├── .gitignore ├── .nojekyll ├── GM.jpg ├── README.html ├── README.md ├── SierraMadreAptRegulations.pdf ├── _site.yml ├── before.Rmd ├── before.html ├── gulf.jpg ├── index.Rmd ├── index.html ├── lessons.Rmd ├── lessons.html ├── nceas.png ├── oss-2017.Rproj ├── reading.html ├── readings.Rmd ├── readings.html ├── schedule.Rmd ├── schedule.html ├── schedule ├── wk1.csv ├── wk2.csv └── wk3.csv ├── site_libs ├── bootstrap-3.3.5 │ ├── css │ │ ├── bootstrap-theme.css │ │ ├── bootstrap-theme.css.map │ │ ├── bootstrap-theme.min.css │ │ ├── bootstrap.css │ │ ├── bootstrap.css.map │ │ ├── bootstrap.min.css │ │ ├── cerulean.min.css │ │ ├── cosmo.min.css │ │ ├── flatly.min.css │ │ ├── fonts │ │ │ ├── Lato.ttf │ │ │ ├── LatoBold.ttf │ │ │ ├── LatoItalic.ttf │ │ │ ├── NewsCycle.ttf │ │ │ ├── NewsCycleBold.ttf │ │ │ ├── OpenSans.ttf │ │ │ ├── OpenSansBold.ttf │ │ │ ├── OpenSansBoldItalic.ttf │ │ │ ├── OpenSansItalic.ttf │ │ │ ├── OpenSansLight.ttf │ │ │ ├── OpenSansLightItalic.ttf │ │ │ ├── Raleway.ttf │ │ │ ├── RalewayBold.ttf │ │ │ ├── Roboto.ttf │ │ │ ├── RobotoBold.ttf │ │ │ ├── RobotoLight.ttf │ │ │ ├── RobotoMedium.ttf │ │ │ ├── SourceSansPro.ttf │ │ │ ├── SourceSansProBold.ttf │ │ │ ├── SourceSansProItalic.ttf │ │ │ ├── SourceSansProLight.ttf │ │ │ └── Ubuntu.ttf │ │ ├── journal.min.css │ │ ├── lumen.min.css │ │ ├── paper.min.css │ │ ├── readable.min.css │ │ ├── sandstone.min.css │ │ ├── simplex.min.css │ │ ├── spacelab.min.css │ │ ├── united.min.css │ │ └── yeti.min.css │ ├── fonts │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.svg │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 │ ├── js │ │ ├── bootstrap.js │ │ ├── bootstrap.min.js │ │ └── npm.js │ └── shim │ │ ├── html5shiv.min.js │ │ └── respond.min.js ├── highlightjs-1.1 │ ├── default.css │ ├── highlight.js │ └── textmate.css ├── jquery-1.11.3 │ └── jquery.min.js └── navigation-1.1 │ ├── FileSaver.min.js │ ├── codefolding.js │ ├── sourceembed.js │ └── tabsets.js ├── wk1.Rmd ├── wk1.html ├── wk2.Rmd ├── wk2.html ├── wk3.Rmd └── wk3.html /.gitignore: -------------------------------------------------------------------------------- 1 | #OSX 2 | *.DS_Store 3 | .AppleDouble 4 | .LSOverride 5 | 6 | 7 | #R stuffs 8 | .Rproj.user 9 | .Rhistory 10 | .RData 11 | .Ruserdata 12 | -------------------------------------------------------------------------------- /.nojekyll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NCEAS/oss-2017/39d9f873d5e2b50bcdd5834aca4a71ccc6f4641c/.nojekyll -------------------------------------------------------------------------------- /GM.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NCEAS/oss-2017/39d9f873d5e2b50bcdd5834aca4a71ccc6f4641c/GM.jpg -------------------------------------------------------------------------------- /README.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 207 | 208 | 209 |
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Open Science for Synthesis 2017: Gulf Research Program

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Open Science for Synthesis: Gulf Research Program is a hands-on data science course for both early career and established researchers to gain skills in data science, including scientific synthesis, reproducible science, and data management. These skills are critical for understanding the complex environmental, human, and energy systems in the Gulf of Mexico, especially following large disturbance events like the Deepwater Horizon oil spill in 2010. This 3-week intensive training, convening in July 2017 at the National Center for Ecological Analysis and Synthesis (NCEAS) in Santa Barbara, CA, will revolve around scientific computing and scientific software for reproducible science. Funding for the program is through a grant from the Gulf Research Program of the National Academies of Science.

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218 | 219 | 231 | 232 | 233 | 241 | 242 | 243 | 244 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Open Science for Synthesis 2017: Gulf Research Program 2 | 3 | [Open Science for Synthesis: Gulf Research Program](https://www.nceas.ucsb.edu/OSS2017) is a hands-on data science course for both early 4 | career and established researchers to gain skills in data science, including scientific synthesis, reproducible science, and 5 | data management. These skills are critical for understanding the complex environmental, human, and energy systems in the Gulf of Mexico, 6 | especially following large disturbance events like the Deepwater Horizon oil spill in 2010. This 3-week intensive training, convening in 7 | July 2017 at the [National Center for Ecological Analysis and Synthesis (NCEAS)](https://www.nceas.ucsb.edu) in Santa Barbara, CA, will 8 | revolve around scientific computing and scientific software for reproducible science. Funding for the program is through a grant from the 9 | [Gulf Research Program](http://www.nationalacademies.org/gulf/about/) of the National Academies of Science. 10 | -------------------------------------------------------------------------------- /SierraMadreAptRegulations.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NCEAS/oss-2017/39d9f873d5e2b50bcdd5834aca4a71ccc6f4641c/SierraMadreAptRegulations.pdf -------------------------------------------------------------------------------- /_site.yml: -------------------------------------------------------------------------------- 1 | name: "OSS-2017" 2 | navbar: 3 | title: "OSS-2017" 4 | left: 5 | - text: "home" 6 | href: index.html 7 | - text: "schedule" 8 | href: schedule.html 9 | - text: "lessons" 10 | href: lessons.html 11 | - text: "readings" 12 | href: readings.html 13 | - text: "logistics" 14 | href: before.html 15 | output_dir: "." 16 | output: 17 | html_document: 18 | theme: yeti -------------------------------------------------------------------------------- /before.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Before you arrive" 3 | output: html_document 4 | draft: true 5 | --- 6 | 7 | ## Travel & Logistics 8 | 9 | ### Upon Arrival in Santa Barbara 10 | 11 | Sierra Madre Apartments provides a shuttle service to/from Santa Barbara Airport or the Santa Barbara Airbus Goleta Station. The shuttle operates between 7am and 10pm. Call the Sierra Madre front desk at 805-893-8001 upon arrival for shuttle pick-up. For arrival by other means (e.g. train) or outside of these hours, you will need to take a taxi/lyft/uber. 12 | 13 | ### Lodging Information 14 | 15 | #### Address: 16 | 17 | Sierra Madre Apartments, University of California, Santa Barbara, 555 Storke Road (cross street is Sierra Madre Ct.), Isla Vista, CA 93117 (http://www.conferences.ucsb.edu/sierra-madre-villages) 18 | 19 | There will be a check in table on July 9th, from 10.30am - 4.00pm in the apartment courtyard where you can pick up keys to access your apartment. If needed, Sierra Madre Office hours are 10:30 am - 4 pm and located at Laguna Village apartment 1104. (Proceed down the walkway and look for check-in signs to the left--across from the Administration building). 20 | If you arrive outside these hours, please call 805-893-8001 ahead of time. A staff member is available 24 hours to meet you. 21 | 22 | Apartments are equipped with plates, bowls, cutlery, bedding and towels. Towels are replaced daily and housekeeping is weekly. Cooking pots/pans and utensils are being provided by NCEAS and will in the apartments upon arrival. 23 | 24 | Please note that Sierra Madre Apartments are non-smoking. The full regulations can be reviewed [here](https://github.com/NCEAS/oss-2017/blob/gh-pages/SierraMadreAptRegulations.pdf). 25 | 26 | ### Daily Transportation to/from NCEAS from Sierra Madre Apartments 27 | 28 | All participants will be given a “30-day unlimited ride” bus pass to use while in Santa Barbara. A representative from NCEAS will meet you at the Sierra Madre Apartments on the first day of the training to give you your bus pass and ride the bus with you to NCEAS. Please meet in the courtyard of the Sierra Madre Apartment Complex at 7:00 am on Monday, July 10. The 24X bus picks up in front of the Sierra Madre Apartments on Storke Road and drops off at the Downtown Transit Center, which is three blocks from NCEAS. It is roughly a 20-minute ride. The complete bus schedule can be found here: http://sbmtd.gov/maps-and-schedules/system-map.html 29 | 30 | ### Workshop Location: 31 | 32 | National Center for Ecological Analysis and Synthesis, 735 State Street Suite 300, Santa Barbara, CA 93101 33 | 34 | ### Meals 35 | 36 | NCEAS will provide snacks and lunch Monday through Friday during the training. You will be responsible for coordinating your own breakfast and dinner and will receive a meal allowance to offset these costs. There are numerous restaurants and grocery stores close to NCEAS and to your apartments in Isla Vista. 37 | 38 | 39 | ## Computer hardware 40 | 41 | You will be using a laptop on a daily basis. Because you will be doing most (if not all) of your work by connecting to a server and not directly on your computer (more on this at the workshop), it's not especially important that you bring a high-powered laptop. A relatively recent (2010 or later) laptop should suffice: 42 | 43 | - Minimum recommended specs: 44 | - Processor: 2.00 GHz or higher 45 | - Memory (RAM): 4 GB or more 46 | - Storage: Ideally, you're hard drive should not be full. You should have at least 10GB of free space. 47 | - Operating system: Windows (7+), Mac OS X / macOS (all versions), Linux/BSD (any) 48 | - Administrator access: You shouldn't have to install any/much software for the workshop but you may want to. Therefore, we recommend you have sufficient privileges to install software on the laptop you bring but we also realize this may not be possibe for some users. 49 | 50 | ***If your computer is below these specifications or you have any questions, please contact us via Slack on the [#OSS](https://nceas.slack.com/messages/C4UHC7K17) channel***. ([get an invite](http://slack.nceas.ucsb.edu)). 51 | 52 | 53 | ## Software 54 | 55 | You will be doing most of your work by connecting to server that already has all of the required software installed (more on this at the workshop) but please make sure you have the following programs installed before you arrive: 56 | 57 | ### Web browser: 58 | 59 | - Your choice, but a recent version of Chrome or Firefox is preferred 60 | 61 | ### Code editor: 62 | 63 | If you already have something you like, feel free to use that code editor. Popular code editors include: 64 | 65 | - Sublime Text 66 | - Notepad++ 67 | - Atom 68 | - Visual Studio Code 69 | - Emacs 70 | - vi(m) 71 | 72 | If you don't know if you have a code editor or know you don't have one, we recommend downloading [Atom](https://atom.io). 73 | 74 | ### Version control - git (and git bash): 75 | 76 | Please install git on your system: https://git-scm.com/downloads and follow the instructions. 77 | 78 | - Windows - you can set the options to default during the installation, until you reach `Configuring the terminal emulator to use with Git Bash` -> be sure `Use MinTTY` is selected. This will install both git and a set of useful command-line tools using a trimmed down Bash shell. 79 | - Mac OSX - depending your OS version, you might have to run few commands from the terminal. Please refer to the `README.txt` that comes with the download regarding the exact steps to follow. 80 | 81 | ### QGIS: 82 | 83 | If you are facing trouble during the installation or prefer to do it at NCEAS, we are happy to assist you as the GIS session will be held in the second week of the workshop. You can download the installer here: 84 | 85 | - Windows: https://www.qgis.org/en/site/forusers/download.html and follow the installation wizzard 86 | - macOS: http://www.kyngchaos.com/software/qgis ; *Be sure to follow the order of installation of the different components*. 87 | 88 | Note: You do not need to install Python separately when installing QGIS. 89 | 90 | ### R: 91 | 92 | We recommend you install the latest version of [R](https://cloud.r-project.org/) on your machine. If you have any reason to want to keep R to a previous version, it is fine as most of the work will be done on a remote server 93 | 94 | ### RStudio: 95 | 96 | We recommend you install the latest free version of [RStudio Desktop](https://www.rstudio.com/products/rstudio/download2/) on your machine. If you have any reason to want to keep RStudio to a previous version, it is fine as most of the work will be done on a remote server 97 | 98 | 99 | ***If you run into any problems or having any questions, please let us know in [#OSS](https://nceas.slack.com/messages/C4UHC7K17)*** ([get an invite](http://slack.nceas.ucsb.edu)). 100 | -------------------------------------------------------------------------------- /before.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | Before you arrive 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 208 | 209 | 210 |
211 |

Travel & Logistics

212 |
213 |

Upon Arrival in Santa Barbara

214 |

Sierra Madre Apartments provides a shuttle service to/from Santa Barbara Airport or the Santa Barbara Airbus Goleta Station. The shuttle operates between 7am and 10pm. Call the Sierra Madre front desk at 805-893-8001 upon arrival for shuttle pick-up. For arrival by other means (e.g. train) or outside of these hours, you will need to take a taxi/lyft/uber.

215 |
216 |
217 |

Lodging Information

218 |
219 |

Address:

220 |

Sierra Madre Apartments, University of California, Santa Barbara, 555 Storke Road (cross street is Sierra Madre Ct.), Isla Vista, CA 93117 (http://www.conferences.ucsb.edu/sierra-madre-villages)

221 |

There will be a check in table on July 9th, from 10.30am - 4.00pm in the apartment courtyard where you can pick up keys to access your apartment. If needed, Sierra Madre Office hours are 10:30 am - 4 pm and located at Laguna Village apartment 1104. (Proceed down the walkway and look for check-in signs to the left–across from the Administration building). If you arrive outside these hours, please call 805-893-8001 ahead of time. A staff member is available 24 hours to meet you.

222 |

Apartments are equipped with plates, bowls, cutlery, bedding and towels. Towels are replaced daily and housekeeping is weekly. Cooking pots/pans and utensils are being provided by NCEAS and will in the apartments upon arrival.

223 |

Please note that Sierra Madre Apartments are non-smoking. The full regulations can be reviewed here.

224 |
225 |
226 |
227 |

Daily Transportation to/from NCEAS from Sierra Madre Apartments

228 |

All participants will be given a “30-day unlimited ride” bus pass to use while in Santa Barbara. A representative from NCEAS will meet you at the Sierra Madre Apartments on the first day of the training to give you your bus pass and ride the bus with you to NCEAS. Please meet in the courtyard of the Sierra Madre Apartment Complex at 7:00 am on Monday, July 10. The 24X bus picks up in front of the Sierra Madre Apartments on Storke Road and drops off at the Downtown Transit Center, which is three blocks from NCEAS. It is roughly a 20-minute ride. The complete bus schedule can be found here: http://sbmtd.gov/maps-and-schedules/system-map.html

229 |
230 |
231 |

Workshop Location:

232 |

National Center for Ecological Analysis and Synthesis, 735 State Street Suite 300, Santa Barbara, CA 93101

233 |
234 |
235 |

Meals

236 |

NCEAS will provide snacks and lunch Monday through Friday during the training. You will be responsible for coordinating your own breakfast and dinner and will receive a meal allowance to offset these costs. There are numerous restaurants and grocery stores close to NCEAS and to your apartments in Isla Vista.

237 |
238 |
239 |
240 |

Computer hardware

241 |

You will be using a laptop on a daily basis. Because you will be doing most (if not all) of your work by connecting to a server and not directly on your computer (more on this at the workshop), it’s not especially important that you bring a high-powered laptop. A relatively recent (2010 or later) laptop should suffice:

242 | 252 |

If your computer is below these specifications or you have any questions, please contact us via Slack on the #OSS channel. (get an invite).

253 |
254 |
255 |

Software

256 |

You will be doing most of your work by connecting to server that already has all of the required software installed (more on this at the workshop) but please make sure you have the following programs installed before you arrive:

257 |
258 |

Web browser:

259 |
    260 |
  • Your choice, but a recent version of Chrome or Firefox is preferred
    • 261 |
262 |
263 |
264 |

Code editor:

265 |

If you already have something you like, feel free to use that code editor. Popular code editors include:

266 |
    267 |
  • Sublime Text
    • 268 |
  • Notepad++
    • 269 |
  • Atom
    • 270 |
  • Visual Studio Code
    • 271 |
  • Emacs
    • 272 |

  • vi(m)

    273 |

    If you don’t know if you have a code editor or know you don’t have one, we recommend downloading Atom.

    • 274 |
275 |
276 |
277 |

Version control - git (and git bash):

278 |

Please install git on your system: https://git-scm.com/downloads and follow the instructions.

279 |
    280 |
  • Windows - you can set the options to default during the installation, until you reach Configuring the terminal emulator to use with Git Bash -> be sure Use MinTTY is selected. This will install both git and a set of useful command-line tools using a trimmed down Bash shell.
    281 |
    • 282 |
  • Mac OSX - depending your OS version, you might have to run few commands from the terminal. Please refer to the README.txt that comes with the download regarding the exact steps to follow.
    • 283 |
284 |
285 |
286 |

QGIS:

287 |

If you are facing trouble during the installation or prefer to do it at NCEAS, we are happy to assist you as the GIS session will be held in the second week of the workshop. You can download the installer here:

288 | 292 |

Note: You do not need to install Python separately when installing QGIS.

293 |
294 |
295 |

R:

296 |

We recommend you install the latest version of R on your machine. If you have any reason to want to keep R to a previous version, it is fine as most of the work will be done on a remote server

297 |
298 |
299 |

RStudio:

300 |

We recommend you install the latest free version of RStudio Desktop on your machine. If you have any reason to want to keep RStudio to a previous version, it is fine as most of the work will be done on a remote server

301 |

If you run into any problems or having any questions, please let us know in #OSS (get an invite).

302 |
303 |
304 | 305 | 306 | 307 | 308 |
309 | 310 | 322 | 323 | 324 | 332 | 333 | 334 | 335 | -------------------------------------------------------------------------------- /gulf.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NCEAS/oss-2017/39d9f873d5e2b50bcdd5834aca4a71ccc6f4641c/gulf.jpg -------------------------------------------------------------------------------- /index.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | output: html_document 4 | --- 5 |
6 | 7 | 8 | ![](./gulf.jpg) 9 | 10 |
11 | 12 | **Course overview** 13 | 14 | The primary goal of the Open Science for Synthesis: Gulf Research Program Workshop is to provide hands-on experience with contemporary open science tools from command line to data to communication. Team science is promoted. Practice and real data are used in groups to apply skills we explore. 15 | 16 | **Week 1.** Fundamental collaboration skills 17 | Introduction to command line, communicating science, R, meta-analysis and data management. 18 | 19 | **Week 2.** Advanced topics 20 | Tabular data, programming, Python, workflows, reproducible science and metagenomics. 21 | 22 | **Week 3.** Advanced topics & group projects 23 | Communication, geospatial analysis, data viz, and group project sharing. 24 | 25 | All participants detail listed [here](https://www.nceas.ucsb.edu/OSS2017). 26 | 27 | Discussion on [Slack OSS channel](https://nceas.slack.com/messages/C4UHC7K17). 28 | 29 | If you aren't already a member of the Slack team, you need to [invite yourself](http://slack.nceas.ucsb.edu/). 30 | 31 | 32 | -------------------------------------------------------------------------------- /index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 207 | 208 | 209 |


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211 | 212 | 213 |
214 |


215 |

Course overview

216 |

The primary goal of the Open Science for Synthesis: Gulf Research Program Workshop is to provide hands-on experience with contemporary open science tools from command line to data to communication. Team science is promoted. Practice and real data are used in groups to apply skills we explore.

217 |

Week 1. Fundamental collaboration skills
218 | Introduction to command line, communicating science, R, meta-analysis and data management.

219 |

Week 2. Advanced topics
220 | Tabular data, programming, Python, workflows, reproducible science and metagenomics.

221 |

Week 3. Advanced topics & group projects
222 | Communication, geospatial analysis, data viz, and group project sharing.

223 |

All participants detail listed here.

224 |

Discussion on Slack OSS channel.

225 |

If you aren’t already a member of the Slack team, you need to invite yourself.

226 | 227 | 228 | 229 | 230 |
231 | 232 | 244 | 245 | 246 | 254 | 255 | 256 | 257 | -------------------------------------------------------------------------------- /lessons.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | output: html_document 4 | --- 5 |
6 | 7 | ## **Lessons** 8 | 9 | [All lessons provided by NCEAS and collaborators here on GitHub.](https://github.com/NCEAS/oss-lessons) 10 | 11 |
12 | 13 | ## **Lessons by Day** 14 | 15 |
16 | 17 | ### Day 1: Mon Jul 10 18 | - [Course Overview](https://nceas.github.io/oss-lessons/course-overview/course-overview.html#/) 19 | - [Networks and Servers](https://nceas.github.io/oss-lessons/servers-networks-command-line/1-servers-net.html) 20 | - [Unix Command Line](https://nceas.github.io/oss-lessons/servers-networks-command-line/2-commandline-intro.html) 21 | - [Thinking Preferences](https://nceas.github.io/oss-lessons/thinking-preferences/thinking-preferences.html#/) 22 | - [R Markdown and R studio](https://github.com/NCEAS/oss-lessons/blob/gh-pages/rmarkdown-rstudio/rmarkdown-rstudio.Rmd) 23 | 24 | ### Day 2: Tue Jul 11 25 | - [Version control: git basics](https://nceas.github.io/oss-lessons/version-control/1-git-basics.html) 26 | - [Version control: remote collaboration with git and GitHub](https://nceas.github.io/oss-lessons/version-control/2-git-remote-collaboration.html) 27 | - [Version control: branches and merge conflicts](https://nceas.github.io/oss-lessons/version-control/3-git-advanced.html) 28 | - [Version control: Rstudio and git](https://nceas.github.io/oss-lessons/version-control/4-getting-started-with-git-in-RStudio.html) 29 | - [The message box](https://nceas.github.io/oss-lessons/message-box/message-box.html#/) 30 | 31 | ### Day 3: Wed Jul 12 32 | - [Unix tools](https://nceas.github.io/oss-lessons/servers-networks-command-line/2-commandline-intro.html) 33 | - [Bash shell scripts](https://nceas.github.io/oss-lessons/servers-networks-command-line/3-bash-loops.html) 34 | - [R Review & Assessment](https://nceas.github.io/oss-lessons/r-review-and-assessment/r-review-and-assessment.html) 35 | - [Data management and repositories](https://nceas.github.io/oss-lessons/data-repositories/data-repositories.html) 36 | - [Data publishing](https://nceas.github.io/oss-lessons/publishing-data/upload-data.html) 37 | 38 | ### Day 4: Thu Jul 13 39 | - [Ecological metadata](https://nceas.github.io/oss-lessons/ecological-metadata/ecological-metadata.html) 40 | - [Open data](https://nceas.github.io/oss-lessons/open-data-in-r/open-data-in-R.html) 41 | - [Data liberation - Web scraping](https://nceas.github.io/oss-lessons/data-liberation/intro-webscraping.html) 42 | - [Data liberation - Text mining](https://nceas.github.io/oss-lessons/data-liberation/intro-text-mining.html) 43 | - [Regular expressions](https://nceas.github.io/oss-lessons/regular-expressions/regular-expressions.html) 44 | 45 | ### Day 5: Fri Jul 14 46 | - Collaboration 47 | - [Facilitation techniques](https://nceas.github.io/oss-lessons/meeting-facilitation/meeting-facilitation.html#/) 48 | - [Data wrangling: Tidyverse](https://nceas.github.io/oss-lessons/data-wrangling/tidyverse.html) 49 | - Data Munging 50 | 51 | ### Day 6: Mon Jul 17 52 | - [Meta analysis intro](https://nceas.github.io/oss-lessons/meta-analysis/index.html) 53 | - [Meta analysis I](https://nceas.github.io/oss-lessons/meta-analysis/step1.html) 54 | - [Meta analysis II](https://nceas.github.io/oss-lessons/meta-analysis/step2.html) 55 | - [Meta analysis III](https://nceas.github.io/oss-lessons/meta-analysis/step3.html) 56 | - [Meta analysis IV](https://nceas.github.io/oss-lessons/meta-analysis/step4.html) 57 | - [Meta analysis V](https://nceas.github.io/oss-lessons/meta-analysis/step5.html) 58 | 59 | ### Day 7: Tue Jul 18 60 | - [Good enough data modeling](https://nceas.github.io/oss-lessons/sql-database/01-sql-database-intro.html) 61 | - [Start SQL with PostgresQL](https://nceas.github.io/oss-lessons/sql-database/02-sql-start.html) 62 | - [SQL and database access in R](https://nceas.github.io/oss-lessons/sql-database-access-in-r/sql-database-access-in-r.html) 63 | 64 | ### Day 8: Wed Jul 19 65 | - [Data wrangling](https://nceas.github.io/oss-lessons/data-munging-qa-qc-cleaning/data-munging-qa-qc-cleaning.html) 66 | - [Creating R Functions](https://nceas.github.io/oss-lessons/creating-r-functions/creating-r-functions.html) 67 | - [Creating R packages](https://nceas.github.io/oss-lessons/creating-r-packages/creating-r-packages.html) 68 | - Testing R code 69 | 70 | ### Day 9: Thu Jul 20 71 | 72 | - [Publishing Data](https://github.com/NCEAS/oss-lessons/tree/gh-pages/publishing-data) 73 | - [Reproducible Papers with RMarkdown](https://nceas.github.io/oss-lessons/reproducible-papers-with-rmd/reproducible-papers-with-rmd.html) 74 | 75 | 76 | ### Day 10: Fri Jul 21 77 | - [Metagenomics](https://nceas.github.io/oss-lessons/metagenomics/) 78 | 79 | ### Day 11: Mon Jul 24 80 | - GIS and geopspatial concepts 81 | - [Intro to spatial data concepts](https://nceas.github.io/oss-lessons/spatial-data-gis-law/1-mon-spatial-data-intro.html) 82 | - [QGIS - an open alternative to ArcGIS](https://nceas.github.io/oss-lessons/spatial-data-gis-law/2-mon-intro-to-open-gis-qgis.html) 83 | - [Plot & manage raster and vector data in R](https://nceas.github.io/oss-lessons/spatial-data-gis-law/3-mon-intro-gis-in-r.html) 84 | - [Publishing maps to the web in R](https://nceas.github.io/oss-lessons/publishing-maps-to-the-web-in-r/publishing-maps-to-the-web-in-r.html) 85 | - [Publication ready maps in R](https://github.com/NCEAS/oss-lessons/tree/gh-pages/publication-ready-maps-in-r) (R scripts examples) 86 | 87 | ### Day 12: Tue Jul 25 88 | - [Getting started with spatial analysis in R](https://nceas.github.io/oss-lessons/spatial-data-gis-law/4-tues-spatial-analysis-in-r.html) 89 | - [NetCDF and HDF5](https://nceas.github.io/oss-lessons/spatial-data-gis-law/5-tues-intro-hierarchical-formats.html) 90 | 91 | ### Day 13: Wed Jul 26 92 | - [Dataviz and Interactive Tools](https://nceas.github.io/oss-lessons/dataviz-and-interactive-tools/dataviz-and-interactive-tools.html) 93 | - [Submodule: ggplot2](https://nceas.github.io/oss-lessons/dataviz-and-interactive-tools/module-1-ggplot2.html) 94 | - [Submodule: Shiny](https://nceas.github.io/oss-lessons/dataviz-and-interactive-tools/module-2-shiny.html) 95 | - [Perfunctory Python](https://nceas.github.io/oss-lessons/why-python/python-the-why.html) 96 | 97 | ### Day 14: Thu Jul 27 98 | - [Parallel Computing in R](https://nceas.github.io/oss-lessons/parallel-computing-in-r/parallel-computing-in-r.html) 99 | - [Open Science](https://speakerdeck.com/cjlortie/open-science-and-the-spells-that-you-ought-to-know) 100 | 101 | ### Day 15: Fri Jul 28 102 | - Group Presentations 103 | 104 | -------------------------------------------------------------------------------- /lessons.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 41 | 42 | 43 | 44 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 97 | 98 | 99 | 132 | 133 | 150 | 151 | 152 |
153 | 154 | 155 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 202 | 203 | 209 | 210 | 211 |


212 |
213 |

Lessons

214 |

All lessons provided by NCEAS and collaborators here on GitHub.

215 |


216 |
217 |
218 |

Lessons by Day

219 |


220 |
221 |

Day 1: Mon Jul 10

222 | 229 |
230 | 240 |
241 |

Day 3: Wed Jul 12

242 | 249 |
250 |
251 |

Day 4: Thu Jul 13

252 | 259 |
260 |
261 |

Day 5: Fri Jul 14

262 | 268 |
269 |
270 |

Day 6: Mon Jul 17

271 | 279 |
280 |
281 |

Day 7: Tue Jul 18

282 | 287 |
288 |
289 |

Day 8: Wed Jul 19

290 | 296 |
297 |
298 |

Day 9: Thu Jul 20

299 | 303 |
304 |
305 |

Day 10: Fri Jul 21

306 | 309 |
310 |
311 |

Day 11: Mon Jul 24

312 | 322 |
323 |
324 |

Day 12: Tue Jul 25

325 | 329 |
330 |
331 |

Day 13: Wed Jul 26

332 | 340 |
341 |
342 |

Day 14: Thu Jul 27

343 | 347 |
348 |
349 |

Day 15: Fri Jul 28

350 |
    351 |
  • Group Presentations
    • 352 |
353 |
354 |
355 | 356 | 357 | 358 | 359 |
360 | 361 | 373 | 374 | 375 | 383 | 384 | 385 | 386 | -------------------------------------------------------------------------------- /nceas.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NCEAS/oss-2017/39d9f873d5e2b50bcdd5834aca4a71ccc6f4641c/nceas.png -------------------------------------------------------------------------------- /oss-2017.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | BuildType: Website 16 | -------------------------------------------------------------------------------- /reading.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 207 | 208 | 209 |


210 |
211 |

Readings

212 |

Day 1:

213 | 216 |

Day 2:

217 | 220 |
221 | 222 | 223 | 224 | 225 |
226 | 227 | 239 | 240 | 241 | 249 | 250 | 251 | 252 | -------------------------------------------------------------------------------- /readings.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | output: html_document 4 | --- 5 |
6 | 7 | ## **Readings** 8 | 9 | Day 1: 10 | 11 | - Hampton and Parker. 2011. Collaboration and Productivity in Scientific Synthesis. [Download PDF](https://github.com/NCEAS/oss-2014/raw/master/day-01/HamptonParker_BioSci_2011.pdf) 12 | 13 | Day 2: 14 | 15 | - Baron. Escape from the Ivory Tower. [Download PDF](https://github.com/NCEAS/oss-2014/raw/master/day-01/Baron_Escape_from_the_Ivory_Tower_Chap_8.pdf) 16 | - Compass. The Message Box Workbook. [Download PDF](https://docs.wixstatic.com/ugd/e58a91_26905f568b1f42b78ba712ac6bb9db65.pdf) 17 | 18 | Day 3: 19 | 20 | - [Some Simple Guidelines for Effective Data Management](http://matt.magisa.org/pubs/borer-esa-2009.pdf) 21 | 22 | 23 | Day 5: 24 | 25 | - [Data wrangling cheatsheet](https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf) 26 | 27 | - [tidyr](https://cran.r-project.org/web/packages/tidyr/README.html) 28 | 29 | - [dplyr 0.7.0 release notes](https://github.com/tidyverse/dplyr/releases/tag/v0.7.0) 30 | 31 | - [R for Open Science: Open Sesame](https://ojs.library.queensu.ca/index.php/IEE/article/view/6559) 32 | 33 | - [A review of R for Data Science](https://www.jstatsoft.org/article/view/v077b01) 34 | 35 | Day 6: 36 | 37 | - [How to read a meta-analysis](http://onlinelibrary.wiley.com/doi/10.1002/jrsm.1109/abstract) 38 | 39 | - [How to do a meta-analysis](http://onlinelibrary.wiley.com/wol1/doi/10.1348/000711010X502733/full) 40 | 41 | - [How to write your papers for others to use in meta-analyses](http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12758/full) 42 | 43 | Day 13: 44 | 45 | - [The Tao of open science for ecology](http://onlinelibrary.wiley.com/wol1/doi/10.1890/ES14-00402.1/abstract) 46 | 47 | - [Data reuse and the citation advantage](https://peerj.com/articles/175.pdf) -------------------------------------------------------------------------------- /readings.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 207 | 208 | 209 |


210 |
211 |

Readings

212 |

Day 1:

213 | 216 |

Day 2:

217 | 221 |

Day 3:

222 | 225 |

Day 5:

226 | 233 |

Day 6:

234 | 239 |

Day 13:

240 | 244 |
245 | 246 | 247 | 248 | 249 |
250 | 251 | 263 | 264 | 265 | 273 | 274 | 275 | 276 | -------------------------------------------------------------------------------- /schedule.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | output: html_document 4 | --- 5 | 6 | ```{r library loads, warnings = FALSE, message=FALSE, echo=FALSE} 7 | #library loads 8 | library(tidyverse) 9 | library(knitr) 10 | ``` 11 | 12 |
13 | 14 | ####**Week 1** 15 | ```{r wk1, warnings = FALSE, message=FALSE, echo=FALSE} 16 | #wk1 17 | wk1 <- read_csv("schedule/wk1.csv") 18 | kable(wk1) 19 | 20 | ``` 21 | 22 |
23 | 24 | ####**Week 2** 25 | ```{r wk2, warnings = FALSE, message=FALSE, echo=FALSE} 26 | #wk2 27 | wk2 <- read_csv("schedule/wk2.csv") 28 | kable(wk2) 29 | 30 | ``` 31 | 32 |
33 | 34 | ####**Week 3** 35 | ```{r wk3, warnings = FALSE, message=FALSE, echo=FALSE} 36 | #wk3 37 | wk3 <- read_csv("schedule/wk3.csv") 38 | kable(wk3) 39 | 40 | ``` 41 | 42 | -------------------------------------------------------------------------------- /schedule.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 207 | 208 | 209 |


210 |
211 |

Week 1

212 | 213 | 214 | 215 | 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 | 239 | 240 | 241 | 242 | 243 | 244 | 245 | 246 | 247 | 248 | 249 | 250 | 251 | 252 | 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 262 | 263 | 264 | 265 | 266 | 267 | 268 | 269 | 270 | 271 | 272 | 273 | 274 | 275 | 276 | 277 | 278 | 279 | 280 | 281 | 282 | 283 | 284 | 285 | 286 | 287 | 288 | 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 298 | 299 | 300 | 301 | 302 | 303 | 304 | 305 | 306 | 307 | 308 | 309 | 310 | 311 | 312 | 313 | 314 | 315 | 316 | 317 | 318 | 319 | 320 | 321 |
AgendaDay 1. Synthesis & UnixDay 2. Communication and Version ControlDay 3. Advanced Unix and Data toolsDay 4. Open Data and RDay 5. People and Data Wrangling
8:15-8:30Welcome (Jones, Budden)Feedback, questions, and discussionFeedback, questions, and discussionFeedback, questions, and discussionFeedback, questions, and discussion
8:30-9:00Participant intros; brief bio, project interests, goals for course (all)Activity: Version control, Git, Github, Git in RStudio (Brun)Advanced unix tools (awk, sed, iconv, etc.) (Jones)Ecological Metadata in R (Mecum)Social aspects of collaboration, high-performing groups, data policies (Budden and Jones)
9:00-9:30Course overview, discussion of expectations (Jones, Budden)Activity: Version control, Git, Github, Git in RStudio (Brun)Advanced unix tools (awk, sed, iconv, etc.) (Jones)Open data in R and ROpenSci (Mecum & Jones)Facilitating group discussions (Budden)
9:30-9:45BreakBreakBreakBreakBreak
9:45-11:00Intro to servers, networks, and the unix command line (Jones)Activity: Version control, Git, Github, Git in RStudio (Brun)Bash shell scripts (Jones)Data liberation (scraping, text mining) (Brun)Introduction to tidyverse wrangling (Lortie)
11:00-12:00Thinking preferences activity (Budden)Activity: Version control, Git, Github, Git in RStudio (Brun)R Review/ Assessment (Mecum)Data liberation (scraping, text mining) (Brun)Tutorial and exercises wrangling to filter, sort, and merge (Lortie)
Noon-1:00LunchLunchLunchLunchLunch
1:00-1:30R Markdown & Rstudio setup (Mecum)Communications: The message box (Budden)Data Management & Scientific data repositories (Budden)Regular expressions (Mecum)Data munging, QA/QC, cleaning (Mecum)
1:30-2:00R Markdown & Rstudio setup (Mecum)Group work on message box (Budden)Publishing Data in R (Jones)Message box 2: Group exchange and feedback (Budden)Data munging, QA/QC, cleaning (Mecum)
2:00-2:15BreakBreakBreakBreakBreak
2:15-5:00Pre-Assessment (Budden) and Synthesis Groups (Jones)Synthesis GroupsSynthesis GroupsSynthesis GroupsSynthesis Groups
5:00-5:15Peanut GalleryPeanut GalleryPeanut GalleryPeanut GalleryPeanut Gallery
322 |


323 |
324 |
325 |

Week 2

326 | 327 | 328 | 329 | 330 | 331 | 332 | 333 | 334 | 335 | 336 | 337 | 338 | 339 | 340 | 341 | 342 | 343 | 344 | 345 | 346 | 347 | 348 | 349 | 350 | 351 | 352 | 353 | 354 | 355 | 356 | 357 | 358 | 359 | 360 | 361 | 362 | 363 | 364 | 365 | 366 | 367 | 368 | 369 | 370 | 371 | 372 | 373 | 374 | 375 | 376 | 377 | 378 | 379 | 380 | 381 | 382 | 383 | 384 | 385 | 386 | 387 | 388 | 389 | 390 | 391 | 392 | 393 | 394 | 395 | 396 | 397 | 398 | 399 | 400 | 401 | 402 | 403 | 404 | 405 | 406 | 407 | 408 | 409 | 410 | 411 | 412 | 413 | 414 | 415 | 416 | 417 | 418 | 419 | 420 | 421 | 422 | 423 | 424 | 425 | 426 | 427 | 428 | 429 | 430 | 431 | 432 | 433 | 434 | 435 |
AgendaDay 6. Open Meta-analysisDay 7. Tabular DataDay 8. Programming and WorkflowsDay 9. Reproducible researchDay 10. Metagenomics
8:15-8:30Feedback, questions, and discussionFeedback, questions, and discussionMid-term assessmentFeedback, questions, and discussionFeedback, questions, and discussion
8:30-9:00Metas and systematic reviews (Lortie)Overview of tabular data modeling (Jones)Lecture: Workflows and software modeling (Jones)LECTURE: Science in the open: Provenance and Reproducibility (Jones)Introduction to metagenomic data (Teal)
9:00-9:30Metas steps 1-3 (Lortie)Data Modeling Exercise with Group projects (Jones)Wrangling followup: tidyr’s separate, gather, and spreadActivity: Asserting provenance in R (Jones)Metagenomics (Teal)
9:30-9:45BreakBreakBreakBreakBreak
9:45-11:00Metas step 4 (Lortie)Activity: SQL and PostgreSQL (Jones)Activity: Functions and modular code in R (Jones)Practical provenance (Lowndes)Metagenomics (Teal)
11:00-12:00Metas step 5 (Lortie)Activity: SQL and PostgreSQL (Jones)Activity: Creating R Packages (Jones)Activity: Recording provenance with recordr (Jones)Metagenomics (Teal)
Noon-1:00Lunch (starts 11:45)LunchLunchLunchLunch
1:00-1:30LAB: complete group metas (Lortie)SQL and database access in R (Mecum)Testing R code and analysis (Mecum)Activity: Reproducible papers with Rmd (Mecum and Jones)Advanced Metagenomics (Teal)
1:30-2:00Presentations by groups of meta-analysesSQL and database access in R (Mecum)Workflow design activity (Group projects) (Jones)Activity: Reproducible papers with RmdHands-on exercise and workflow (Teal)
2:00-2:15BreakBreakBreakBreakBreak
2:15-5:00Synthesis GroupsSynthesis GroupsSynthesis GroupsSynthesis GroupsSynthesis Groups
5:00-5:15Peanut GalleryPeanut GalleryPeanut GalleryPeanut GalleryPeanut Gallery
436 |


437 |
438 |
439 |

Week 3

440 | 441 | 442 | 443 | 444 | 445 | 446 | 447 | 448 | 449 | 450 | 451 | 452 | 453 | 454 | 455 | 456 | 457 | 458 | 459 | 460 | 461 | 462 | 463 | 464 | 465 | 466 | 467 | 468 | 469 | 470 | 471 | 472 | 473 | 474 | 475 | 476 | 477 | 478 | 479 | 480 | 481 | 482 | 483 | 484 | 485 | 486 | 487 | 488 | 489 | 490 | 491 | 492 | 493 | 494 | 495 | 496 | 497 | 498 | 499 | 500 | 501 | 502 | 503 | 504 | 505 | 506 | 507 | 508 | 509 | 510 | 511 | 512 | 513 | 514 | 515 | 516 | 517 | 518 | 519 | 520 | 521 | 522 | 523 | 524 | 525 | 526 | 527 | 528 | 529 | 530 | 531 | 532 | 533 | 534 | 535 | 536 | 537 | 538 | 539 | 540 | 541 | 542 | 543 | 544 | 545 | 546 | 547 | 548 | 549 |
AgendaDay 11. Geospatial DataDay 12. Geospatial analysis and Algorithmic ApproachesDay 13. Data VizDay 14. Scaling up analysisDay 15. Group projects! Publications. Group reports
8:15-8:30Feedback, questions, and discussionFeedback, questions, and discussionFeedback, questions, and discussionFeedback, questions, and discussionFeedback, questions, and discussion
8:30-9:00Intro to GIS - geospatial data concepts (Wasser)LAB: geospatial analysis (Wasser)Data Viz and interactive tools (Mecum)Parallel processing (in R)(Jones)Group 1 presentation and discussion
9:00-9:30Go from an Excel-like set of data to QGIS (Brun)LAB: geospatial analysis (Wasser)Data Viz and interactive tools (Mecum)Parallel processing (in R)(Jones)Group 1 presentation and discussion
9:30-9:45BreakBreakBreakBreakBreak
9:45-11:00Intro to GIS in R (Wasser & Mecum)LAB: geospatial analysis (Wasser)Data Viz and interactive tools (Mecum)Open Science (Lortie) (10-10:30)
Synthesis Groups		Group 2 presentation and discussion
11:00-12:00Intro to GIS in R (Wasser & Mecum)LAB: geospatial analysis (Wasser)Perfunctory Python (Brun) (30 mins)Synthesis GroupsGroup 3 presentation and discussion
Noon-1:00LunchLunchLunchLunchLunch
1:00-1:30Publishing maps to the web in R (Mecum)LAB: NetCDF and HDF5 (Wasser & Mecum)Synthesis GroupsSynthesis GroupsPost-course assessment
1:30-2:00Publication ready maps in R (Mecum)LAB: NetCDF and HDF5 (Wasser & Mecum)Synthesis GroupsSynthesis GroupsDiscussion: open science for synthesis and course feedback
2:00-2:15BreakBreakBreakBreakBreak
2:15-5:00Synthesis GroupsSynthesis GroupsSynthesis GroupsSynthesis GroupsAdjourn
5:00-5:15Peanut GalleryPeanut GalleryPeanut GalleryPeanut GalleryCelebration
550 |
551 | 552 | 553 | 554 | 555 |
556 | 557 | 569 | 570 | 571 | 579 | 580 | 581 | 582 | -------------------------------------------------------------------------------- /schedule/wk1.csv: -------------------------------------------------------------------------------- 1 | Agenda,Day 1. Synthesis & Unix,Day 2. Communication and Version Control,Day 3. Advanced Unix and Data tools,Day 4. Open Data and R,Day 5. People and Data Wrangling 2 | 8:15-8:30,"Welcome (Jones, Budden)","Feedback, questions, and discussion","Feedback, questions, and discussion","Feedback, questions, and discussion","Feedback, questions, and discussion" 3 | 8:30-9:00,"Participant intros; brief bio, project interests, goals for course (all)","Activity: Version control, Git, Github, Git in RStudio (Brun)","Advanced unix tools (awk, sed, iconv, etc.) (Jones)",Ecological Metadata in R (Mecum),"Social aspects of collaboration, high-performing groups, data policies (Budden and Jones)" 4 | 9:00-9:30,"Course overview, discussion of expectations (Jones, Budden)","Activity: Version control, Git, Github, Git in RStudio (Brun)","Advanced unix tools (awk, sed, iconv, etc.) (Jones)",Open data in R and ROpenSci (Mecum & Jones),Facilitating group discussions (Budden) 5 | 9:30-9:45,Break,Break,Break,Break,Break 6 | 9:45-11:00,"Intro to servers, networks, and the unix command line (Jones)","Activity: Version control, Git, Github, Git in RStudio (Brun)",Bash shell scripts (Jones),"Data liberation (scraping, text mining) (Brun)",Introduction to tidyverse wrangling (Lortie) 7 | 11:00-12:00,Thinking preferences activity (Budden),"Activity: Version control, Git, Github, Git in RStudio (Brun)",R Review/ Assessment (Mecum),"Data liberation (scraping, text mining) (Brun)","Tutorial and exercises wrangling to filter, sort, and merge (Lortie)" 8 | Noon-1:00,Lunch,Lunch,Lunch,Lunch,Lunch 9 | 1:00-1:30,R Markdown & Rstudio setup (Mecum),Communications: The message box (Budden),Data Management & Scientific data repositories (Budden),Regular expressions (Mecum),"Data munging, QA/QC, cleaning (Mecum)" 10 | 1:30-2:00,R Markdown & Rstudio setup (Mecum),Group work on message box (Budden),Publishing Data in R (Jones),Message box 2: Group exchange and feedback (Budden),"Data munging, QA/QC, cleaning (Mecum)" 11 | 2:00-2:15,Break,Break,Break,Break,Break 12 | 2:15-5:00,Pre-Assessment (Budden) and Synthesis Groups (Jones),Synthesis Groups,Synthesis Groups,Synthesis Groups,Synthesis Groups 13 | 5:00-5:15,Peanut Gallery,Peanut Gallery,Peanut Gallery,Peanut Gallery,Peanut Gallery -------------------------------------------------------------------------------- /schedule/wk2.csv: -------------------------------------------------------------------------------- 1 | Agenda,Day 6. Open Meta-analysis,Day 7. Tabular Data,Day 8. Programming and Workflows,Day 9. Reproducible research,Day 10. Metagenomics 2 | 8:15-8:30,"Feedback, questions, and discussion","Feedback, questions, and discussion",Mid-term assessment,"Feedback, questions, and discussion","Feedback, questions, and discussion" 3 | 8:30-9:00,Metas and systematic reviews (Lortie),Overview of tabular data modeling (Jones),Lecture: Workflows and software modeling (Jones),LECTURE: Science in the open: Provenance and Reproducibility (Jones),Introduction to metagenomic data (Teal) 4 | 9:00-9:30,Metas steps 1-3 (Lortie),Data Modeling Exercise with Group projects (Jones),"Wrangling followup: tidyr's separate, gather, and spread",Activity: Asserting provenance in R (Jones),Metagenomics (Teal) 5 | 9:30-9:45,Break,Break,Break,Break,Break 6 | 9:45-11:00,Metas step 4 (Lortie),Activity: SQL and PostgreSQL (Jones),Activity: Functions and modular code in R (Jones),Practical provenance (Lowndes),Metagenomics (Teal) 7 | 11:00-12:00,Metas step 5 (Lortie),Activity: SQL and PostgreSQL (Jones),Activity: Creating R Packages (Jones),Activity: Recording provenance with recordr (Jones),Metagenomics (Teal) 8 | Noon-1:00,Lunch (starts 11:45),Lunch,Lunch,Lunch,Lunch 9 | 1:00-1:30,LAB: complete group metas (Lortie),SQL and database access in R (Mecum),Testing R code and analysis (Mecum),Activity: Reproducible papers with Rmd (Mecum and Jones),Advanced Metagenomics (Teal) 10 | 1:30-2:00,Presentations by groups of meta-analyses,SQL and database access in R (Mecum),Workflow design activity (Group projects) (Jones),Activity: Reproducible papers with Rmd,Hands-on exercise and workflow (Teal) 11 | 2:00-2:15,Break,Break,Break,Break,Break 12 | 2:15-5:00,Synthesis Groups,Synthesis Groups,Synthesis Groups,Synthesis Groups,Synthesis Groups 13 | 5:00-5:15,Peanut Gallery,Peanut Gallery,Peanut Gallery,Peanut Gallery,Peanut Gallery -------------------------------------------------------------------------------- /schedule/wk3.csv: -------------------------------------------------------------------------------- 1 | Agenda,Day 11. Geospatial Data,Day 12. Geospatial analysis and Algorithmic Approaches,Day 13. Data Viz,Day 14. Scaling up analysis,Day 15. Group projects! Publications. Group reports 2 | 8:15-8:30,"Feedback, questions, and discussion","Feedback, questions, and discussion","Feedback, questions, and discussion","Feedback, questions, and discussion","Feedback, questions, and discussion" 3 | 8:30-9:00,Intro to GIS - geospatial data concepts (Wasser),LAB: geospatial analysis (Wasser),Data Viz and interactive tools (Mecum),Parallel processing (in R)(Jones),Group 1 presentation and discussion 4 | 9:00-9:30,Go from an Excel-like set of data to QGIS (Brun),LAB: geospatial analysis (Wasser),Data Viz and interactive tools (Mecum),Parallel processing (in R)(Jones),Group 1 presentation and discussion 5 | 9:30-9:45,Break,Break,Break,Break,Break 6 | 9:45-11:00,Intro to GIS in R (Wasser & Mecum),LAB: geospatial analysis (Wasser),Data Viz and interactive tools (Mecum),Open Science (Lortie) (10-10:30)
Synthesis Groups,Group 2 presentation and discussion 7 | 11:00-12:00,Intro to GIS in R (Wasser & Mecum),LAB: geospatial analysis (Wasser), Perfunctory Python (Brun) (30 mins),Synthesis Groups,Group 3 presentation and discussion 8 | Noon-1:00,Lunch,Lunch,Lunch,Lunch,Lunch 9 | 1:00-1:30,Publishing maps to the web in R (Mecum),LAB: NetCDF and HDF5 (Wasser & Mecum),Synthesis Groups,Synthesis Groups,Post-course assessment 10 | 1:30-2:00,Publication ready maps in R (Mecum),LAB: NetCDF and HDF5 (Wasser & Mecum),Synthesis Groups,Synthesis Groups,Discussion: open science for synthesis and course feedback 11 | 2:00-2:15,Break,Break,Break,Break,Break 12 | 2:15-5:00,Synthesis Groups,Synthesis Groups,Synthesis Groups,Synthesis Groups,Adjourn 13 | 5:00-5:15,Peanut Gallery,Peanut Gallery,Peanut Gallery,Peanut Gallery,Celebration -------------------------------------------------------------------------------- /site_libs/bootstrap-3.3.5/css/bootstrap-theme.css: 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| .btn-primary[disabled]:active, 141 | fieldset[disabled] .btn-primary:active, 142 | .btn-primary.disabled.active, 143 | .btn-primary[disabled].active, 144 | fieldset[disabled] .btn-primary.active { 145 | background-color: #265a88; 146 | background-image: none; 147 | } 148 | .btn-success { 149 | background-image: -webkit-linear-gradient(top, #5cb85c 0%, #419641 100%); 150 | background-image: -o-linear-gradient(top, #5cb85c 0%, #419641 100%); 151 | background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#419641)); 152 | background-image: linear-gradient(to bottom, #5cb85c 0%, #419641 100%); 153 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff419641', GradientType=0); 154 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 155 | background-repeat: repeat-x; 156 | border-color: #3e8f3e; 157 | } 158 | .btn-success:hover, 159 | .btn-success:focus { 160 | background-color: #419641; 161 | background-position: 0 -15px; 162 | } 163 | .btn-success:active, 164 | .btn-success.active { 165 | background-color: #419641; 166 | border-color: #3e8f3e; 167 | } 168 | .btn-success.disabled, 169 | .btn-success[disabled], 170 | fieldset[disabled] .btn-success, 171 | .btn-success.disabled:hover, 172 | .btn-success[disabled]:hover, 173 | fieldset[disabled] .btn-success:hover, 174 | .btn-success.disabled:focus, 175 | .btn-success[disabled]:focus, 176 | fieldset[disabled] .btn-success:focus, 177 | .btn-success.disabled.focus, 178 | .btn-success[disabled].focus, 179 | fieldset[disabled] .btn-success.focus, 180 | .btn-success.disabled:active, 181 | .btn-success[disabled]:active, 182 | fieldset[disabled] .btn-success:active, 183 | .btn-success.disabled.active, 184 | .btn-success[disabled].active, 185 | fieldset[disabled] .btn-success.active { 186 | background-color: #419641; 187 | background-image: none; 188 | } 189 | .btn-info { 190 | background-image: -webkit-linear-gradient(top, #5bc0de 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.btn-info.disabled:focus, 216 | .btn-info[disabled]:focus, 217 | fieldset[disabled] .btn-info:focus, 218 | .btn-info.disabled.focus, 219 | .btn-info[disabled].focus, 220 | fieldset[disabled] .btn-info.focus, 221 | .btn-info.disabled:active, 222 | .btn-info[disabled]:active, 223 | fieldset[disabled] .btn-info:active, 224 | .btn-info.disabled.active, 225 | .btn-info[disabled].active, 226 | fieldset[disabled] .btn-info.active { 227 | background-color: #2aabd2; 228 | background-image: none; 229 | } 230 | .btn-warning { 231 | background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #eb9316 100%); 232 | background-image: -o-linear-gradient(top, #f0ad4e 0%, #eb9316 100%); 233 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#eb9316)); 234 | background-image: linear-gradient(to bottom, #f0ad4e 0%, #eb9316 100%); 235 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffeb9316', GradientType=0); 236 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 237 | background-repeat: repeat-x; 238 | border-color: #e38d13; 239 | } 240 | .btn-warning:hover, 241 | .btn-warning:focus { 242 | background-color: #eb9316; 243 | background-position: 0 -15px; 244 | } 245 | .btn-warning:active, 246 | .btn-warning.active { 247 | background-color: #eb9316; 248 | border-color: #e38d13; 249 | } 250 | .btn-warning.disabled, 251 | .btn-warning[disabled], 252 | fieldset[disabled] .btn-warning, 253 | .btn-warning.disabled:hover, 254 | .btn-warning[disabled]:hover, 255 | fieldset[disabled] .btn-warning:hover, 256 | .btn-warning.disabled:focus, 257 | .btn-warning[disabled]:focus, 258 | fieldset[disabled] .btn-warning:focus, 259 | .btn-warning.disabled.focus, 260 | .btn-warning[disabled].focus, 261 | fieldset[disabled] .btn-warning.focus, 262 | .btn-warning.disabled:active, 263 | .btn-warning[disabled]:active, 264 | fieldset[disabled] .btn-warning:active, 265 | .btn-warning.disabled.active, 266 | .btn-warning[disabled].active, 267 | fieldset[disabled] .btn-warning.active { 268 | background-color: #eb9316; 269 | background-image: none; 270 | } 271 | .btn-danger { 272 | background-image: -webkit-linear-gradient(top, #d9534f 0%, #c12e2a 100%); 273 | background-image: -o-linear-gradient(top, #d9534f 0%, #c12e2a 100%); 274 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c12e2a)); 275 | background-image: linear-gradient(to bottom, #d9534f 0%, #c12e2a 100%); 276 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc12e2a', GradientType=0); 277 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 278 | background-repeat: repeat-x; 279 | border-color: #b92c28; 280 | } 281 | .btn-danger:hover, 282 | .btn-danger:focus { 283 | background-color: #c12e2a; 284 | background-position: 0 -15px; 285 | } 286 | .btn-danger:active, 287 | .btn-danger.active { 288 | background-color: #c12e2a; 289 | border-color: #b92c28; 290 | } 291 | .btn-danger.disabled, 292 | .btn-danger[disabled], 293 | fieldset[disabled] .btn-danger, 294 | .btn-danger.disabled:hover, 295 | .btn-danger[disabled]:hover, 296 | fieldset[disabled] .btn-danger:hover, 297 | .btn-danger.disabled:focus, 298 | .btn-danger[disabled]:focus, 299 | fieldset[disabled] .btn-danger:focus, 300 | .btn-danger.disabled.focus, 301 | .btn-danger[disabled].focus, 302 | fieldset[disabled] .btn-danger.focus, 303 | .btn-danger.disabled:active, 304 | .btn-danger[disabled]:active, 305 | fieldset[disabled] .btn-danger:active, 306 | .btn-danger.disabled.active, 307 | .btn-danger[disabled].active, 308 | fieldset[disabled] .btn-danger.active { 309 | background-color: #c12e2a; 310 | background-image: none; 311 | } 312 | .thumbnail, 313 | .img-thumbnail { 314 | -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 315 | box-shadow: 0 1px 2px rgba(0, 0, 0, .075); 316 | } 317 | .dropdown-menu > li > a:hover, 318 | .dropdown-menu > li > a:focus { 319 | background-color: #e8e8e8; 320 | background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 321 | background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%); 322 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8)); 323 | background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%); 324 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0); 325 | background-repeat: repeat-x; 326 | } 327 | .dropdown-menu > .active > a, 328 | .dropdown-menu > .active > a:hover, 329 | .dropdown-menu > .active > a:focus { 330 | background-color: #2e6da4; 331 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 332 | background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 333 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4)); 334 | background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%); 335 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0); 336 | background-repeat: repeat-x; 337 | } 338 | .navbar-default { 339 | background-image: -webkit-linear-gradient(top, #fff 0%, #f8f8f8 100%); 340 | background-image: -o-linear-gradient(top, #fff 0%, #f8f8f8 100%); 341 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#f8f8f8)); 342 | background-image: linear-gradient(to bottom, #fff 0%, #f8f8f8 100%); 343 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#fff8f8f8', GradientType=0); 344 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 345 | background-repeat: repeat-x; 346 | border-radius: 4px; 347 | -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075); 348 | box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075); 349 | } 350 | .navbar-default .navbar-nav > .open > a, 351 | .navbar-default .navbar-nav > .active > a { 352 | background-image: -webkit-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%); 353 | background-image: -o-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%); 354 | background-image: -webkit-gradient(linear, left top, left bottom, from(#dbdbdb), to(#e2e2e2)); 355 | background-image: linear-gradient(to bottom, #dbdbdb 0%, #e2e2e2 100%); 356 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdbdbdb', endColorstr='#ffe2e2e2', GradientType=0); 357 | background-repeat: repeat-x; 358 | -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075); 359 | box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075); 360 | } 361 | .navbar-brand, 362 | .navbar-nav > li > a { 363 | text-shadow: 0 1px 0 rgba(255, 255, 255, .25); 364 | } 365 | .navbar-inverse { 366 | background-image: -webkit-linear-gradient(top, #3c3c3c 0%, #222 100%); 367 | background-image: -o-linear-gradient(top, #3c3c3c 0%, #222 100%); 368 | background-image: -webkit-gradient(linear, left top, left bottom, from(#3c3c3c), to(#222)); 369 | background-image: linear-gradient(to bottom, #3c3c3c 0%, #222 100%); 370 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3c3c3c', endColorstr='#ff222222', GradientType=0); 371 | filter: progid:DXImageTransform.Microsoft.gradient(enabled = false); 372 | background-repeat: repeat-x; 373 | border-radius: 4px; 374 | } 375 | .navbar-inverse .navbar-nav > .open > a, 376 | .navbar-inverse .navbar-nav > .active > a { 377 | background-image: -webkit-linear-gradient(top, #080808 0%, #0f0f0f 100%); 378 | background-image: -o-linear-gradient(top, #080808 0%, #0f0f0f 100%); 379 | background-image: -webkit-gradient(linear, left top, left bottom, from(#080808), to(#0f0f0f)); 380 | background-image: linear-gradient(to bottom, #080808 0%, #0f0f0f 100%); 381 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff080808', endColorstr='#ff0f0f0f', GradientType=0); 382 | background-repeat: repeat-x; 383 | -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25); 384 | box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25); 385 | } 386 | .navbar-inverse .navbar-brand, 387 | .navbar-inverse .navbar-nav > li > a { 388 | text-shadow: 0 -1px 0 rgba(0, 0, 0, .25); 389 | } 390 | .navbar-static-top, 391 | .navbar-fixed-top, 392 | .navbar-fixed-bottom { 393 | border-radius: 0; 394 | } 395 | @media (max-width: 767px) { 396 | .navbar .navbar-nav .open .dropdown-menu > .active > a, 397 | .navbar .navbar-nav .open .dropdown-menu > .active > a:hover, 398 | .navbar .navbar-nav .open .dropdown-menu > .active > a:focus { 399 | color: #fff; 400 | background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 401 | background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%); 402 | background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4)); 403 | background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%); 404 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0); 405 | background-repeat: repeat-x; 406 | } 407 | } 408 | .alert { 409 | text-shadow: 0 1px 0 rgba(255, 255, 255, .2); 410 | -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05); 411 | box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05); 412 | } 413 | .alert-success { 414 | background-image: -webkit-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%); 415 | background-image: -o-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%); 416 | background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#c8e5bc)); 417 | background-image: linear-gradient(to bottom, #dff0d8 0%, #c8e5bc 100%); 418 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffc8e5bc', GradientType=0); 419 | background-repeat: repeat-x; 420 | border-color: #b2dba1; 421 | } 422 | .alert-info { 423 | background-image: -webkit-linear-gradient(top, #d9edf7 0%, #b9def0 100%); 424 | background-image: -o-linear-gradient(top, #d9edf7 0%, #b9def0 100%); 425 | background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#b9def0)); 426 | background-image: linear-gradient(to bottom, #d9edf7 0%, #b9def0 100%); 427 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffb9def0', GradientType=0); 428 | background-repeat: repeat-x; 429 | border-color: #9acfea; 430 | } 431 | .alert-warning { 432 | background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%); 433 | background-image: -o-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%); 434 | background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#f8efc0)); 435 | background-image: linear-gradient(to bottom, #fcf8e3 0%, #f8efc0 100%); 436 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fff8efc0', GradientType=0); 437 | background-repeat: repeat-x; 438 | border-color: #f5e79e; 439 | } 440 | .alert-danger { 441 | background-image: -webkit-linear-gradient(top, #f2dede 0%, #e7c3c3 100%); 442 | background-image: -o-linear-gradient(top, #f2dede 0%, #e7c3c3 100%); 443 | background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#e7c3c3)); 444 | background-image: linear-gradient(to bottom, #f2dede 0%, #e7c3c3 100%); 445 | filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffe7c3c3', GradientType=0); 446 | background-repeat: repeat-x; 447 | border-color: #dca7a7; 448 | } 449 | .progress { 450 | background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%); 451 | background-image: -o-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%); 452 | background-image: -webkit-gradient(linear, left top, left bottom, from(#ebebeb), to(#f5f5f5)); 453 | background-image: linear-gradient(to bottom, #ebebeb 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'); 44 | 45 | buttonCol.append(showCodeButton); 46 | buttonRow.append(buttonCol); 47 | 48 | div.before(buttonRow); 49 | 50 | // update state of button on show/hide 51 | div.on('hidden.bs.collapse', function () { 52 | showCodeText.text('Code'); 53 | }); 54 | div.on('show.bs.collapse', function () { 55 | showCodeText.text('Hide'); 56 | }); 57 | }); 58 | 59 | } 60 | -------------------------------------------------------------------------------- /site_libs/navigation-1.1/sourceembed.js: -------------------------------------------------------------------------------- 1 | 2 | 3 | window.initializeSourceEmbed = function(filename) { 4 | $("#rmd-download-source").click(function() { 5 | var src = window.atob($("#rmd-source-code").html()); 6 | var blob = new Blob([src], {type: "text/x-r-markdown"}); 7 | saveAs(blob, filename); 8 | }); 9 | }; 10 | -------------------------------------------------------------------------------- /site_libs/navigation-1.1/tabsets.js: -------------------------------------------------------------------------------- 1 | 2 | 3 | /** 4 | * jQuery Plugin: Sticky Tabs 5 | * 6 | * @author Aidan Lister 7 | * adapted by Ruben Arslan to activate parent tabs too 8 | * http://www.aidanlister.com/2014/03/persisting-the-tab-state-in-bootstrap/ 9 | */ 10 | (function($) { 11 | "use strict"; 12 | $.fn.rmarkdownStickyTabs = function() { 13 | var context = this; 14 | // Show the tab corresponding with the hash in the URL, or the first tab 15 | var showStuffFromHash = function() { 16 | var hash = window.location.hash; 17 | var selector = hash ? 'a[href="' + hash + '"]' : 'li.active > a'; 18 | var $selector = $(selector, context); 19 | if($selector.data('toggle') === "tab") { 20 | $selector.tab('show'); 21 | // walk up the ancestors of this element, show any hidden tabs 22 | $selector.parents('.section.tabset').each(function(i, elm) { 23 | var link = $('a[href="#' + $(elm).attr('id') + '"]'); 24 | if(link.data('toggle') === "tab") { 25 | link.tab("show"); 26 | } 27 | }); 28 | } 29 | }; 30 | 31 | 32 | // Set the correct tab when the page loads 33 | showStuffFromHash(context); 34 | 35 | // Set the correct tab when a user uses their back/forward button 36 | $(window).on('hashchange', function() { 37 | showStuffFromHash(context); 38 | }); 39 | 40 | // Change the URL when tabs are clicked 41 | $('a', context).on('click', function(e) { 42 | history.pushState(null, null, this.href); 43 | showStuffFromHash(context); 44 | }); 45 | 46 | return this; 47 | }; 48 | }(jQuery)); 49 | 50 | window.buildTabsets = function(tocID) { 51 | 52 | // build a tabset from a section div with the .tabset class 53 | function buildTabset(tabset) { 54 | 55 | // check for fade and pills options 56 | var fade = tabset.hasClass("tabset-fade"); 57 | var pills = tabset.hasClass("tabset-pills"); 58 | var navClass = pills ? "nav-pills" : "nav-tabs"; 59 | 60 | // determine the heading level of the tabset and tabs 61 | var match = tabset.attr('class').match(/level(\d) /); 62 | if (match === null) 63 | return; 64 | var tabsetLevel = Number(match[1]); 65 | var tabLevel = tabsetLevel + 1; 66 | 67 | // find all subheadings immediately below 68 | var tabs = tabset.find("div.section.level" + tabLevel); 69 | if (!tabs.length) 70 | return; 71 | 72 | // create tablist and tab-content elements 73 | var tabList = $('
    '); 74 | $(tabs[0]).before(tabList); 75 | var tabContent = $('
    '); 76 | $(tabs[0]).before(tabContent); 77 | 78 | // build the tabset 79 | var activeTab = 0; 80 | tabs.each(function(i) { 81 | 82 | // get the tab div 83 | var tab = $(tabs[i]); 84 | 85 | // get the id then sanitize it for use with bootstrap tabs 86 | var id = tab.attr('id'); 87 | 88 | // see if this is marked as the active tab 89 | if (tab.hasClass('active')) 90 | activeTab = i; 91 | 92 | // remove any table of contents entries associated with 93 | // this ID (since we'll be removing the heading element) 94 | $("div#" + tocID + " li a[href='#" + id + "']").parent().remove(); 95 | 96 | // sanitize the id for use with bootstrap tabs 97 | id = id.replace(/[.\/?&!#<>]/g, '').replace(/\s/g, '_'); 98 | tab.attr('id', id); 99 | 100 | // get the heading element within it, grab it's text, then remove it 101 | var heading = tab.find('h' + tabLevel + ':first'); 102 | var headingText = heading.html(); 103 | heading.remove(); 104 | 105 | // build and append the tab list item 106 | var a = $('' + headingText + ''); 107 | a.attr('href', '#' + id); 108 | a.attr('aria-controls', id); 109 | var li = $('
  • '); 110 | li.append(a); 111 | tabList.append(li); 112 | 113 | // set it's attributes 114 | tab.attr('role', 'tabpanel'); 115 | tab.addClass('tab-pane'); 116 | tab.addClass('tabbed-pane'); 117 | if (fade) 118 | tab.addClass('fade'); 119 | 120 | // move it into the tab content div 121 | tab.detach().appendTo(tabContent); 122 | }); 123 | 124 | // set active tab 125 | $(tabList.children('li')[activeTab]).addClass('active'); 126 | var active = $(tabContent.children('div.section')[activeTab]); 127 | active.addClass('active'); 128 | if (fade) 129 | active.addClass('in'); 130 | 131 | if (tabset.hasClass("tabset-sticky")) 132 | tabset.rmarkdownStickyTabs(); 133 | } 134 | 135 | // convert section divs with the .tabset class to tabsets 136 | var tabsets = $("div.section.tabset"); 137 | tabsets.each(function(i) { 138 | buildTabset($(tabsets[i])); 139 | }); 140 | }; 141 | 142 | -------------------------------------------------------------------------------- /wk1.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | output: html_document 4 | --- 5 |
    6 | 7 | ####**Fundamental collaboration and open sciences skills** 8 | 9 |
    10 | 11 | [Lessons](https://github.com/NCEAS/oss-lessons) -------------------------------------------------------------------------------- /wk1.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
    151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 207 | 208 | 209 |


    210 |
    211 |

    Fundamental collaboration and open sciences skills

    212 |


    213 |

    Lessons

    214 |
    215 | 216 | 217 | 218 | 219 |
    220 | 221 | 233 | 234 | 235 | 243 | 244 | 245 | 246 | -------------------------------------------------------------------------------- /wk2.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | output: html_document 4 | --- 5 |
    6 | 7 | ####**Advanced skills** 8 | 9 |
    10 | -------------------------------------------------------------------------------- /wk2.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
    151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 207 | 208 | 209 |


    210 |
    211 |

    Advanced skills

    212 |


    213 |
    214 | 215 | 216 | 217 | 218 |
    219 | 220 | 232 | 233 | 234 | 242 | 243 | 244 | 245 | -------------------------------------------------------------------------------- /wk3.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "" 3 | output: html_document 4 | --- 5 |
    6 | 7 | ####**Advanced topics & group projects** 8 | 9 |
    10 | 11 | -------------------------------------------------------------------------------- /wk3.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 32 | 39 | 40 | 41 | 42 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 95 | 96 | 97 | 130 | 131 | 148 | 149 | 150 |
    151 | 152 | 153 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 200 | 201 | 207 | 208 | 209 |


    210 |
    211 |

    Advanced topics & group projects

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    213 |
    214 | 215 | 216 | 217 | 218 |
    219 | 220 | 232 | 233 | 234 | 242 | 243 | 244 | 245 | --------------------------------------------------------------------------------