Georeferencing for Research Use: Difference between revisions

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= Post Workshop Publication =
Organizers and participants co-wrote a summation from this workshop of lessons learned and key observations and published these results as
*Seltmann K, Lafia S, Paul D, James S, Bloom D, Rios N, Ellis S, Farrell U, Utrup J, Yost M, Davis E, Emery R, Motz G, Kimmig J, Shirey V, Sandall E, Park D, Tyrrell C, Thackurdeen R, Collins M, O'Leary V, Prestridge H, Evelyn C, Nyberg B (2018) Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers. Research Ideas and Outcomes 4: e32449. https://doi.org/10.3897/rio.4.e32449
== iDigBio - CCBER GWG Georeferencing for Research Use, a short course  ==
{| class="wikitable" style="float:right;"
{| class="wikitable" style="float:right;"
! colspan="2" style="background:#D58B28;width:200px;font-size:10pt" | Georeferencing for Research Use, a short course
! colspan="2" style="background:#D58B28;width:200px;font-size:10pt" | Georeferencing for Research Use, a short course
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!colspan="2" style="background:#D58B28;text-align:center;font-size:9pt" | Quick Links for GWG Second Train the Trainers Workshop  
!colspan="2" style="background:#D58B28;text-align:center;font-size:9pt" | Quick Links for GWG Second Train the Trainers Workshop  
|-  
|-  
|Georeferencing for Research Use - link to agenda
|[[Georeferencing_for_Research_Use#Schedule_of_Events_-_Agenda|Georeferencing for Research Use - link to agenda]]
|-  
|-  
|Biblio entries<br>
|Biblio entries<br>
|-  
|-  
| Georeferencing for Research Use, short course report
|[https://www.idigbio.org/content/georeferencing-and-visualizing-biodiversity-data-research Georeferencing for Research Use, short course report]
|}
|}
[[Category:Workshop]]
[[Category:Workshop]][[Category:Georeferencing]][[Category:Research]]
= Wiki URLs =
[[File:Capture.PNG|200px|thumb|right|hotel and NCEAS map]]
# Agenda (this page)
October 4 - 7, 2016 at (https://www.nceas.ucsb.edu/) NCEAS, Santa Barbara California
# Logistics
# Useful links
# Photos
 
= iDigBio - CCBER GWG Georeferencing for Research Use, a short course  =
 
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.
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.
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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.
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.
Some anticipated course content includes discussion and activities about georeferencing integration, georeferenced data visualization, and georeferences for modeling and research.
 
=== Logistics: ===
* [[Media:HOTEL_MAP_NCEAS.pdf|Hotel and NCEAS Map]]
* NCEAS is 3rd floor of the Balboa Building,  735 State Street
* [https://www.idigbio.org/wiki/images/8/89/Local_Restaurants.pdf Local restaurant list]


==== Logistics: ====
=== Course Instructor List ===
* link to logistics page or pdf
(''in alphabetical order'') David Bloom, Matt Collins, Una Farrell, Shelley James, Sara Lafia, Deborah Paul, Marcy Revelez, Nelson Rios, Katja Seltmann, Jessica Utrup, Mike Yost
=== 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.


==== Meet the Participants: ====
Participants must bring their own laptops and '''everyone will have wired access''' to facilitate the best possible workshop experience.
* Participant list
* Map of [http://tinyurl.com/idbtttmap Participants and Instructors for TTT1 and TTT2]
* Wiki for all [[TTT1TTT2| TTT1 and TTT2 Participants]]


==== Reading Materials and Resources:  ====
==== Reading Materials and Resources:  ====


#[http://georeferencing.org/ Georeferencing.org]
#[https://www.idigbio.org/sites/default/files/workshop-presentations/geotrain/GeoreferencingQuickReferenceGuide20121008.pdf Georeferencing Quick Reference Guide]<br> version 2012-10-08. John Wieczorek, David Bloom, Heather Constable, Janet Fang, Michelle Koo, Carol Spencer, Kristina Yamamoto  
#[https://www.idigbio.org/sites/default/files/workshop-presentations/geotrain/GeoreferencingQuickReferenceGuide20121008.pdf Georeferencing Quick Reference Guide]<br> version 2012-10-08. John Wieczorek, David Bloom, Heather Constable, Janet Fang, Michelle Koo, Carol Spencer, Kristina Yamamoto  
<!--#[http://manisnet.org/GeoreferencingQuickReferenceGuide.pdf Georeferencing Quick Reference Guide] version 2012-10-08. John Wieczorek, David Bloom, Heather Constable, Janet Fang, Michelle Koo, Carol Spencer, Kristina Yamamoto-->
<!--#[http://manisnet.org/GeoreferencingQuickReferenceGuide.pdf Georeferencing Quick Reference Guide] version 2012-10-08. John Wieczorek, David Bloom, Heather Constable, Janet Fang, Michelle Koo, Carol Spencer, Kristina Yamamoto-->
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#[https://www.idigbio.org/wiki/index.php/Georeferencing iDigBio Georeferencing Wiki] http://tinyurl.com/idbgeowiki
#[https://www.idigbio.org/wiki/index.php/Georeferencing iDigBio Georeferencing Wiki] http://tinyurl.com/idbgeowiki
#[http://herpnet.org/Gazetteer/GeorefResources.htm HerpNET Georeferencing Resources]
#[http://herpnet.org/Gazetteer/GeorefResources.htm HerpNET Georeferencing Resources]
# Pre Workshop Survey Questions and Summary Results
#Take Workshop Notes Together Here
# Take Workshop Notes Together Here
#Post - Workshop Survey Questions
# Post - Workshop Survey Questions
#[https://www.idigbio.org/wiki/index.php/IDigBio_Listservs#Georeferencing_Working_Group Got a Georeferencing Question? Post it on the iDigBio Georeferencing List Serve]
#[https://www.idigbio.org/wiki/index.php/IDigBio_Listservs#Georeferencing_Working_Group Got a Georeferencing Question? Post it on the iDigBio Georeferencing List Serve]
 
#[https://plus.google.com/events/c0sjgu7mjp85vjel5rj8enq9ib0 BITC Global Online Seminar #25: Simple Workflow for Data Cleaning]
==== Bring your Datasets and Laptops: ====
'''Participants are strongly encouraged to bring representative datasets''' from their collections 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.


==== Wireless / Wired Access Issues: ====
==== Wireless / Wired Access Issues: ====
Both wired and wireless access provided to workshop participants. Connectivity instructions will be provided at the workshop.
Both wired and wireless access provided to workshop participants. Connectivity instructions will be provided at the workshop.


== Overview:  ==
== Goals of the Workshop:  ==
*Best practices for researchers for in-the-field creating of new locality data and legacy data georeferencing.
**Tools (hardware and software) and standards (what to document, datum etc.).
**How to re-patriate data and/or best practices for putting data into data repository if can’t be repatriated (what the obstacles are and minimization of data loss).
*How to evaluate already georeferenced data. Current tools for visualization and evaluation.
**Metrics to look for
**Current tools for georeferencing
**Online tools
**R
**QGIS
*Researchers give input on the challenges for georeferencing, using existing georeferences.
*Workflow review for some research review of using georeferenced data (Katja, Shelley, ...)


== Goals of the Workshop:  ==
Ultimate goal: Participant can point to aspects they have learned (tool, standard etc.) during the workshop and can indicate how they will use those aspects for their research goal/purpose (present or future).


== Workshop Objectives:  ==
== Workshop Objectives:  ==
'''Topics to be covered'''<br>
''Pre-workshop materials''<br>
*Introductory information about datums, mapping, coordinate systems<br>
*Basic georeferencing how-to<br>
''During workshop''<br>
*Data standards, DwC terminology and fields (e.g. lat, long, datum), differences among disciplines (neo- and paleontological fields)<br>
*Georeferencing toolkit and workflow examples (GEOLocate, maps, other resources, pros and cons)<br>
*Best practices for field collection of data (locality strings and GPS units, precision, datum) <br>
*How best to record and store georeferencing notes and other data sources (database/CMS dependant)<br>
*Best practices for georeferencing of legacy data given:<br>
**Varied research requirements for accuracy and precision
**Project and collection management limitations
**Uncertainty data - polygon vs. point radius, description and metadata, etc.
**Datum - georectify to a standard versus verbatim
*Workflows for incorporating data into different collections databases
**Best practice syntax in locality descriptions for use in automation vs verbatim strings
**Database limitations
**Multiple geopoint values and storage (verbatim, automated-non-vetted value, nearest named place, update to more accurate value, etc.)
*Downloading datasets - sources, different mechanisms
**Assessing data quality
**Uncertainty data - availability in data sources and interpretation
*Tools for aggregating, cleaning, visualizing and analyzing data
**R, QGIS, OpenRefine
**Creating maps
**Spatial analyses
**Automated, online tools and applications using geospatial data (e.g. LifeMapper)
*Difficult cases, such as geopolitically fluid locations over time, offshore localities<br>
*Hands-on practice & case studies<br>


== Schedule of Events - Agenda ==
Breakfast, Lunch and Dinner every day is on our own (not provided).
=== Day 1, Tuesday October 4th  ===
[https://vimeo.com/album/2163673/video/192472653 Recording Day 1]


=== Desired Outcomes:  ===
{| cellspacing="2" cellpadding="5" border="1"
 
 
<br>Informal Dinner or social event tbd
 
== Schedule of Events<br>  ==
 
Breakfast every day is on our own.
 
{| cellspacing="1" cellpadding="1" border="1" align="center"
|+
=== Day 1, Monday August 12th  ===
|-
|-
! width="49" scope="col" | '''Time '''<br>  
! width="49" scope="col" | '''Time '''<br>  
! width="400" scope="col" | '''Activity'''<br>  
! width="400" scope="col" | '''Activity'''<br>  
! width="150" scope="col" | '''Presenter'''<br>
! width="150" scope="col" | '''Presenter'''<br>
|-
|-
| 8:45<br>
| 8:45<br>
| Pick up Name Tags, Wireless Log-In, Wired Setup<br>  
| Pick up Name Tags, Wireless Log-In, Wired Setup, [https://docs.google.com/document/d/1m9cdERGtJkukb3EHUXPmCg58G08WWMA2HyBv28k6PUo/edit# Collaborative Notes (google doc)]<br>  
| <br>  
| <br>  
|-
|-
| 9:00<br>  
| 9:00<br>  
| Welcome, Overview and [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/TTT2_IntroToiDigBio_0.pptx Introduction to iDigBio]<br>
| Welcome by NCEAS host, Logistics, Trainer Introductions, Introduction to iDigBio, CCBER<br>
| iDigBio PI - Pam Soltis and Debbie Paul - Informatics Analyst / User Services<br>
| Katja Seltmann - CCBER, Debbie Paul - iDigBio, Ben Halpern - Director NCEAS, Ginger Gillquist - Logistics NCEAS <br>
|-
|-
| 9:15<br>  
| 9:20<br>  
| Trainer Introductions<br>  
| From the participants and instructors: a quick informal survey
| David Bloom<br>
Quick Name/Rank/Serial# introductions<br>
:tools you use<br>
:what you’d like to be able to do, tools you'd like to be able to use<br>  
|Deb Paul<br>
|-
|-
| <br>
| 10:00<br>  
| Participants Introductions -[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/BrindaLBCCgeoref.slide_.pptx LBCC TCN]<br>
| Standards, Terms & Fields: [http://rs.tdwg.org/dwc/terms/index.htm Darwin Core Standard], Key Terminology
| John Brinda, Missouri Botanical Garden<br>
[https://www.idigbio.org/wiki/images/5/52/Georef_iDigBio_terms.pdf iDigBio Recommended fields]<br>  
| David Bloom, Shelley James<br>
|-
|-
| <br>
| 10:15<br>  
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Riley-TTT2.ppt SCAN TCN]<br>
| [https://www.idigbio.org/sites/default/files/workshop-presentations/geotrain/GeoreferencingQuickReferenceGuide20121008.pdf Georeferencing Quick Reference Guide], and [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_GeoreferencingTemplate(CONCAT).xls Georeferencing Template]
| Edward Riley, <br>Texas A & M<br>
| Una Farrell
|-
| <br>  
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Pace_TTT2iDigBio.pptx TTD TCN]<br>
| Danielle Pace, AMNH<br>
|-
| <br>
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/MenardKatrinaidigBio_Menard.pptx InvertNet TCN]<br>
| Katrina Menard, Sam Noble Museum<br>
|-
| <br>
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/CaseyPaleonichesLightning.pptx Paleoniches TCN]<br>
| Michelle Casey, University of Kansas<br>
|-
| <br>
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GrantSharonTTT2FMNH_iDigBio2013.ppt Georeferencing at the Field Museum]<br>
| Sharon Grant, Field Museum<br>
|-
|-
| 10:30<br>
| Coffee Klatch w/ NCEAS<br>
| <br>
| <br>
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Wallace_TTT_workshop_slide.pptx Magnolia grandiFLORA]<br>
| Lisa Wallace, Mississippi State University<br>
|-
|-
| <br>
| 11:15<br>  
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/barroso-UMMZ-lightning-presentation-PPT.pptx FishNet2]<br>
| [https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/GeoreferencingConceptsandLocalityTypes2016.pptx Locality Types]
| Diego Barroso, University of Michigan<br>
| Una Farrell
|-
|-
| <br>
| 11:45<br>  
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/HarrisKari_TTT2_August2013-1.pptx Arkansas State University & SERNEC]<br>
| [http://manisnet.org/gci2.html Georeferencing Calculator], [http://goo.gl/G5RM9 Calculator Manual]<br>  
| Kari Harris, Arkansas State University<br>  
| David Bloom<br>
|-
|-
| <br>
| 12:10<br>  
| Participants Introductions - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Traggis_Hannah_LightningTalk_TTT2_Workshop-1.pptx Macroalgal Herbarium Consortium TCN]<br>
| Lunch<br>  
| Hannah Traggis, University of New Hampshire<br>
|  
|-
|-
| <br>  
| 13:10<br>  
| Participants Introductions - All other projects<br>
|[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_GeorefCalculatorExample.ppt Georeferencing Calculator Example] and Exercises, [http://manisnet.org/GeorefGuide.html MaNIS/HerpNET/ORNIS Georeferencing Guidelines]<br>  
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/BesterCathyGTTT2_lightningtalk_bester-2.pptx Cathy Bester, iDigBio]<br>
| David Bloom
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Uhrenlightning-1.pdf Mark Uhen, Paleobiology Database - PaleoDB]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/RevelezMarcyiDigBio2013-2.pptx Marcia Revelez, Angelo State Natural History Collections]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/FrablelightningTTT.pptx Benjamin Frable, Oregon State Ichthyology Collection]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/AllanJR_iDigBioTTT2013.pptx J Ryan Allen, University of Colorado Museum of Natural History]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Johansen_TTT2_2013.pptx Rebecca Johansen, Austin Peay State University]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Stevens_nysm_georef_intro.ppt Ellen Stevens, New York State Museum]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/CodyBryanGeorefTTT2Lightning.pptx Bryan Cody, North Carolina State University]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/ThomasJGeorefKUEnto.pptx Jennifer Thomas, University of Kansas]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/OrleusLunideIcthyology.pptx Lunide Orleus, University of Florida]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/BarkworthMaryGainesville-1.pptx Mary Barkworth, Utah State University]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Weru_Larry.pptx Lawrence Weru, Florida State University]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GoddenGrantTTT2_Godden_LightningTalk.pptx Grant Godden, University of Florida]<br>
Elana Benamy, ANSP at Drexel<br>
 
| Everyone<br>
|-
|-
| 10:00<br>  
| 13:40<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_Workshop_Overview.pptx Workshop Overview], Introduction to Georeferencing, and Thinking like a Trainer<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/InternetResources2016.pptx Internet Resources] - Where to Begin? [http://georeferencing.org georeferencing.org] <br>  
| David Bloom<br>
[http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/2015_OnlineExercises11CONCAT.xls Exercises using online resources - Version 2]
| Una Farrell
|-
|-
| 10:20<br>
| 14:40<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Georeferencing%20TTT2%20presentation.pptx Selected Survey Results], Train-the-Trainers Second Georeferencing Pre-workshop Survey Report and Update from TTT1 Participants Pay-It-Forward Efforts<br>
| Shari Ellis<br>
|-
| 10:35<br>  
| Break<br>  
| Break<br>  
| <br>
| <br>
|-
|-
| 11:00<br>
| 15:10<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_CollaborationToAutomation.ppt Georeferencing Introduction: Collaboration to Automation]<br>
| Exercises cont.<br>  
| Dave Bloom<br>
|-
| 11:30<br>
| [https://www.idigbio.org/sites/default/files/workshop-presentations/geotrain/idigbio_tdt_geog_concepts.pptx Geographical Concepts]<br>
| Nelson Rios<br>
|-
| 11:50<br>
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_PointRadiusBestPractices.ppt Point-Radius Method and Best Practices] <br>
| Jessica Utrup<br>
|-
| 12:10<br>  
| [http://rs.tdwg.org/dwc/terms/index.htm Darwin Core Standard], Key Terminology<br>[https://docs.google.com/spreadsheet/ccc?key=0AtzqKK80tdzhdDg1aFJwNnVsRXNhRFNrUE1tMWxBQ1E#gid=0 iDigBio Recommended fields]
| Dave Bloom<br>
|-
| 12:30<br>
| Lunch (Provided)<br>  
| <br>
| <br>
|-
| 13:30<br>
| [https://www.idigbio.org/sites/default/files/workshop-presentations/geotrain/GeoreferencingQuickReferenceGuide20121008.pdf Georeferencing Quick Reference Guide], [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GeoreferencingConceptsandLocalityTypes2013.pptx Locality Types], and [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_GeoreferencingTemplate(CONCAT).xls Georeferencing Template]<br>
| Una Farrell<br>
|-
| 14:40<br>
| [http://manisnet.org/gci2.html Georeferencing Calculator], [http://goo.gl/G5RM9 Calculator Manual]<br>
| Dave Bloom<br>
|-
|-
| 15:30<br>  
| 15:30<br>  
| Break<br>
| [http://www.museum.tulane.edu/geolocate/ GEOLocate]: Overview, Basics & Demos<br>  
| <br>
[http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/idigbio_ttt3_geolocate.pptx GEOLocate Introduction]<br>
|-
[http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/cogef2_sernec.pptx '''Co'''llaborative '''Ge'''oreferencing using CoGe] by GEOLocate
| 16:00<br>  
| Nelson Rios<br>
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_GeorefCalculatorExample.ppt Georeferencing Calculator Example] and Exercises, [http://manisnet.org/GeorefGuide.html MaNIS/HerpNET/ORNIS Georeferencing Guidelines]<br>
| Dave Bloom<br>
|-
|-
| 17:00<br>  
| 17:00<br>  
| Day in Review and Considerations for Trainers-to-be<br>Trivia Question of the Day<br>[http://idigbio.adobeconnect.com/p9cfrts7nom/ A.M. Recording: Start-10:30]<br>[http://idigbio.adobeconnect.com/p3svd7e8gse/ A.M. Recording: 10:40-12:30]<br>
| Day in Review<br>Trivia Question of the Day<br>Survey (15 min)
[http://idigbio.adobeconnect.com/p7acqka9r44/ P.M. Recording: 1:30-3:30]<br>
|  
[http://idigbio.adobeconnect.com/p844nmpspes/ P.M. Recording 3:30-5:15]<br>
| David Bloom<br>Debbie Paul<br>
|-
|-
| 17:30<br>  
| 17:30<br>  
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| <br>
| <br>
|}
|}
<br>
'''Dinner on our own''' - See list of [http://goo.gl/maps/CN0tP local restaurants]. You'll be reimbursed at the standard per diem rates.


'''Optional Evening Activity is''': TBA
'''Dinner on our own''' - See [https://www.idigbio.org/wiki/images/8/89/Local_Restaurants.pdf list of local restaurants]. '''Optional Evening Activity''': Happy hour and joyful GeoGathering at [http://www.hoffmannbrathaus.com/ Hoffmann Brat Haus]
 
=== Day 2, Wednesday October 5th  ===
[https://vimeo.com/album/2163673/video/192472654 Recording Day 2]


{| cellspacing="1" cellpadding="1" border="1"
{| cellspacing="2" cellpadding="5" border="1"
|+
|+
=== Day 2, Tuesday August 13th  ===
|-
|-
! width="49" | '''Time<br>'''  
! width="49" | '''Time<br>'''  
! width="400" | '''Activity<br>'''  
! width="400" | '''Activity<br>'''  
! width="150" | '''Presenter<br>'''
! width="150" | '''Presenter<br>'''
|-
| 8:50<br>
|Please complete Survey for Day 1!
|
|-
|-
| 9:00<br>  
| 9:00<br>  
| Review and Questions<br>  
| Two! Trivia Questions<br>Review and Questions<br>Software Installs check for tomorrow<br>
| All<br>
| All<br>
|-
|-
| 9:10<br>  
| 9:10<br>  
| Group Photo<br>
|GEOLocate: Advanced Features, Collaborative Georeferencing and the GEOLocate API<br>  
| All, Joanna McCaffrey, photographer<br>
|Nelson Rios<br>
|-
| 9:30<br>
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/OnlineResources2013.pptx Internet Resources] - Where to Begin?<br>  
| Una Farrell<br>
|-
|-
| 10:00<br>  
| 10:00<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_OnlineExercises11(CONCAT).xls Exercises: Internet Resources]<br>  
| [http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/Georeferencing%20Presentation%20INTRO%20-%20Polygons_FINAL.pptx Importance of Polygons]<br>  
| All<br>
| Mike Yost, Nelson Rios<br>
|-
|-
| 10:30<br>  
| 10:30<br>  
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|-
|-
| 11:00<br>  
| 11:00<br>  
| Exercises: Internet Resources (continued)<br>  
| GPS Units and APPs: [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GPS_EXERCISE.docx Exercise Introduction]<br>
| David Bloom, Mike Yost, Shelley James, Katja Seltmann<br>
|-
| 11:15<br>
| GPS Exercises (continued outside)<br>  
| All<br>
| All<br>
|-
|-
| 12:15<br>  
| 12:15<br>  
| More Online Resources (resources used by/requested by participants)<br>  
| Lunch<br>  
| David Bloom<br>
| <br>
|-
|-
| 12:30<br>  
| 13:15<br>  
| Lunch (Provided)<br>  
| GPS Exercises (continued outside)<br>Please [https://goo.gl/X3LkQO upload your GPS Data here]
| <br>
|All<br>
|-
|-
| 13:30<br>  
| 13:30<br>  
| GPS Exercise Introduction<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_GoodAndBadLocalities.ppt Good and Bad Localities], [http://www.idigbio.org/sites/default/files/working-groups/gwg/GoodBadLocalitiesV27Oct2015.doc Field Locality Handout]: MVZ and iDigBio GWG Guide for Recording Localities in Field Notes, <br>[http://biscicol.org/template Field Information Management Systems (FIMS)]<br> [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/HandoutPaperMaps.doc Paper maps]
| Dave Bloom<br>
| David Bloom<br>
|-
|-
| 13:45<br>  
| 14:15<br>  
| GPS Exercises (outside)<br>  
| Georeferencing Workflows: presentations and discussion<br>
Researcher and Collections perspectives: Producers and Consumers<br>
:[http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/WorkflowKickOffQuestionsRCollectionManagers.pptx Collection and Data Managers]
:[http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/WorkflowKickOffQuestionsResearchers.pptx Researchers]
:[https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/WorkflowKickOffQuestionsRCollectionManagers_YOST.pptx Mike Yost]
:[https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/WorkflowKickOffQuestionsJessicaUtrup.pptx Jessica Utrup]
:[https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/WorkflowKickOffQuestionsResearchers_SLafia.pptx Sara Lafia]
:[https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/WorkflowKickOffQuestionsResearchers-seltmann.pptx Katja Seltmann]
:[https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/WorkflowKickOffQuestionsResearchers_SAJ.pptx Shelley James]
:[http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/WorkflowKickOffQuestionsEBD.pptx Edward Davis]
<br>
:[https://www.idigbio.org/content/digitization-workflows Digitization Workflows at iDigBio]
:[https://www.idigbio.org/wiki/index.php/Georeferencing#Georeferencing_Community_Protocols_and_Workflows Georeferencing Protocols and Workflows - from a collections viewpoint]
| All<br>
| All<br>
|-
|-
| 15:15<br>  
| 15:15<br>  
| Break<br>  
| Break<br>  
| All<br>
|
|-
|-
| 15:30<br>  
| 15:45<br>  
| Online Exercises<br>Review of known answers<br>  
| Online Exercises, Review of known answers<br>  
| Una Farrell
| <br>
|-
|-
| 16:15<br>  
| 16:30<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_PaperMaps.ppt Georeferencing Using Paper Maps], [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/HandoutPaperMaps.doc Paper Maps Handout]<br>  
| GPS Exercise - Review (.kmz), Summary Spreadsheet, Field Worksheet, Locality Descriptions<br>  
| Jessica Utrup<br>
:GPSTour
:GPS Status
:Geopaparazzi
:Camera GPS
:Theodolite
| David Bloom, Jessica Utrup<br>
|-
|-
| 16:45<br>  
| 16:45<br>  
| Day in Review and Considerations for Trainers-to-be<br>
| Day in Review<br>
Your Input Needed - Mapping Functions in the iDigBio Portal<br>
Download dataset for tomorrow<br>
Trivia Question of the Day<br>
Trivia Question of the Day<br>
'''Hotelwork: create/document your project workflow(s)''' for discussion on Wednesday<br>[http://idigbio.adobeconnect.com/p8zbma8akf6/ A.M. Recording: Start-10:30]<br>[http://idigbio.adobeconnect.com/p4v5jqkvx5w/ A.M. Recording: 10:30-12:30]<br>[http://idigbio.adobeconnect.com/p5wq7gx5d87/ P.M. Recording: 4:30-5:30]<br>  
|
| David Bloom<br>Joanna McCaffrey<br>Debbie Paul<br>
|-
| 17:15<br>
| Survey (15 min)<br>
|
|-
|-
| 17:30<br>  
| 17:30<br>  
| END<br>  
| End<br>  
| <br>
| <br>
|}
|}
'''Dinner on our own''' - See list of [http://goo.gl/maps/CN0tP local restaurants]. You'll be reimbursed at the standard per diem rates.
'''Dinner on our own''' - See [https://www.idigbio.org/wiki/images/8/89/Local_Restaurants.pdf list of local restaurants].  
 
'''Optional Evening Activities:''' TBA
'''Optional Evening Activities are:''' TBA
 
{| cellspacing="1" cellpadding="1" border="1"
|+
 
=== Day 3, Wednesday August 14th  ===
 


=== Day 3, Thursday October 6th  ===
[http://s.idigbio.org/idigbio-downloads/a69d1541-4726-465d-84ad-50c7ed556eee.zip 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.<br/>
[https://vimeo.com/album/2163673/video/192472656 Recording Day 3]


{| cellspacing="2" cellpadding="5" border="1"
|-
|-
! width="49" | '''Time''' <br>  
! width="49" | '''Time''' <br>  
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| All<br>
| All<br>
|-
|-
| 9:15<br>  
| 9:05<br>  
| GPS Exercise - [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GPSResults.kmz Review (.kmz)], [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GPSResults.xlsx Summary Spreadsheet], [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GPS_EXERCISE.docx Field Worksheet]<br>
| [https://docs.google.com/presentation/d/1ORWr2krUhwpNWteDXmNyoUaUjFkJ8PAc-mj7tNW1Rng/edit?usp=sharing​ Georeferencing for Research Use Workshop - iDigBio Datasets]
| Dave Bloom<br>
* [https://docs.google.com/presentation/d/1ORWr2krUhwpNWteDXmNyoUaUjFkJ8PAc-mj7tNW1Rng/edit?usp=sharing​ Downloading datasets from iDigBio] - get data from portal and explain each component to the dataset.
filter and get the dataset
* What is raw vs not raw?
* Similar or different from GBIF?
* [https://github.com/iDigBio/idigbio-search-api/wiki/Data-Quality-Flags List of iDigBio Flags]:
* Walk through steps of download, but provide dataset.
* iDigBio Data set: http://s.idigbio.org/idigbio-downloads/a69d1541-4726-465d-84ad-50c7ed556eee.zip
|Matthew Collins (remote), Katja Seltmann, Shelley James<br>
|-
|-
| 9:35<br>  
| 10:00<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_ExercisesPaperMaps_SA_CR(CONCAT).xls Exercises: Using Paper Maps]<br>
| Data Quality: How to evaluate existing georeferenced data/Fitness for Use
| All<br>
* Data quality flags
* What do you need the data for (differences in use-cases)
* http://s.idigbio.org/idigbio-downloads/a69d1541-4726-465d-84ad-50c7ed556eee.zip
* 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
| Katja Seltmann, Shelley James<br>
|-
|-
| 10:30<br>  
| 10:30<br>  
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|-
|-
| 11:00<br>  
| 11:00<br>  
| Exercises: Using Paper Maps (continued)<br>  
|Cleaning Datasets: Spreadsheets, Open Refine, tracking your work<br>  
| All<br>
| Deb Paul, Nelson Rios, Katja Seltmann<br>
|-
|-
| 12:30<br>  
| 12:00<br>  
| Lunch on our own. See [http://goo.gl/maps/CN0tP local restaurant map]<br>  
| Lunch<br>  
| <br>
| <br>
|-
| 13:00<br>
| [https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/GRU_spreadsheetsRefine6Oct2016.pptx Cleaning Datasets: Spreadsheets, Open Refine, tracking your work] (2)<br>
| Deb Paul, Nelson Rios, Katja Seltmann<br>
|-
|-
| 13:30<br>  
| 13:30<br>  
| Exercises: Using Paper Maps (continued)<br>  
| Visualizing datasets: Set up QGIS and load data
| All<br>
* vector: points, lines, polygons
* raster: images<br>
Auxiliary [https://ucsb.box.com/s/10v6jzr6lrdmafazfvm2aukhpphr2q55 datasets]: Download any additional datasets of interest. Online [https://docs.google.com/document/d/16X0rmTqdMWzWUJIq87Pkap5IVHn3sl3bOp0jr7sev6w/edit?usp=sharing Tutorial]
| Sara Lafia<br>
|-
|-
| 14:30<br>  
| 15:00<br>  
| Online Exercises - Participant Georeferences Review<br>
| Break<br>  
Group Results and Answers available upon request
| <br>
| All<br>
|-
| 14:45<br>
| Examples and Discussion: Process, Workflows, Priorities, and Collaborations<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_EMuGeoRef.pptx EMu], [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/KUMIP_Georeferencing_Protocol_AUG2013.pdf KUMIP and Specify]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/idigbio_ttt2_fishnet.pptx FishNet2]<br>
ORNIS [http://www.ornisnet.org/georeferencing/workflownew Workflow] and [http://www.ornisnet.org/georeferencing/repatriationguide/repatriationprocess Repatriation]<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Paul_WorkflowsExpertorNoviceTTT2.pptx Workflows and Expert or Novice: an Experiment in Progress]<br>
*[https://www.idigbio.org/sites/default/files/workshop-presentations/geotrain/FSU_Georef-Protocol.doc FSU Georeferencing Protocol (Collaborative using GEOLocate)]<br>
*[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Mast_Protocol.docx FSU Georeferencing Protocol (Excel and GEOLocate)]<br>
*Online Videos: [http://symbiota.org/tiki/tikimovies/georef1.htm Georeferencing and Symbiota], [https://vimeo.com/50943206 Georeferencing and Specify]<br>
*[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/ShortSurvey.xlsx Documentation Check: Short Questionnaire], [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/LongSurvey.xlsx Long Questionnaire]<br>  
| Jessica Utrup, Una Farrell, Nelson Rios, Deb Paul, Dave Bloom<br>
|-
|-
| 15:30<br>  
| 15:30<br>  
| Break<br>
| Visualizing datasets: Preview and explore toolkits & saving your maps and data<br>
| <br>
| Sara Lafia<br>
|-
| 16:00<br>
| Process, Workflows, Priorities, and Collaborations (continued)<br>Discuss Hotelwork: Participant Project workflow(s)<br>
*Danielle Pace, AMNH, Arthropod Easy Capture<br>
*Katrina Menard, Sam Noble Museum<br>
*Mark Uhen, Paleodb.org<br>  
| Jessica Utrup, Una Farrell, Nelson Rios, Deb Paul, Dave Bloom<br>
|-
|-
| 17:00<br>  
| 17:15<br>
| Day in Review and Considerations for Trainers-to-be,<br>
| Survey (15 min)
'''Volunteers for Training Demos'''<br>
|
*Kari Harris, Arkansas State University<br>
*Edward Riley, Texas A & M<br>
*Sharon Grant, The Field Museum<br>
*Marcia Revelez, Angelo State Natural History Collections<br>
Trivia Question of the Day<br>
[http://idigbio.adobeconnect.com/p6tc7p1kpj5/ A.M. Recording: Start-9:30]<br>
[http://idigbio.adobeconnect.com/p81nbwrgkgt/ P.M. Recording: 2:30-4]<br>
[http://idigbio.adobeconnect.com/p3txnfajdno/ P.M. Recording: 4:15-Finish]<br>
| David Bloom<br>Debbie Paul<br>
|-
|-
|17:30<br>  
|17:30<br>  
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| <br>
| <br>
|}
|}
'''Evening Activity is''': Group Dinner,  [http://leonardosgainesville.com/706menu.pdf Leonardo's 706], 7PM - 9PM, short walk due east of the hotel, on the north side of the street.
'''Dinner''': TBD<br>
 
'''Today in Gainesville''': <br>Downtown Gainesville, Union Street Farmers Market, 4 - 7 PM. Food and live music.<br>http://unionstreetfarmersmkt.com/index.php/vendors<br>
 
{| cellspacing="1" cellpadding="1" border="1"
|+
 
=== Day 4, Thursday August 15th  ===
 
 


=== Day 4, Friday October 7th  ===
[https://ucsb.box.com/s/5qqiiqw237jr5mb7ip8hm5yspl4b8hcn Download zipped QGIS project] The project to the point we completed on Day 3 is available for download in the same folder as the auxiliary data. Launch the QGIS project from the '''Tutorial.qgs''' file. <br/>
[https://vimeo.com/album/2163673/video/192472655 Recording Day 4]
 
{| cellspacing="2" cellpadding="5" border="1"
|-
|-
! width="49" | '''Time<br>'''  
! width="49" | '''Time<br>'''  
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|-
|-
| 9:00<br>  
| 9:00<br>  
| Questions and Review<br>  
| Questions and Review
| David Bloom<br>
Share your datasets! [https://ucsb.box.com/s/hwddmd4cxgvxte1gn0a2lyf70k7ab6px]: Upload your research datasets that you'd like to work on.<br>  
| All <br>
|-
|-
| 9:10<br>  
| 9:10<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_PaperMapsReview.ppt Paper Maps Review]<br>  
|Exploring datasets: Aggregating by Regions
| Jessica Utrup<br>
* Join, aggregate, or summarize records by county
* Summarize observations intersecting counties
* Finding altitude
* Why do this?
<br>  
| Sara Lafia, Katja Seltmann, Nelson Rios<br>
|-
|-
| 9:40<br>  
| 9:50<br>  
| Results: Paper Maps<br>
| Exploring datasets: Time animation
Group Results and Answers available upon request
* By collecting event date or collector (to show biases in collection)
| Dave Bloom<br>
* Check for errors with dates or transcriptions
| Sara Lafia<br>
|-
|-
| 10:30<br>  
| 10:30<br>  
Line 416: Line 398:
|-
|-
| 11:00<br>  
| 11:00<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/2013_GoodAndBadLocalities.ppt Good and Bad Localities], [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GoodBadLocalities.doc Field Locality Handout], Review of GPS Locality Descriptions<br>
| Exploring datasets: Uncertainty
| David Bloom<br>
* Bin points based on uncertainty rank
* Symbolize uncertainty by collector, data quality score - systematic error
| Sara Lafia<br>
|-
|-
| 11:30<br>  
| 11:30<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/idigbio_ttt2_geolocate.pptx Introduction to GEOLocate]<br>[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GEOLocate_What_to_Do.ppt What To Do]<br>
| Exploring datasets: Spatial autocorrelation
| Nelson Rios<br>Michelle Vanderwel<br>
* Distribution/clustering prevalence based on species, collector, etc.
* Date-collector correlation
| Sara Lafia<br>
|-
|-
| 12:15<br>  
| 12:00<br>  
| Lunch on our own. See [http://goo.gl/maps/CN0tP local restaurant map]<br>
| Lunch on our own.
| <br>
| <br>
|-
| 13:00<br>
| LifeMapper LIVE DEMO<br>
| Jeffrey Cavner, James Beach, et al<br>
|-
|-
| 13:15<br>  
| 13:15<br>  
| Using GEOLocate: Basics (Web Application)<br>  
| Work on own data sets/Open question time/Practice. Polygon practice<br>  
| Nelson Rios<br>
| Nelson Rios, et al<br>
|-
|-
| 13:45<br>  
| 13:45<br>  
| Using GEOLocate: Batch Processing (Web App and Excel)<br>  
| ''Breakout sessions''<br>
| Nelson Rios<br>
Cleaning data using r <br>
|-
Accessing APIs using r <br>
| 14:25<br>  
More with QGIS<br>
| Using GEOLocate: Collaborative Georeferencing Administrative Portal<br>  
GEOLocate in Symbiota<br>
| Nelson Rios<br>
Advanced GEOLocate<br>
GPS Apps<br>
Georectification<br>
Try GeoODK [http://geoodk.com/ http://geoodk.com/]
| <br>
|-
|-
| 15:30<br>  
| 15:30<br>  
Line 444: Line 438:
|-
|-
| 16:00<br>  
| 16:00<br>  
| Using GEOLocate: Collaborative Georeferencing Web Client<br>  
| Research Use of the Data. A conversation from the collective point-of-view of the researchers present.<br> Challenges? Experiences? Needs (software, skills, infrastructure)? What changes might you make now to your workflows?<br>  
| Nelson Rios<br>
| Ed Davis, Katja Seltmann, Shelley James, Nelson Rios, Sara Lafia<br>
|-
|-
| 16:20<br>  
| 16:30<br>  
| [https://www.idigbio.org/content/advanced-geolocate-course-services-integration-end-end-workflows Advanced GEOLocate]: Taxon validation, Web services &amp; integration, Building end-to-end georeferencing workflows<br>Note this topic was covered in a [http://idigbio.adobeconnect.com/p47ekqz7lum/ remote recorded session] after TTT2.
| Day & workshop in Review<br>[https://www.idigbio.org/content/webinar-isn%E2%80%99t-spatial-discover-how-geo-enable-your-research-and-teaching-today%E2%80%99s-interactive iDigBio Webinar On Your Calendar Oct 12th, 2016 - Isn't that Spatial?]<br>Post Workshop Survey
| Nelson Rios<br>
| <br>
|-
|-
| 17:00<br>
| Day in Review and Considerations for Trainers-to-be<br>
Trivia Question of the Day<br>
[http://idigbio.adobeconnect.com/p8gjag8hri2/ A.M. Recording: Start-10:20]<br>
[http://idigbio.adobeconnect.com/p8kfnsa6lyf/ A.M. Recording: 11-12:30]<br>
[http://idigbio.adobeconnect.com/p66niiv7irq/ P.M. Recording: 1:30-5]<br>
| David Bloom<br>Debbie Paul<br>
|-
|-
| 17:30<br>  
| 17:30<br>  
| End<br>  
| Beer<br>  
| <br>
| <br>
|-
|-
|}
|}
'''Dinner on our own''' - See list of [http://goo.gl/maps/CN0tP local restaurants]. You'll be reimbursed at the standard per diem rates.
'''Dinner on our own''' - See [https://www.idigbio.org/wiki/images/8/89/Local_Restaurants.pdf list of local restaurants].  
<br>
<br>


{| cellspacing="1" cellpadding="1" border="1"
|+


=== Day 5, Friday August 16th ===
<br/>
Some software [http://www.datacarpentry.org/workshop-template/install.html install instructions] from Data and Software Carpentry
 
== Requests for the Future ==
* Scripts/tools for repeated cleaning/analysis
* Using the iDigBio API (API for dummies)
* Inselect (note we provided links for more on this tool - to the workshop participants, see [https://docs.google.com/document/d/1m9cdERGtJkukb3EHUXPmCg58G08WWMA2HyBv28k6PUo/edit?usp=sharing google doc])
* Automated data cleaning - iDigBio and VertNet activities
* What to do with quantified uncertainties & polygons - Jorge Soberon (KU team, others in the fitness for use GBIF working group - see [https://www.gbif.org/document/82612/report-of-the-task-group-on-gbif-data-fitness-for-use-in-distribution-modelling Final Report of the Task Group on GBIF Data Fitness for Use in Distribution Modelling]
* QGIS layers - use cases (e.g. elevation)
* Detailed Workflows - for georeferencing, when not to georeference (see iDigBio Georeferencing Working Group - https://www.idigbio.org/wiki/index.php/IDigBio_Working_Groups#Georeferencing_Working_Group_.28GWG.29), cleaning
* Documentation for tutorials
* Standards/possibility for storing multiple georeferences (and other possibilities such as annotations within iDigBio)
* QGIS tutorial as a Software/Data Carpentry format
* QGIS working group
* Geolocate with r webinar (follow on from Symbiota  webinar https://www.idigbio.org/content/symbiota-webinar-geolocate-toolkit https://www.idigbio.org/content/coge-collaborative-georeferencing-demo-webinar
 


|-
== Trained Georeferencers ==
! width="49" | '''Time<br>'''
* Map of [http://tinyurl.com/idbtttmap Participants and Instructors for TTT1 and TTT2]
! width="400" | '''Activity<br>'''
* Wiki for all [[TTT1TTT2| TTT1 and TTT2 Participants]]
! width="150" | '''Presenter<br>'''
|-
| 9:00<br>
| Review and Questions<br>
| David Bloom<br>
|-
| 9:10<br>
| Data Cleaning, Processing, and Analysis<br>
[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/OpenRefineTTT22013.pptx Cleaning, Validating, and Enhancing Data with Open Refine]<br>[https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/OpenRefineTTT2Demo.csv sample CSV] and [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/openrefinettt2demoscripts.txt sample script] to use with this presentation
<br>([http://www.gpsvisualizer.com/ GPS Vizualizer], [http://code.google.com/p/google-refine/ Google Refine] which is now [https://github.com/OpenRefine Open Refine], [https://gist.github.com/3880547 Example of a Refine Call to GEOLocate], [http://www.r-project.org/ r-project], [http://rstudio.org/download/desktop RStudio], [http://www.qgis.org/ QuantumGIS], [https://www.idigbio.org/sites/default/files/workshop-presentations/geotrain/QGIS1.8BasicOperations-vectors.doc QGIS Basic Operations)]<br>
| Debbie Paul, Nelson Rios, Dave Bloom<br>
|-


| 10:30<br>
== Pre-Workshop Assignments ==
| Break<br>
# Attend pre-workshop online meeting. Two options, choose one.
| <br>
## Thursday September 15th - two times to choose from:
|-
### 11am EDT (10am CDT, 9am MDT, 8am PDT)
| 11:00<br>
### 3pm EDT (2pm CDT, 1pm MDT, 12pm PDT)
| Open Work Session - Participant/TCN Georeferencing Projects (use those data sets)<br>
## Sign Up Here: https://goo.gl/forms/WmJO6z79rx5nHlv32
| All<br>
## 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.''
| 12:00<br>
## Collaboration to Automation: https://vimeo.com/53006304 (25 min lecture, 10 min discussion)
| Open Work Session (continued)<br>
## Geographical Concepts: https://vimeo.com/53008556 (4 min lecture, 2 min discussion)
| All<br>
### https://vimeo.com/album/2163673/video/63692461 (4 min lecture only)
|-
## Point Radius Method and Best Practices: https://vimeo.com/53006303 (20 min lecture, 5 min discussion)
| 12:30<br>  
## '''OPTIONAL video''': [https://plus.google.com/events/c0sjgu7mjp85vjel5rj8enq9ib0 BITC Global Online Seminar #25: Simple Workflow for Data Cleaning] (1 hour)
| Lunch on our own. See [http://goo.gl/maps/CN0tP local restaurant map]<br>
# Please '''install the following software'''
| <br>
## '''QGIS''' and then [http://plugins.qgis.org/plugins/ QGIS Plugins]. '''NOTE it's easy to install all the plugins from inside QGIS once you have it installed.''' [[File:QGISPlugins2.png|300px|thumb|right|QGIS plugins menu - Manage and Install]][[File:plugins.png|300px|thumb|right|QGIS plugins menu]]
|-
### '''QGIS''': http://qgis.org/en/site/forusers/download.html
| 13:30<br>
### ''' 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, GPS Tools, Heatmap, Interpolation, OpenLayers, Processing, TimeManager, and Lifemapper.
| Open Work Session (continued)<br>
#### [https://plugins.qgis.org/plugins/clipper/ Clipper] (clip intersecting vector features)
| All<br>
#### [https://docs.qgis.org/2.2/en/docs/user_manual/plugins/plugins_coordinate_capture.html?highlight=coordinate Coordinate Capture] (find coordinates in various coordinate reference systems (CRS) via mouse-over)
|-
#### [https://github.com/mixedbredie/qgis-gazetteer-search?highlight=gazetteer Gazetteer Search] (finding named places via a search bar): NOTE: The Gazetteer Plugin is not "discoverable" through the Plugins manager in QGIS. You'll need to follow the installation steps listed here: https://github.com/AstunTechnology/QGIS-Gazetteer-Plugin#Installation
| 14:15<br>
##### Manual
| Batch Georeferencing in Symbiota<br>
###### find where your QGIS is installed on your machine
| John Brinda, Missouri Botanical Garden<br>
###### right click the folder to see contents and find the folder for Plugins
|-
####### for example, on Deb's Windows 10 laptop, the path to the correct QGIS plugins folder is C:\Users\dlpss\.qgis2\python\plugins
| 14:30<br>
###### make a folder called gazetteersearch inside of the QGIS Plugins directory
| Volunteer Training Demos - <br>
###### download the contents from GitHub and move them into the gazetteersearch folder
*Kari Harris, Arkansas State University ([https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/iDigBio_TTT2_August_2013_DemoPresentation_Kari_Harris.pptx .ppt]) <br>
###### close and reopen QGIS in order for the plugin to show up
*Edward Riley, Texas A & M ([https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Insect_Specimen_labeling.ppt .ppt])<br>
##### via Git
*Sharon Grant, The Field Museum ([https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/idigbio_polar_projections.ppt .ppt])<br>
###### clone the repository into your QGIS Plugins folder following the steps from the link above. Please let Sara know if you have any other questions.
*Marcia Revelez, Angelo State Natural History Collections ([https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/Workflow_Marcy.pptx .ppt])<br>
#### [http://docs.qgis.org/2.0/en/docs/user_manual/working_with_gps/plugins_gps.html?highlight=GPS GPS Tools] (loading and importing GPS data)
| Trainees<br>
#### [http://documentation.qgis.org/2.0/en/docs/user_manual/plugins/plugins_heatmap.html?highlight=heatmap Heatmap] (generate a heatmap raster given input vector points)
|-
#### [http://documentation.qgis.org/2.0/en/docs/user_manual/plugins/plugins_interpolation.html?highlight=interpolation Interpolation] (interpolation techniques given vertices of a vector layer)
| 15:30<br>
#### [http://documentation.qgis.org/2.0/en/docs/training_manual/qgis_plugins/plugin_examples.html?highlight=openlayers OpenLayers] (load basemaps from OpenStreetMap, Google, etc.)
| Break<br>
#### Processing (spatial data processing framework)
| <br>
#### [https://plugins.qgis.org/plugins/timemanager/?highlight=time TimeManager] (event-visualization animation for vector features)
|-
#### [http://plugins.qgis.org/plugins/lifemapperTools/ Lifemapper]: Plugin for Lifemapper webservices for SDM modeling, and multispecies Presence Absence Matrix (PAM) analysis. The tool allows you to build SDM models using GBIF, iDigBio, or user supplied species occurrence data.
| 16:00<br>
### ''' [https://github.com/AstunTechnology/QGIS-Gazetteer-Plugin Gazetteer Search] requires an additional step; follow these steps to install (manual):
| [https://ufl.qualtrics.com/SE/?SID=SV_eD1wtiXhHUS0zB3 Post-Workshop Survey]<br>  
#### find where your QGIS is installed on your machine
| All<br>
#### right click the folder to see contents and find the folder for Plugins
|-
#### make a folder called gazetteersearch inside of the QGIS Plugins directory
| 16:30<br>  
#### download the contents from GitHub and move them into the gazetteersearch folder
| Day in Review and Considerations for Trainers-you-now-be<br>
#### close and reopen QGIS in order for the plugin to show up
Your Input Needed - Mapping Functions in the iDigBio Portal - Part 2<br>
#### OR install via command line (using Git - see instructions in link above)
Trivia Question of the Day<br>  
#### clone the repository into your QGIS Plugins folder following the steps from the link above.
| David Bloom<br>Joanna McCaffrey<br>Debbie Paul<br>
## '''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 [https://swissbib.github.io/2016-06-23-basel/ Open Refine Install] or [https://github.com/OpenRefine/OpenRefine/wiki/Installation-Instructions Install Open Refine] for more help if you run into any Open Refine install issues).
|-
### '''Windows'''
| 17:00<br>  
#### Go to the OpenRefine [http://openrefine.org/download.html download page].
| Workshop Summary and Certificates<br>  
#### Click on <i>Windows kit</i> to download the install file
[http://idigbio.adobeconnect.com/p66niiv7irq/ A.M. Recording: 9:30-11]<br>
#### To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead)
[http://idigbio.adobeconnect.com/p5x2ywuctc2/ P.M. Recording: 2:15-3:45]<br>
#### OpenRefine will then open in your web browser.
| All Instructors<br>
#### If it doesn't open automatically, open a web broswer after you've started the program and go to the URL <code>http://localhost:3333</code> and you should see OpenRefine.
|-
### '''MacOS'''
| 17:30<br>  
#### Go to the OpenRefine [http://openrefine.org/download.html download page].
| End<br>  
#### Click on <i>Mac kit</i> to download the install file
| <br>
#### Open the downloaded .dmg file
|}
#### Drag the icon in to the Applications folder
'''Dinner on our own''' - See list of [http://goo.gl/maps/CN0tP local restaurants]. You'll be reimbursed at the standard per diem rates. Leaving tomorrow? Want to get together for dinner or hang out at the hotel pool?
#### Double click on the icon and Google Refine will then open in your web browser.
#### If it doesn't open automatically, open a web broswer after you've started the program and go to the URL <code>http://localhost:3333</code> and you should see OpenRefine.
###'''Linux'''
#### Go to the OpenRefine [http://openrefine.org/download.html download page].
#### Click on <i>Linux kit</i> to download the install file
#### Download and extract
#### Type <code>./refine</code> in your terminal and Google Refine will then open in your web browser.
#### If it doesn't open automatically, open a web broswer after you've started the program and go to the URL <code>http://localhost:3333</code> and you should see OpenRefine.
## '''Spreadsheet''' software (your choice, Libre Office, Excel, etc.,)
### 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/
## '''Java''': Please make sure you have [https://java.com/en/download/ Java installed] (needed for Open Refine to work).
# OPTIONAL software install and tutorials - if you are interested in the R breakout section we will offer at the workshop.
## '''R & RStudio''': R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
### '''Windows'''
#### [https://www.youtube.com/watch?v=q0PjTAylwoU Video Tutorial]
#### Install R by downloading and running [http://cran.r-project.org/bin/windows/base/release.htm this .exe file] from CRAN (http://cran.r-project.org/index.html).
#### Also, please [http://www.rstudio.com/ide/download/desktop install the RStudio IDE].
### '''Mac OS X'''
#### [https://www.youtube.com/watch?v=5-ly3kyxwEg Video Tutorial]
#### Install R by downloading and running [http://cran.r-project.org/bin/macosx/R-latest.pkg this .pkg file] from CRAN (http://cran.r-project.org/index.html).
#### Also, please [http://www.rstudio.com/ide/download/desktop install the RStudio IDE].
### '''Linux'''
#### You can download the binary files for your distribution from [http://cran.r-project.org/index.html CRAN]. Or you can use your package manager
##### e.g. for Debian/Ubuntu run <code>sudo apt-get install r-base</code> and for Fedora run <code>sudo yum install R</code>.
#### Also, please [http://www.rstudio.com/ide/download/desktop install the RStudio IDE].
## Then install packages:
## 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:
###[http://tryr.codeschool.com/ Try R] (Code School course)
### Beginner Course: [http://www.lynda.com/R-training-tutorials/1570-0.html?category=beginner_337 Up and Running with R with Barton Poulson] (course at lynda.com)
### Intermediate Course: [http://www.lynda.com/R-training-tutorials/1570-0.html?category=intermediate_33 R Statistics Essential Training with Barton Poulson](course at lynda.com)
### For the future you could take a Coursera class. [https://www.coursera.org/course/rprog intro to R](Coursera course started August 22nd).
## Georeferencing using Apps: please install either of these on your device, if you want to try georeferencing this way to compare with results from a GPS unit.
### '''GPS Status''': available for [https://play.google.com/store/apps/details?id=com.eclipsim.gpsstatus2&hl=en android] and [https://itunes.apple.com/us/app/gps-status/id378085995?mt=8 iOS] devices.
### '''Geopaparazzi''': [https://play.google.com/store/apps/details?id=eu.hydrologis.geopaparazzi&hl=en android] only


'''Optional Friday night activities:'''<br>free concerts downtown (same location as the wed night farmers mkt) - http://www.gvlculturalaffairs.org/website/programs_events/plaza_series/plaza.html<br><br><br><br>
== Updates  ==

Latest revision as of 13:28, 1 May 2019

Post Workshop Publication

Organizers and participants co-wrote a summation from this workshop of lessons learned and key observations and published these results as

  • Seltmann K, Lafia S, Paul D, James S, Bloom D, Rios N, Ellis S, Farrell U, Utrup J, Yost M, Davis E, Emery R, Motz G, Kimmig J, Shirey V, Sandall E, Park D, Tyrrell C, Thackurdeen R, Collins M, O'Leary V, Prestridge H, Evelyn C, Nyberg B (2018) Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers. Research Ideas and Outcomes 4: e32449. https://doi.org/10.3897/rio.4.e32449

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

Georeferencing for Research Use, a short course
GWG3Version2a.png

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.

Logistics:

Course Instructor List

(in alphabetical order) David Bloom, Matt Collins, Una Farrell, Shelley James, Sara Lafia, Deborah Paul, Marcy Revelez, Nelson Rios, Katja Seltmann, Jessica Utrup, Mike Yost

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.

Reading Materials and Resources:

  1. Georeferencing.org
  2. Georeferencing Quick Reference Guide
    version 2012-10-08. John Wieczorek, David Bloom, Heather Constable, Janet Fang, Michelle Koo, Carol Spencer, Kristina Yamamoto
  3. Guide to Best Practices for Georeferencing - Chapman, A.D. and J. Wieczorek (eds). 2006
  4. Georeferencing Working Group Training Videos
  5. 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
  6. iDigBio Georeferencing Wiki http://tinyurl.com/idbgeowiki
  7. HerpNET Georeferencing Resources
  8. Take Workshop Notes Together Here
  9. Post - Workshop Survey Questions
  10. Got a Georeferencing Question? Post it on the iDigBio Georeferencing List Serve
  11. 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.

Goals of the Workshop:

  • Best practices for researchers for in-the-field creating of new locality data and legacy data georeferencing.
    • Tools (hardware and software) and standards (what to document, datum etc.).
    • How to re-patriate data and/or best practices for putting data into data repository if can’t be repatriated (what the obstacles are and minimization of data loss).
  • How to evaluate already georeferenced data. Current tools for visualization and evaluation.
    • Metrics to look for
    • Current tools for georeferencing
    • Online tools
    • R
    • QGIS
  • Researchers give input on the challenges for georeferencing, using existing georeferences.
  • Workflow review for some research review of using georeferenced data (Katja, Shelley, ...)

Ultimate goal: Participant can point to aspects they have learned (tool, standard etc.) during the workshop and can indicate how they will use those aspects for their research goal/purpose (present or future).

Workshop Objectives:

Topics to be covered
Pre-workshop materials

  • Introductory information about datums, mapping, coordinate systems
  • Basic georeferencing how-to

During workshop

  • Data standards, DwC terminology and fields (e.g. lat, long, datum), differences among disciplines (neo- and paleontological fields)
  • Georeferencing toolkit and workflow examples (GEOLocate, maps, other resources, pros and cons)
  • Best practices for field collection of data (locality strings and GPS units, precision, datum)
  • How best to record and store georeferencing notes and other data sources (database/CMS dependant)
  • Best practices for georeferencing of legacy data given:
    • Varied research requirements for accuracy and precision
    • Project and collection management limitations
    • Uncertainty data - polygon vs. point radius, description and metadata, etc.
    • Datum - georectify to a standard versus verbatim
  • Workflows for incorporating data into different collections databases
    • Best practice syntax in locality descriptions for use in automation vs verbatim strings
    • Database limitations
    • Multiple geopoint values and storage (verbatim, automated-non-vetted value, nearest named place, update to more accurate value, etc.)
  • Downloading datasets - sources, different mechanisms
    • Assessing data quality
    • Uncertainty data - availability in data sources and interpretation
  • Tools for aggregating, cleaning, visualizing and analyzing data
    • R, QGIS, OpenRefine
    • Creating maps
    • Spatial analyses
    • Automated, online tools and applications using geospatial data (e.g. LifeMapper)
  • Difficult cases, such as geopolitically fluid locations over time, offshore localities
  • Hands-on practice & case studies

Schedule of Events - Agenda

Breakfast, Lunch and Dinner every day is on our own (not provided).

Day 1, Tuesday October 4th

Recording Day 1

Time
Activity
Presenter
8:45
Pick up Name Tags, Wireless Log-In, Wired Setup, Collaborative Notes (google doc)

9:00
Welcome by NCEAS host, Logistics, Trainer Introductions, Introduction to iDigBio, CCBER
Katja Seltmann - CCBER, Debbie Paul - iDigBio, Ben Halpern - Director NCEAS, Ginger Gillquist - Logistics NCEAS
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, tools you'd like to be able to use
Deb Paul
10:00
Standards, Terms & Fields: Darwin Core Standard, Key Terminology

iDigBio Recommended fields

David Bloom, Shelley James
10:15
Georeferencing Quick Reference Guide, and Georeferencing Template Una Farrell
10:30
Coffee Klatch w/ NCEAS

11:15
Locality Types Una Farrell
11:45
Georeferencing Calculator, Calculator Manual
David Bloom
12:10
Lunch
13:10
Georeferencing Calculator Example and Exercises, MaNIS/HerpNET/ORNIS Georeferencing Guidelines
David Bloom
13:40
Internet Resources - Where to Begin? georeferencing.org

Exercises using online resources - Version 2

Una Farrell
14:40
Break

15:10
Exercises cont.

15:30
GEOLocate: Overview, Basics & Demos

GEOLocate Introduction
Collaborative Georeferencing using CoGe by GEOLocate

Nelson Rios
17:00
Day in Review
Trivia Question of the Day
Survey (15 min)
17:30
End

Dinner on our own - See list of local restaurants. Optional Evening Activity: Happy hour and joyful GeoGathering at Hoffmann Brat Haus

Day 2, Wednesday October 5th

Recording Day 2

Time
Activity
Presenter
8:50
Please complete Survey for Day 1!
9:00
Two! Trivia Questions
Review and Questions
Software Installs check for tomorrow
All
9:10
GEOLocate: Advanced Features, Collaborative Georeferencing and the GEOLocate API
Nelson Rios
10:00
Importance of Polygons
Mike Yost, Nelson Rios
10:30
Break

11:00
GPS Units and APPs: Exercise Introduction
David Bloom, Mike Yost, Shelley James, Katja Seltmann
11:15
GPS Exercises (continued outside)
All
12:15
Lunch

13:15
GPS Exercises (continued outside)
Please upload your GPS Data here
All
13:30
Good and Bad Localities, Field Locality Handout: MVZ and iDigBio GWG Guide for Recording Localities in Field Notes,
Field Information Management Systems (FIMS)
Paper maps
David Bloom
14:15
Georeferencing Workflows: presentations and discussion

Researcher and Collections perspectives: Producers and Consumers

Collection and Data Managers
Researchers
Mike Yost
Jessica Utrup
Sara Lafia
Katja Seltmann
Shelley James
Edward Davis


Digitization Workflows at iDigBio
Georeferencing Protocols and Workflows - from a collections viewpoint
All
15:15
Break
15:45
Online Exercises, Review of known answers

16:30
GPS Exercise - Review (.kmz), Summary Spreadsheet, Field Worksheet, Locality Descriptions
GPSTour
GPS Status
Geopaparazzi
Camera GPS
Theodolite
David Bloom, Jessica Utrup
16:45
Day in Review

Download dataset for tomorrow
Trivia Question of the Day

17:15
Survey (15 min)
17:30
End

Dinner on our own - See list of local restaurants. Optional Evening Activities: 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.
Recording Day 3

Time
Activity
Presenter
9:00
Review and Questions
All
9:05
Georeferencing for Research Use Workshop - iDigBio Datasets

filter and get the dataset

Matthew Collins (remote), Katja Seltmann, Shelley James
10:00
Data Quality: How to evaluate existing georeferenced data/Fitness for Use Katja Seltmann, Shelley James
10:30
Break

11:00
Cleaning Datasets: Spreadsheets, Open Refine, tracking your work
Deb Paul, Nelson Rios, Katja Seltmann
12:00
Lunch

13:00
Cleaning Datasets: Spreadsheets, Open Refine, tracking your work (2)
Deb Paul, Nelson Rios, Katja Seltmann
13:30
Visualizing datasets: Set up QGIS and load data
  • vector: points, lines, polygons
  • raster: images

Auxiliary datasets: Download any additional datasets of interest. Online Tutorial

Sara Lafia
15:00
Break

15:30
Visualizing datasets: Preview and explore toolkits & saving your maps and data
Sara Lafia
17:15
Survey (15 min)
17:30
End

Dinner: TBD

Day 4, Friday October 7th

Download zipped QGIS project The project to the point we completed on Day 3 is available for download in the same folder as the auxiliary data. Launch the QGIS project from the Tutorial.qgs file.
Recording Day 4

Time
Activity
Presenter
9:00
Questions and Review

Share your datasets! [1]: Upload your research datasets that you'd like to work on.

All
9:10
Exploring datasets: Aggregating by Regions
  • Join, aggregate, or summarize records by county
  • Summarize observations intersecting counties
  • Finding altitude
  • 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
LifeMapper LIVE DEMO
Jeffrey Cavner, James Beach, et al
13:15
Work on own data sets/Open question time/Practice. Polygon practice
Nelson Rios, et al
13:45
Breakout sessions

Cleaning data using r
Accessing APIs using r
More with QGIS
GEOLocate in Symbiota
Advanced GEOLocate
GPS Apps
Georectification
Try GeoODK http://geoodk.com/


15:30
Break

16:00
Research Use of the Data. A conversation from the collective point-of-view of the researchers present.
Challenges? Experiences? Needs (software, skills, infrastructure)? What changes might you make now to your workflows?
Ed Davis, Katja Seltmann, Shelley James, Nelson Rios, Sara Lafia
16:30
Day & workshop in Review
iDigBio Webinar On Your Calendar Oct 12th, 2016 - Isn't that Spatial?
Post Workshop Survey

17:30
Beer

Dinner on our own - See list of local restaurants.



Some software install instructions from Data and Software Carpentry

Requests for the Future


Trained Georeferencers

Pre-Workshop Assignments

  1. 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
  2. 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)
  3. 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 - Manage and Install
      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, GPS Tools, Heatmap, Interpolation, OpenLayers, Processing, TimeManager, and Lifemapper.
        1. Clipper (clip intersecting vector features)
        2. Coordinate Capture (find coordinates in various coordinate reference systems (CRS) via mouse-over)
        3. Gazetteer Search (finding named places via a search bar): NOTE: The Gazetteer Plugin is not "discoverable" through the Plugins manager in QGIS. You'll need to follow the installation steps listed here: https://github.com/AstunTechnology/QGIS-Gazetteer-Plugin#Installation
          1. Manual
            1. find where your QGIS is installed on your machine
            2. right click the folder to see contents and find the folder for Plugins
              1. for example, on Deb's Windows 10 laptop, the path to the correct QGIS plugins folder is C:\Users\dlpss\.qgis2\python\plugins
            3. make a folder called gazetteersearch inside of the QGIS Plugins directory
            4. download the contents from GitHub and move them into the gazetteersearch folder
            5. close and reopen QGIS in order for the plugin to show up
          2. via Git
            1. clone the repository into your QGIS Plugins folder following the steps from the link above. Please let Sara know if you have any other questions.
        4. GPS Tools (loading and importing GPS data)
        5. Heatmap (generate a heatmap raster given input vector points)
        6. Interpolation (interpolation techniques given vertices of a vector layer)
        7. OpenLayers (load basemaps from OpenStreetMap, Google, etc.)
        8. Processing (spatial data processing framework)
        9. TimeManager (event-visualization animation for vector features)
        10. Lifemapper: Plugin for Lifemapper webservices for SDM modeling, and multispecies Presence Absence Matrix (PAM) analysis. The tool allows you to build SDM models using GBIF, iDigBio, or user supplied species occurrence data.
      3. Gazetteer Search requires an additional step; follow these steps to install (manual):
        1. find where your QGIS is installed on your machine
        2. right click the folder to see contents and find the folder for Plugins
        3. make a folder called gazetteersearch inside of the QGIS Plugins directory
        4. download the contents from GitHub and move them into the gazetteersearch folder
        5. close and reopen QGIS in order for the plugin to show up
        6. OR install via command line (using Git - see instructions in link above)
        7. clone the repository into your QGIS Plugins folder following the steps from the link above.
    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).
  4. OPTIONAL software install and tutorials - if you are interested in the R breakout section we will offer at the workshop.
    1. R & RStudio: 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).
    4. Georeferencing using Apps: please install either of these on your device, if you want to try georeferencing this way to compare with results from a GPS unit.
      1. GPS Status: available for android and iOS devices.
      2. Geopaparazzi: android only

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