PNW workshop

NeotomaDB · Mar 2, 2023 · a189e59 · a189e59
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diff --git a/PNW-March2023/.DS_Store b/PNW-March2023/.DS_Store
diff --git a/PNW-March2023/LICENSE b/PNW-March2023/LICENSE
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+MIT License
+
+Copyright (c) 2022 Socorro Dominguez Vidana
+
+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.
diff --git a/PNW-March2023/NeotomaWorkshopAgenda.md b/PNW-March2023/NeotomaWorkshopAgenda.md
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+# neotoma2 PNW Virtual Workshop Workshop
+
+March 1st, 2023
+
+8:30am - 11:20am Pacific Standard Time [Time Zone Converter](https://dateful.com/convert/pst-pdt-pacific-time?t=0830&d=2023-03-01)
+
+## Socorro Dominguez Vidaña, Simon Goring
+
+# Overview
+
+This workshop is designed to provide users of the Neotoma Database with an overview of the new [`neotoma2` R package](https://github.com/NeotomaDB/neotoma2), and its use in obtaining data from the Neotoma Paleoecology Database.
+
+At the end of this workshop, users will understand the following concepts:
+
+1. How data is structured within Neotoma and in the R package
+2. How to search for data in space and time
+3. How to extract summary objects from individual sites and collections of sites
+4. How to manipulate data to add new chronologies
+
+Online resources for users include links embedded within the agenda, as well as:
+
+* Participant slides: [Google Slides](https://docs.google.com/presentation/d/1lDZAam5zPBf0aK0zrcOgqb9f8-OPCCZk7bOiCw9QFLc/edit?usp=sharing)
+* Online slides: [Google Slides](https://docs.google.com/presentation/d/1SN308n1-3q94lV_oF7NMI04Rs-X4kutiI29eJp2B-Vg/edit?usp=sharing)
+* An online version of RStudio built for this workshop: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NeotomaDB/Current_Workshop/main?urlpath=rstudio)
+* The code repository for the workshop: [https://github.com/NeotomaDB/Current_Workshop](https://github.com/NeotomaDB/Current_Workshop)
+
+## Getting Started
+
+The course is designed to be run using RStudio in your browser. You will not need to install any files or packages, however, if you do want to install the R package on your computer, you can simply open your R session and type:
+
+```
+install.packages('devtools')
+devtools::install_github('NeotomaDB/neotoma2')
+```
+
+# Resources
+
+Neotoma maintains an online community on Slack that includes a channel for help using R and Neotoma (#it_r).  Come join our community: [https://bit.ly/3PT8zuP](https://bit.ly/3PT8zuP)
+
+This allows us to better help you during the workshop and in the future.
+
+* The Neotoma Database Manual: [https://open.neotomadb.org/manual/](https://open.neotomadb.org/manual/)
+* The `neotoma2` GitHub Repository: [https://github.com/neotomadb/neotoma2](https://github.com/neotomadb/neotoma2)
+
+# Agenda
+
+3 Hours (8:30am - 11:20pm)
+
+<table>
+  <tr>
+   <td>Time
+   </td>
+   <td>Topic
+   </td>
+   <td>Overview
+   </td>
+   <td>Link
+   </td>
+  </tr>
+  <tr>
+   <td>8:30 - 8:45am
+   </td>
+   <td>Introductions
+   </td>
+   <td>Run through each individual’s profile quickly, say hi & introduce ourselves.
+   </td>
+   <td><a href="https://docs.google.com/presentation/d/1lDZAam5zPBf0aK0zrcOgqb9f8-OPCCZk7bOiCw9QFLc/edit?usp=sharing">Participant Slides</a>
+   </td>
+  </tr>
+  <tr>
+   <td>8:45 - 8:50am
+   </td>
+   <td>Why `neotoma2`?
+   </td>
+   <td>Explaining why we’ve moved to a new package, rather than updating the `neotoma` R package.
+   </td>
+   <td><a href="https://docs.google.com/presentation/d/1UhIJ3HJskE9ymmFZ109ktsKKuqzW21JZc8fiWQLkyZw/edit?usp=sharing">Why neotoma2?</a>
+   </td>
+  </tr>
+  <tr>
+   <td><strong>8:50 - 9:00am</strong>
+   </td>
+   <td><strong>A simple workflow</strong>
+   </td>
+   <td colspan="2" ><a href="https://open.neotomadb.org/Current_Worksop/simple_workflow.html">https://open.neotomadb.org/EPD_binder/simple_workflow.html</a>
+   </td>
+  </tr>
+  <tr>
+   <td>9:20 - 9:30
+   </td>
+   <td>Simple Site Search
+   </td>
+   <td>How to search for sites by space & name.
+   </td>
+   <td>
+   </td>
+  </tr>
+  <tr>
+   <td>9:30 - 9:35
+   </td>
+   <td>Independent Searching
+   </td>
+   <td>Individuals will use the geoJSON site to select an area, perform a search and plot the results. Paste the image on your personal slide.
+   </td>
+   <td>
+   </td>
+  </tr>
+  <tr>
+   <td>9:35 - 9:40
+   </td>
+   <td>Quick Debrief
+   </td>
+   <td>One or two people, what did you find?
+   </td>
+   <td>
+   </td>
+  </tr>
+  <tr>
+   <td>9:40 - 9:50am
+   </td>
+   <td>Searching for Datasets and Filtering
+   </td>
+   <td>How to extract datasets by dataset type & see summary information about records.
+   </td>
+   <td>
+   </td>
+  </tr>
+  <tr>
+   <td>9:50 - 10:00am
+   </td>
+   <td>Independent filtering
+   </td>
+   <td>Users will filter by time, space &cetera.
+   </td>
+   <td>
+   </td>
+  </tr>
+  <tr>
+   <td>10:05 - 10:10am
+   </td>
+   <td>Quick debrief
+   </td>
+   <td>What do you need from Neotoma?
+   </td>
+   <td>
+   </td>
+  </tr>
+  <tr>
+   <td>10:10 - 10:30am
+   </td>
+   <td>Samples & Stratigraphic plotting
+   </td>
+   <td>How to pull them from sites/datasets. Key features, filtering.
+   </td>
+   <td>Intro to taxonomic harmonization is in the simple_workflow.html
+   </td>
+  </tr>
+  <tr>
+   <td>10:30 - 11:00am
+   </td>
+   <td>Break
+   </td>
+   <td>
+   </td>
+   <td>
+   </td>
+  </tr>
+  <tr>
+   <td>11:00 - 11:20am
+   </td>
+   <td>Spatial Analysis
+   </td>
+   <td>Using climate data from WorldClim rasters, examine taxon distributions in climate space
+   </td>
+   <td>
+   </td>
+  </tr>
+  <tr>
+   <td>11:20am - end
+   </td>
+   <td>Independent Breakout 1
+   </td>
+   <td>See instructions in the slide
+   </td>
+   <td>Link removed for online version.
+   </td>
+  </tr>
+</table>
diff --git a/PNW-March2023/README.md b/PNW-March2023/README.md
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+[![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![NSF-1948926](https://img.shields.io/badge/NSF-1948926-blue.svg)](https://nsf.gov/awardsearch/showAward?AWD_ID=1948926)
+
+# Neotoma Current R Workshop
+
+A repository to host interactive R workshops. This repository will always be set up for the most recent/current Neotoma Workshop. All past workshops will be archived in the [Neotoma Workshops](https://github.com/NeotomaDB/Workshops) repository.
+
+This repository is built with the structure required to serve the content through an interactive, online RStudio session using Binder (and Docker). Clicking the Binder link will open RStudio in the user's browser.
+
+**Currently, this repo hosts the Workshop to be delivered for the Pacific North West Virtual Workshop.**
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NeotomaDB/Current_Workshop/main?urlpath=rstudio)
+
+## Contributors
+
+This is an open project and contributions are welcome from any individual.  All contributors to this project are bound by a [code of conduct](CODE_OF_CONDUCT.md).  Please review and follow this code of conduct as part of your contribution.
+
+* [![orcid](https://img.shields.io/badge/orcid-0000--0002--7926--4935-brightgreen.svg)](https://orcid.org/0000-0002-7926-4935) [Socorro Dominguez Vidana](https://sedv8808.github.io/)
+
+* [![orcid](https://img.shields.io/badge/orcid-0000--0002--2700--4605-brightgreen.svg)](https://orcid.org/0000-0002-2700-4605) [Simon Goring](http://goring.org)
+
+## How to use this repository 
+
+This repository contains two different R workflows, a complex workflow that shows how to manage and modify chronologies with the R package, and a simple workflow that shows how to access data and perform relatively simple analysis. These workflows may be modified for content (e.g., focusing on different dataset types or geospatial contexts).
+
+Users may clone this workshop and modify the content, but be aware that the Binder links are specific to this repository, and must be modified through the users' own Binder setup.
+
+* `runtime.txt` is used to define the R environment to be used by Docker/Binder
+* `apt.txt` defines a set of packages required by Binder/Docker to enable the spatial tools in the `neotoma2` R package.
diff --git a/PNW-March2023/apt.txt b/PNW-March2023/apt.txt
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+libudunits2-dev
+libgdal-dev
+libgeos-dev
+libproj-dev
+libglpk-dev