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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  ==
== iDigBio - CCBER GWG 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]]
[[File:Capture.PNG|200px|thumb|right|hotel and NCEAS map]]
[[File:Capture.PNG|200px|thumb|right|hotel and NCEAS map]]
October 4 - 7, 2016 at (https://www.nceas.ucsb.edu/) NCEAS, Santa Barbara California
October 4 - 7, 2016 at (https://www.nceas.ucsb.edu/) NCEAS, Santa Barbara California
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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: ===
=== Logistics: ===
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=== Course Instructor List ===
=== Course Instructor List ===
(''in alphabetical order'') David Bloom, Matt Collins, Shelley James, Sara Lafia, Deborah Paul, Marcy Revelez, Nelson Rios, Katja Seltmann, Jessica Utrup, Mike Yost
(''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
 
=== Meet the Participants: ===
* Participant list
=== Bring your Datasets and Laptops:  ===
=== 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 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.
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.
## Thursday September 15th - two times to choose from:
### 11am EDT (10am CDT, 9am MDT, 8am PDT)
### 3pm EDT (2pm CDT, 1pm MDT, 12pm PDT)
## Sign Up Here: https://goo.gl/forms/WmJO6z79rx5nHlv32
## 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.''
## Collaboration to Automation: https://vimeo.com/53006304 (25 min lecture, 10 min discussion)
## Geographical Concepts: https://vimeo.com/53008556 (4 min lecture, 2 min discussion)
### 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)
## '''OPTIONAL video''': [https://plus.google.com/events/c0sjgu7mjp85vjel5rj8enq9ib0 BITC Global Online Seminar #25: Simple Workflow for Data Cleaning] (1 hour)
# Please '''install the following software'''
## '''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
### ''' 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.
#### [https://plugins.qgis.org/plugins/clipper/ Clipper] (clip intersecting vector features)
#### [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)
##### 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
###### Manual
####### find where your QGIS is installed on your machine
####### right click the folder to see contents and find the folder for Plugins
####### make a folder called gazetteersearch inside of the QGIS Plugins directory
####### download the contents from GitHub and move them into the gazetteersearch folder
####### close and reopen QGIS in order for the plugin to show up
###### via Git
####### 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.
#### [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)
#### [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)
#### [http://documentation.qgis.org/2.0/en/docs/training_manual/qgis_plugins/plugin_examples.html?highlight=openlayers OpenLayers] (load basemaps from OpenStreetMap, Google, etc.)
#### Processing (spatial data processing framework)
#### [https://plugins.qgis.org/plugins/timemanager/?highlight=time TimeManager] (event-visualization animation for vector features)
#### [http://plugins.qgis.org/plugins/lifemapperTools/ Lifemapper]
### ''' [https://github.com/AstunTechnology/QGIS-Gazetteer-Plugin Gazetteer Search] requires an additional step; follow these steps to install (manual):
#### find where your QGIS is installed on your machine
#### right click the folder to see contents and find the folder for Plugins
#### make a folder called gazetteersearch inside of the QGIS Plugins directory
#### download the contents from GitHub and move them into the gazetteersearch folder
#### close and reopen QGIS in order for the plugin to show up
#### OR install via command line (using Git - see instructions in link above)
#### clone the repository into your QGIS Plugins folder following the steps from the link above.
## '''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'''
#### Go to the OpenRefine [http://openrefine.org/download.html download page].
#### Click on <i>Windows kit</i> to download the install file
#### To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead)
#### OpenRefine 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.
### '''MacOS'''
#### Go to the OpenRefine [http://openrefine.org/download.html download page].
#### Click on <i>Mac kit</i> to download the install file
#### Open the downloaded .dmg file
#### Drag the icon in to the Applications folder
#### 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


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


 
== Schedule of Events - Agenda ==
=== Desired Outcomes:  ===
 
== Schedule of Events - Agenda - in development ==
Breakfast, Lunch and Dinner every day is on our own (not provided).  
Breakfast, Lunch and Dinner every day is on our own (not provided).  
=== Day 1, Tuesday October 4th  ===
=== Day 1, Tuesday October 4th  ===
[https://vimeo.com/album/2163673/video/192472653 Recording Day 1]
{| cellspacing="2" cellpadding="5" border="1"
{| cellspacing="2" cellpadding="5" border="1"
|-
|-
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|-
|-
| 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 by NCEAS host, Logistics, Trainer Introductions, Introduction to iDigBio, CCBER<br>
| Welcome by NCEAS host, Logistics, Trainer Introductions, Introduction to iDigBio, CCBER<br>
| Katja Seltmann, Debbie Paul, (NCEAS person)<br>
| Katja Seltmann - CCBER, Debbie Paul - iDigBio, Ben Halpern - Director NCEAS, Ginger Gillquist - Logistics NCEAS <br>
|-
|-
| 9:20<br>  
| 9:20<br>  
| From the participants and instructors: a quick informal survey
| From the participants and instructors: a quick informal survey
Quick Name/Rank/Serial# introductions<br>  
Quick Name/Rank/Serial# introductions<br>  
tools you use<br>  
:tools you use<br>  
what you’d like to be able to do<br>
:what you’d like to be able to do, tools you'd like to be able to use<br>  
<br>  
|Deb Paul<br>
|Deb Paul<br>
|-
|-
| 10:00<br>  
| 10:00<br>  
| Standards, Terms & Fields: [http://rs.tdwg.org/dwc/terms/index.htm Darwin Core Standard], Key Terminology
| Standards, Terms & Fields: [http://rs.tdwg.org/dwc/terms/index.htm Darwin Core Standard], Key Terminology
iDigBio Recommended fields<br>  
[https://www.idigbio.org/wiki/images/5/52/Georef_iDigBio_terms.pdf iDigBio Recommended fields]<br>  
| David Bloom, Shelley James<br>
| David Bloom, Shelley James<br>
|-
|-
| 10:15<br>  
| 10:15<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]
| [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]
| Una Farell
| Una Farrell
|-
|-
| 10:30<br>  
| 10:30<br>  
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|-
|-
| 11:15<br>  
| 11:15<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/GeoreferencingConceptsandLocalityTypes2013.pptx Locality Types]
| [https://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/GeoreferencingConceptsandLocalityTypes2016.pptx Locality Types]
| Una Farell
| Una Farrell
|-
|-
| 11:45<br>  
| 11:45<br>  
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|-
|-
| 13:40<br>  
| 13:40<br>  
| [https://www.idigbio.org/sites/default/files/workshop-presentations/ttt2/OnlineResources2013.pptx Internet Resources] - Where to Begin? [http://georeferencing.org georeferencing.org] <br> Exercises using online resources
| [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>  
| Una Farell
[http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/2015_OnlineExercises11CONCAT.xls Exercises using online resources - Version 2]
| Una Farrell
|-
|-
| 14:40<br>  
| 14:40<br>  
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| 15:30<br>  
| 15:30<br>  
| [http://www.museum.tulane.edu/geolocate/ GEOLocate]: Overview, Basics & Demos<br>  
| [http://www.museum.tulane.edu/geolocate/ GEOLocate]: Overview, Basics & Demos<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
| Nelson Rios<br>
| Nelson Rios<br>
|-
|-
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=== Day 2, Wednesday October 5th  ===
=== Day 2, Wednesday October 5th  ===
[https://vimeo.com/album/2163673/video/192472654 Recording Day 2]
{| cellspacing="2" cellpadding="5" border="1"
{| cellspacing="2" cellpadding="5" border="1"
|+
|+
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! 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>
|-
|-
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|-
|-
| 10:00<br>  
| 10:00<br>  
| Importance of Polygons<br>  
| [http://www.idigbio.org/sites/default/files/workshop-presentations/georef-research-use/Georeferencing%20Presentation%20INTRO%20-%20Polygons_FINAL.pptx Importance of Polygons]<br>  
| Mike Yost, Nelson Rios<br>
| Mike Yost, Nelson Rios<br>
|-
|-
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|-
|-
| 13:15<br>  
| 13:15<br>  
| GPS Exercises (continued outside)<br>  
| GPS Exercises (continued outside)<br>Please [https://goo.gl/X3LkQO upload your GPS Data here]
|All<br>
|All<br>
|-
|-
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| 14:15<br>  
| 14:15<br>  
| Georeferencing Workflows: presentations and discussion<br>  
| Georeferencing Workflows: presentations and discussion<br>  
Researcher and Collections perspectives
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>
|-
|-
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| 16:30<br>  
| 16:30<br>  
| GPS Exercise - Review (.kmz), Summary Spreadsheet, Field Worksheet, Locality Descriptions<br>  
| GPS Exercise - Review (.kmz), Summary Spreadsheet, Field Worksheet, Locality Descriptions<br>  
:GPSTour
:GPS Status
:Geopaparazzi
:Camera GPS
:Theodolite
| David Bloom, Jessica Utrup<br>
| David Bloom, Jessica Utrup<br>
|-
|-
| 16:45<br>  
| 16:45<br>  
| Day in Review<br>
| Day in Review<br>
Download dataset for tomorrow<br>
Trivia Question of the Day<br>
Trivia Question of the Day<br>
|  
|  
|-
|-
| 17:15<br>
| 17:15<br>
| Survey (15 min)
| Survey (15 min)<br>
|
|
|-
|-
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=== Day 3, Thursday October 6th  ===
=== 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.
[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]
 
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|-
|-
| 9:05<br>  
| 9:05<br>  
| Getting datasets:  
| [https://docs.google.com/presentation/d/1ORWr2krUhwpNWteDXmNyoUaUjFkJ8PAc-mj7tNW1Rng/edit?usp=sharing​ Georeferencing for Research Use Workshop - iDigBio Datasets]
* Downloading datasets from iDigBio - get data from portal and explain each component to the dataset.
* [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
filter and get the dataset
* What is raw vs not raw?
* Similar or different from GBIF?
* Similar or different from GBIF?
* What is raw vs not raw?
* [https://github.com/iDigBio/idigbio-search-api/wiki/Data-Quality-Flags List of iDigBio Flags]:
* Walk through steps of download, but provide dataset.
* Walk through steps of download, but provide dataset.
* Data set: http://s.idigbio.org/idigbio-downloads/a69d1541-4726-465d-84ad-50c7ed556eee.zip
* iDigBio Data set: http://s.idigbio.org/idigbio-downloads/a69d1541-4726-465d-84ad-50c7ed556eee.zip
|Matthew Collins (remote), Katja Seltmann, Shelley James<br>
|Matthew Collins (remote), Katja Seltmann, Shelley James<br>
|-
|-
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|-
|-
| 13:00<br>  
| 13:00<br>  
| Cleaning Datasets: Spreadsheets, Open Refine, tracking your work (2)<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>
| Deb Paul, Nelson Rios, Katja Seltmann<br>
|-
|-
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* vector: points, lines, polygons
* vector: points, lines, polygons
* raster: images<br>
* 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>
| Sara Lafia<br>
|-
|-
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=== Day 4, Friday October 7th  ===
=== 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]
 
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|-
|-
| 9:00<br>  
| 9:00<br>  
| Questions and Review<br>  
| Questions and Review
| <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>  
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* Join, aggregate, or summarize records by county
* Join, aggregate, or summarize records by county
* Summarize observations intersecting counties
* Summarize observations intersecting counties
* Finding altitude
* Why do this?
* Why do this?
<br>  
<br>  
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| 11:00<br>  
| 11:00<br>  
| Exploring datasets: Uncertainty
| Exploring datasets: Uncertainty
* Bin points based on uncertainty rank</li>
* Bin points based on uncertainty rank
* Symbolize uncertainty by collector, data quality score - systematic error
* Symbolize uncertainty by collector, data quality score - systematic error
| Sara Lafia<br>
| Sara Lafia<br>
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|-
|-
| 12:00<br>  
| 12:00<br>  
| Lunch on our own.<br>
| Lunch on our own.
| <br>
| <br>
|-
|-
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GEOLocate in Symbiota<br>
GEOLocate in Symbiota<br>
Advanced GEOLocate<br>
Advanced GEOLocate<br>
GPS Apps
GPS Apps<br>
Georectification<br>
Try GeoODK [http://geoodk.com/ http://geoodk.com/]
Try GeoODK [http://geoodk.com/ http://geoodk.com/]
| <br>
| <br>
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|-
|-
| 16:30<br>  
| 16:30<br>  
| Day & workshop in Review <br>Post Workshop Survey  
| 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
| <br>
| <br>
|-
|-
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<br/>
<br/>
Some software [http://www.datacarpentry.org/workshop-template/install.html install instructions] from Data and Software Carpentry
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 ==
== Trained Georeferencers ==
* Map of [http://tinyurl.com/idbtttmap Participants and Instructors for TTT1 and TTT2]
* Map of [http://tinyurl.com/idbtttmap Participants and Instructors for TTT1 and TTT2]
* Wiki for all [[TTT1TTT2| TTT1 and TTT2 Participants]]
* Wiki for all [[TTT1TTT2| TTT1 and TTT2 Participants]]
== Pre-Workshop Assignments ==
# Attend pre-workshop online meeting. Two options, choose one.
## Thursday September 15th - two times to choose from:
### 11am EDT (10am CDT, 9am MDT, 8am PDT)
### 3pm EDT (2pm CDT, 1pm MDT, 12pm PDT)
## Sign Up Here: https://goo.gl/forms/WmJO6z79rx5nHlv32
## 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.''
## Collaboration to Automation: https://vimeo.com/53006304 (25 min lecture, 10 min discussion)
## Geographical Concepts: https://vimeo.com/53008556 (4 min lecture, 2 min discussion)
### 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)
## '''OPTIONAL video''': [https://plus.google.com/events/c0sjgu7mjp85vjel5rj8enq9ib0 BITC Global Online Seminar #25: Simple Workflow for Data Cleaning] (1 hour)
# Please '''install the following software'''
## '''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
### ''' 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.
#### [https://plugins.qgis.org/plugins/clipper/ Clipper] (clip intersecting vector features)
#### [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
##### Manual
###### find where your QGIS is installed on your machine
###### 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
###### make a folder called gazetteersearch inside of the QGIS Plugins directory
###### download the contents from GitHub and move them into the gazetteersearch folder
###### close and reopen QGIS in order for the plugin to show up
##### via Git
###### 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.
#### [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)
#### [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)
#### [http://documentation.qgis.org/2.0/en/docs/training_manual/qgis_plugins/plugin_examples.html?highlight=openlayers OpenLayers] (load basemaps from OpenStreetMap, Google, etc.)
#### Processing (spatial data processing framework)
#### [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.
### ''' [https://github.com/AstunTechnology/QGIS-Gazetteer-Plugin Gazetteer Search] requires an additional step; follow these steps to install (manual):
#### find where your QGIS is installed on your machine
#### right click the folder to see contents and find the folder for Plugins
#### make a folder called gazetteersearch inside of the QGIS Plugins directory
#### download the contents from GitHub and move them into the gazetteersearch folder
#### close and reopen QGIS in order for the plugin to show up
#### OR install via command line (using Git - see instructions in link above)
#### clone the repository into your QGIS Plugins folder following the steps from the link above.
## '''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'''
#### Go to the OpenRefine [http://openrefine.org/download.html download page].
#### Click on <i>Windows kit</i> to download the install file
#### To use it, unzip, and double-click on openrefine.exe (if you're having issues with openrefine.exe try refine.bat instead)
#### OpenRefine 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.
### '''MacOS'''
#### Go to the OpenRefine [http://openrefine.org/download.html download page].
#### Click on <i>Mac kit</i> to download the install file
#### Open the downloaded .dmg file
#### Drag the icon in to the Applications folder
#### 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
== Updates  ==
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