetteBuilder: knitr
+RoxygenNote: 6.1.1

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2015 Research Institute for Nature and Forest (INBO)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(add_dist_to_colony)
 export(add_dist_travelled)

README.md

@@ -1,27 +1,27 @@
-# UvA-BiTS ETL
+# uvabits
 
-## Background
+> ✋ This package is not ready for use! It was previously called `BirdTrackingEtl` and used exclusively to process UvA-BiTS data for INBO researchers (see [release](https://github.com/inbo/uvabits/releases/tag/bt-etl) and [vignette](vignettes/bird-tracking-etl.Rmd) for that version). We are now expanding its functionality for more general use by UvA-BiTS users. Want to contribute? Check out our [contributing guidelines](.github/CONTRIBUTING.md).
 
-At [the Research Institute for Nature and Forest](http://www.inbo.be), we're tracking large birds as part of [our LifeWatch contribution](http://lifewatch.inbo.be). We are using small solar-powered GPS devices, developed by [UvA-BiTS](http://www.uva-bits.nl). The data are stored in the UvA-BiTS virtual lab and we frequently get a dump from that database on which we work. As tracking data volume grows quicker than human observation data (what we usually work with), we were in need for a data store that contains the cleaned and enriched tracking data in a system that is optimized for querying these *large-ish* data sets. Something like a data warehouse. This R package contains code to extract the data from the UvA-BiTS virtual lab, clean and enrich it, and load it in the data warehouse.
+uvabits provides an R interface to the [UvA-BiTS database](http://www.uva-bits.nl/), which stores bird movement data collected with UvA-BiTS GPS trackers. The package provides functionality to download data and metadata, calculate some metrics, and load the data into a  query-optimized SQLite database for local analysis. It also allows to download the data in a format that can easily be uploaded to [Movebank](https://www.movebank.org/), a free online database for animal tracking data.
 
-## Install the package
+## Installation
 
-The package is not on CRAN. If you want to use it, download a copy of the code here, and [install it from source](http://stackoverflow.com/questions/1474081/how-do-i-install-an-r-package-from-source). You need a few third party packages, as documented in the package [DESCRIPTION](./DESCRIPTION). R should take care of that. If not, install `lubridate`, `data.table`, `geosphere`, `sp` and `DBI`. If you want to run the tests, you'll need `testthat` too.
-
-## Run the tests
-
-Tests are written using [testthat](https://github.com/hadley/testthat). Run the tests in RStudio by opening the package main directory and pressing CTRL/CMD + SHIFT + T.
-
-## Load the package
+You can install uvabits from [GitHub](https://github.com/inbo/uvabits) with:
 
-```
-library(BirdTrackingEtl)
+```r
+# install.packages("devtools")
+devtools::install_github("inbo/uvabits")
 ```
 
-## How to use the package
+Then load the package with:
 
-This is explained in the package [vignette](./vignettes/bird-tracking-etl.Rmd).
+```r
+library(uvabits)
+```
 
-## Get in touch
+## Meta
 
-Should you encounter issues while using this package, get in touch by [filing an issue](https://github.com/LifeWatchINBO/bird-tracking-etl/issues).
+* We welcome [contributions](.github/CONTRIBUTING.md) including bug reports.
+* License: MIT
+* Get citation information for `uvabits` in R doing `citation("uvabits")`.
+* Please note that this project is released with a [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.