Georeferencing for Research Use

iDigBio - CCBER GWG Georeferencing for Research Use, a short course

Georeferencing for Research Use, a short course

Quick Links for GWG Second Train the Trainers Workshop
Georeferencing for Research Use - link to agenda
Biblio entries
Georeferencing for Research Use, short course report

hotel and NCEAS map

October 4 - 7, 2016 at (https://www.nceas.ucsb.edu/) NCEAS, Santa Barbara California

We welcome you to this short course, with a focus on research use of georeferenced natural history collections data. We will include activities and discussions about best practices and tools for georeferencing, capturing locality data in the field, and using georeferenced specimen locality data in research. Attendees must have a basic level of experience with georeferencing techniques and tools and be researchers or directly involved with researchers.

After the workshop, we will encourage our participants to share use cases, any training materials developed, and to offer workshops, webinars, talks, or other events aimed at increasing use of best practices for georeferencing legacy locality data, best practices for capturing the locality data from future biological and paleontological collecting and sampling events, and best practices for using the data in research.

Some anticipated course content includes discussion and activities about georeferencing integration, georeferenced data visualization, and georeferences for modeling and research. Detailed agenda in development.

Logistics:

Hotel and NCEAS Map

Meet the Participants:

Participant list

Bring your Datasets and Laptops:

Participants are strongly encouraged to bring representative datasets from their collections or research that need georeferencing to expose everyone to the variety of locality data georeferencing issues and give the experts and participants a chance to work together to address any challenges.

Participants must bring their own laptops and everyone will have wired access to facilitate the best possible workshop experience.

Pre-Workshop Assignments

Attend pre-workshop online meeting. Two options, choose one.
1. Thursday September 15th - two times to choose from:
  1. 11am EDT (10am CDT, 9am MDT, 8am PDT)
  2. 3pm EDT (2pm CDT, 1pm MDT, 12pm PDT)
2. Sign Up Here: https://goo.gl/forms/WmJO6z79rx5nHlv32
3. Meet: http://idigbio.adobeconnect.com/geotrain
Please watch the following videos - before the workshop. (flipped-classroom). Be sure to note any questions / insights to share with the group.
1. Collaboration to Automation: https://vimeo.com/53006304 (25 min lecture, 10 min discussion)
2. Geographical Concepts: https://vimeo.com/53008556 (4 min lecture, 2 min discussion)
  1. https://vimeo.com/album/2163673/video/63692461 (4 min lecture only)
3. Point Radius Method and Best Practices: https://vimeo.com/53006303 (20 min lecture, 5 min discussion)
4. OPTIONAL video: BITC Global Online Seminar #25: Simple Workflow for Data Cleaning (1 hour)
Please install the following software
1. QGIS and then QGIS Plugins. NOTE it's easy to install all the plugins from inside QGIS once you have it installed.
  
  QGIS plugins menu
  1. QGIS: http://qgis.org/en/site/forusers/download.html
  2. QGIS Plug-ins: Open your QGIS installation on your laptop > navigate to Plugins > Manage and Install Plugins (as seen in the screenshots). You can then add these plugins within QGIS by typing the tool name into the search box and clicking on "Install Plugin": Clipper, Coordinate capture, eVis, Gazetteer Search, GPS tools, Heatmap, Interpolation, OpenLayers, Processing, and Lifemapper
    1. Clipper (clip intersecting vector features)
    2. Coordinate capture (find coordinates in various coordinate reference systems (CRS) via mouse-over)
    3. eVis (event-visualization animation for vector features): eVis is now automatically installed and enabled in new versions of QGIS. http://documentation.qgis.org/2.0/en/docs/user_manual/plugins/plugins_evis.html
    4. Gazetteer Search (finding named places via a search bar)
    5. GPS tools (loading and importing GPS data)
    6. Heatmap (generate a heatmap raster given input vector points)
    7. Interpolation (interpolation techniques given vertices of a vector layer)
    8. OpenLayers (load basemaps from OpenStreetMap, Google, etc.)
    9. Processing (spatial data processing framework)
    10. Lifemapper
2. Open Refine: (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, - should work fine (Explorer not recommended). You will need to download Google Refine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer. (Use these resources Open Refine Install or Install Open Refine for more help if you run into any Open Refine install issues).
  1. Windows
    1. Go to the OpenRefine download page.
    2. Click on Windows kit to download the install file
    3. To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead)
    4. OpenRefine will then open in your web browser.
    5. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.
  2. MacOS
    1. Go to the OpenRefine download page.
    2. Click on Mac kit to download the install file
    3. Open the downloaded .dmg file
    4. Drag the icon in to the Applications folder
    5. Double click on the icon and Google Refine will then open in your web browser.
    6. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.
  3. Linux
    1. Go to the OpenRefine download page.
    2. Click on Linux kit to download the install file
    3. Download and extract
    4. Type ./refine in your terminal and Google Refine will then open in your web browser.
    5. If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.
3. Spreadsheet software (your choice, Libre Office, Excel, etc.,)
  1. We'll be using a spreadsheet program. If you already have a spreadsheet program installed, like LibreOffice, Excel or OpenOffice, you can use whatever you already have. If you don't have a spreadsheet program, please download and install LibreOffice from http://www.libreoffice.org/download/libreoffice-fresh/
4. Java: Please make sure you have Java installed (needed for Open Refine to work).
OPTIONAL software install and tutorials - if you are interested in the R section we will offer at the workshop.
1. R: R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
  1. Windows
    1. Video Tutorial
    2. Install R by downloading and running this .exe file from CRAN (http://cran.r-project.org/index.html).
    3. Also, please install the RStudio IDE.
  2. Mac OS X
    1. Video Tutorial
    2. Install R by downloading and running this .pkg file from CRAN (http://cran.r-project.org/index.html).
    3. Also, please install the RStudio IDE.
  3. Linux
    1. You can download the binary files for your distribution from CRAN. Or you can use your package manager
      1. e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R.
    2. Also, please install the RStudio IDE.
2. Then install packages:
3. R Tutorials. OPTIONAL take a short course in R. If you are a novice, take a beginner course. We don't expect you know know R well, but we do need you be familiar enough to follow along with one of our optional hands-on sessions. There are several good options:
  1. Try R (Code School course)
  2. Beginner Course: Up and Running with R with Barton Poulson (course at lynda.com)
  3. Intermediate Course: R Statistics Essential Training with Barton Poulson(course at lynda.com)
  4. For the future you could take a Coursera class. intro to R(Coursera course started August 22nd).

Reading Materials and Resources:

Georeferencing.Org
Georeferencing Quick Reference Guide
version 2012-10-08. John Wieczorek, David Bloom, Heather Constable, Janet Fang, Michelle Koo, Carol Spencer, Kristina Yamamoto
Guide to Best Practices for Georeferencing - Chapman, A.D. and J. Wieczorek (eds). 2006
Georeferencing Working Group Training Videos
Georeferencing Incidents from Locality Descriptions and its Applications: a Case Study from Yosemite National Park Search and Rescue Transactions in GIS, 2011, 15(6): 775–793 Authors: Doherty, Guo, Liu, Wieczorek, Doke
iDigBio Georeferencing Wiki http://tinyurl.com/idbgeowiki
HerpNET Georeferencing Resources
Take Workshop Notes Together Here
Post - Workshop Survey Questions
Got a Georeferencing Question? Post it on the iDigBio Georeferencing List Serve
BITC Global Online Seminar #25: Simple Workflow for Data Cleaning

Wireless / Wired Access Issues:

Both wired and wireless access provided to workshop participants. Connectivity instructions will be provided at the workshop.

Overview:

Goals of the Workshop:

Workshop Objectives:

Desired Outcomes:

Schedule of Events - Agenda - in development

Breakfast every day is on our own.

Day 1, Tuesday October 4th

Time	Activity	Presenter
8:45	Pick up Name Tags, Wireless Log-In, Wired Setup
9:00	Welcome by NCEAS host, Logistics, Trainer Introductions, Introduction to iDigBio, CCBER	Katja Seltmann, Debbie Paul, (NCEAS person)
9:20	From the participants and instructors: a quick informal survey Quick Name/Rank/Serial# introductions tools you use what you’d like to be able to do	Deb Paul
10:00
10:15	Darwin Core Standard, Key Terminology iDigBio Recommended fields (include FIMS discussion)	David Bloom, Shelley James
10:45	Break
11:15	Locality Types, Georeferencing Quick Reference Guide, and Georeferencing Template
11:35	Georeferencing Calculator, Calculator Manual	David Bloom
12:00	Lunch (Provided)	David Bloom
13:00	Georeferencing Calculator Example and Exercises, MaNIS/HerpNET/ORNIS Georeferencing Guidelines
14:30	Break
15:00
15:30	GEOLocate - Overview, Basics & Demos	Nelson Rios
17:00	Day in Review Trivia Question of the Day
17:30	End

Dinner on our own - See list of local restaurants. Optional Evening Activity is: TBA

Day 2, Wednesday October 5th


Time	Activity	Presenter
9:00	Review and Questions	All
9:10	GEOLocate - Advanced Features, Collaborative Georeferencing and the GEOLocate API	Nelson Rios
10:00	Georeferencing Exercises georeference 5 of these localities, or more, can you do it?	All
10:30	Break
11:00	GPS Exercise Introduction	David Bloom, Mike Yost, Shelley James, Katja Seltmann
11:15	GPS Exercises (outside)	All
12:15	Lunch
13:15	GPS Exercises (outside)	All
13:30	Good and Bad Localities, Field Locality Handout: MVZ and iDigBio GWG Guide for Recording Localities in Field Notes, FIMS	All
14:15	Examples and Discussion: Process, Workflows, Priorities, and Collaborations	All
15:15	Break
16:15	Online Exercises, Review of known answers
16:30	GPS Exercise - Review (.kmz), Summary Spreadsheet, Field Worksheet, Locality Descriptions	David Bloom, Jessica Utrup
16:45	Day in Review and Considerations for Trainers-to-be Your Input Needed - Mapping Functions in the iDigBio Portal Trivia Question of the Day Hotelwork: create/document your project workflow(s) for discussion on Wednesday
17:30	END

Dinner on our own - See list of local restaurants. You'll be reimbursed at the standard per diem rates. Optional Evening Activities are: TBA

Day 3, Thursday October 6th

Download zipped dataset The parameters for this dataset are specimens in the family Carabidae, that have geocoordinates, and are in California. It results in about 25,000 records in total.

Time	Activity	Presenter
9:00	Review and Questions	All
9:05	Getting datasets: Downloading datasets from iDigBio - get data from portal and explain each component to the dataset. filter and get the dataset Similar or different from GBIF? What is raw vs not raw? Walk through steps of download, but provide dataset. Data set https://drive.google.com/file/d/0B_HeAV_gLFNsRkNIN1RBaDF5aHM/view	Matthew Collins (remote), Katja Seltmann, Shelley James
10:00	Data Quality: How to evaluate existing georeferenced data/Fitness for Use Data quality flags What do you need the data for (differences in use-cases) https://drive.google.com/file/d/0B_HeAV_gLFNsUkc5S0xwMVFNRWc/view Thought exercise? Evaluating data for different research project use e.g. http://www.gbif.org/event/82604 http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0063708	All
10:30	Break
11:00	Cleaning Datasets: Spreadsheets, Open Refine, tracking your work	Deb Paul, Nelson, Katja Seltmann
12:00	Lunch on our own.
13:00	Cleaning Datasets: Spreadsheets, Open Refine, tracking your work (2)	Deb Paul, Nelson, Katja Seltmann
13:30	Visualizing datasets: Set up QGIS and load data vector: points, lines, polygons raster: images	Sara Lafia, Mike Yost
15:00	Break
15:30	Visualizing datasets: Preview and explore toolkits & saving your maps and data	Sara Lafia
17:30	End

Evening Activity is: TBD. Today in Santa Barbara:

Day 4, Friday October 7th

Time	Activity	Presenter
9:00	Questions and Review
9:10	Exploring datasets: Aggregating by Regions Join, aggregate, or summarize records by county Summarize observations intersecting counties Why do this?	Sara Lafia, Katja Seltmann, Nelson Rios
9:50	Exploring datasets: Time animation By collecting event date or collector (to show biases in collection) Check for errors with dates or transcriptions	Sara Lafia
10:30	Break
11:00	Exploring datasets: Uncertainty Bin points based on uncertainty rank Symbolize uncertainty by collector, data quality score - systematic error	Sara Lafia
11:30	Exploring datasets: Spatial autocorrelation Distribution/clustering prevalence based on species, collector, etc. Date-collector correlation	Sara Lafia
12:00	Lunch on our own.
13:00	Work on own data sets/Open question time/Practice	Nelson Rios
13:45	Ideas
14:25	Using GEOLocate: Collaborative Georeferencing Administrative Portal	Nelson Rios
15:30	Break
16:00	Research Use of the Data. A conversation from the collective point-of-view of the researchers present. What are your challenges? What is your experience? What needs do you see (software, skills, infrastructure)? After this workshop - what changes might you make now to your workflows?	Ed Davis, Katja Seltmann, Shelley James, Nelson Rios, Sara Lafia
16:30	Post Workshop Questionnaire
17:00	Day & workshop in Review
17:30	Beer

Dinner on our own - See list of local restaurants. You'll be reimbursed at the standard per diem rates.

Some software install instructions from Data and Software Carpentry

Trained Georeferencers

Map of Participants and Instructors for TTT1 and TTT2
Wiki for all TTT1 and TTT2 Participants