Age of Water - User contributions [en]

2014 first Steering Committee Meeting

2015-01-15T02:38:57Z

Jordan: /* List of Collaborators */

[[Category:Task]]

==Date and Venue==

The date for the first advisory committee meeting is Monday November 17, 2014. Rick Hooper and David Tarboton will meet with the team on Sunday from 11:30 noon to 4 pm. They both have prior commitments and will not make the main meeting on Monday.
The meeting will be held near the airport in Denver at:

DoubleTree by Hilton Hotel Denver
3203 Quebec Street, Denver, Colorado, 80207, USA
TEL: +1-303-321-3333
FAX: 1-303-329-5233
http://doubletree3.hilton.com/en/hotels/colorado/doubletree-by-hilton-hotel-denver-RLDV-DT/index.html

==Agenda==

'''Agenda: Sunday 16 Nov, 2014'''

• 12 noon lunch reservations at hotel restaurant for Rick, David, Chris, Paul and Hilary 
• 1-4 pm Briefing on INSPIRE Age of Water project and Organic Data Science Collaboration software (abbreviated but following 17 Nov agenda) 

'''Agenda: Monday 17 Nov, 2014'''

{| class="wikitable"
! Time
! Topic
|-
| {{nowrap|09:00am - 10:00am}}
|
'''Introductions''' 
• Introduce the steering committee and their background (15 min) 
• Introduce the PI’s and the motivation for the research and describe what we intend to accomplish (15)
|-
| {{nowrap|9:30am - 10:30am}}
|
'''Research Overview in Lake-Catchment Data-Models-Collaboration''' 
• Overview of catchment and age research (30 min) (Chris) 
• Overview of lake research (30) (Paul, Jordan) 
• Collaboration concept and overview of organic data science (30) (Yolanda)
|-
| {{nowrap|10:30am - 11:00am}}
|
''Coffee Break'' 
|-
| {{nowrap|11:00am - 12:00pm}}
|
'''Demonstrating the strategy''' 
• Example: Writing a research paper using the Organic Data Science Framework (online) (30) (Yolanda) 
• Training newcomers using the Organic Data Science Framework (online) (15) (Hilary)
• Example: Organizing a workshop using the Organic Data Science Framework (online) (15) (Hilary) 
|-
| {{nowrap|12:00pm - 1:15pm}}
|
''Lunch (~12 people)'' 
|-
| {{nowrap|1:15pm - 2:45pm}}
|
'''Demonstrating the strategy cont’d''' 
• Future work on the Organic Data Science Framework (online) (30) (Yolanda) 
• Jumpstarting new collaboration groups and new communities (30) (Hilary and Yolanda) 
• Creating cross-disciplinary models and data (30)
|-
| {{nowrap|2:45pm - 3:00pm}}
|
''Coffee Break'' 
|-
| {{nowrap|3:00pm - 4:00pm}}
|
'''Open discussion around questions:''' 
• What the INSPIRE Team would like from the Collaborators? 
• What the Collaborators would like from the Team? 
• Strategy for expanded participation?
|-
| {{nowrap|4:00pm - 4:30pm}}
|
''Feedback from Collaborators'' 
|-

| {{nowrap|4:30pm}}
| '''To airport for most, self organized dinner for those staying on'''
|}

==Invitation Letter==

October 1, 2014

To: CyberInfrastructure Collaborators: NSF INSPIRE (1344272)

The Age of Water and Carbon in Hydroecological Systems: A New Paradigm for Science Innovation and Collaboration through Organic Team Science.

Re: Update on activities and request for ½ day meeting in November in Denver

From: Christopher Duffy (PI), Yolanda Gil (Co-PI) and Paul Hanson (Co-PI)

Dear Collaborators,

We have been busily building up the core ideas for this effort over the first 10 months, and are now ready to engage you all as you expressed interest to collaborate on this project. As you may recall, we are investigating Organic Data Science, a new approach aimed to allow scientists to formulate and resolve science processes through an open, task-centered framework that facilitates ad-hoc participation and entices collaborations based on common science goals. We are integrating analytical frameworks from two communities – hydrology and stable water isotope modeling in Critical Zone Observatories (CZOs) and hydrodynamic water quality modeling from the Global Lake Ecological Observatory Network (GLEON) – to quantify water and material fluxes from two research sites, the Shales Hills CZO and the GLEON member site, North Temperate Lakes LTER.

We wanted to kickstart our collaboration activities with all of you with a one-day meeting in Denver this November. Our goal is to review the work we have done to date and plan possible collaboration activities with you for the coming year. We propose three possible dates for this meeting: 10, 17 or 24 November. The expenses for your travel will be covered by the grant. Details for convenient access to the meeting to follow.

Organic Data Science is an open task-centered hierarchical collaboration framework for developing and documenting research activities in the project. The Open Data Science framework is implemented on a semantic wiki, where each task that we are currently engaged in, the participants on that task, the progress to date, and other key information. The website is at www.organicdatascience.org, where you can see the tasks we have laid out and the first year’s activities and progress. The framework itself has been developed in collaboration with our computer science group at USC/ISI. The website outlines not only research activities on the science side, but also the activities concerning the development of the framework proper as well as outreach. Our first outreach activity is being planned to take advantage of the next GLEON annual meeting, where we will hold a workshop on Lake-Catchment Modeling in Jovance, Quebec 26 October, 2014. We will have ~30 invited participants at the workshop.

Please let us know which dates in November in Denver would work for your schedule and if you might like to participate in the GLEON Workshop contact us.

Sincerely,

Christopher J. Duffy, Yolanda Gil and Paul Hanson

==List of Collaborators==

* Supporting Regional Community DATA Infrastructure: '''Gordon Grant''', geomorphologist and chair of the NSF Critical Zone Steering Committee will work with the team to develop a strategy to share important ETV (Essential Terrestrial Variables) geospatial data resources and to consult on new ETV data resources for d18O and d2H in precipitation across the Willamette watershed and Cascade Mountains, an area rich in previous studies of isotopic chemistry and hydrology

* National Data Infrastructure and Social Networking: '''David Tarboton''', lead scientist on the CUAHSI HydroShare funded by NSF effort will work with the PI’s on the social computing aspects the project and in integrating modeling and data resources into the HydroShare community data system.

* Serving a High Resolution Precipitation Isoscape for all Critical Zone Observatories: '''Anthony Aufdenkampe''', lead scientist on NSF funded Integrated Data Management for Critical Zone Observatories and PI on the Christina River basin CZO, will collaborate with the Inspire Team on CZO Data and in building a new database for stable isotope data in precipitation (1979-Pres) for all CZO sites.

* National Geospatial Data Infrastructure and the CUAHSI Water Data Center: '''Rick Hooper & Alva Couch''', Executive Director and lead scientist for CUAHSI and the CUAHSI Water Data Center will collaborate by advising project personnel on standards and services interfaces used by CUAHSI Water Data Center to allow integration and sharing of geospatial services between WDC and Hydroterre.

* National Data and Interoperability Standards: '''Brian Wee''', scientist with NEON (the National Ecological Observing Network) will collaborate by advising project personnel on standards and interoperability of NEON data with CZO’s, GLEON and other observatories.

* Data Publication, Discovery and Access Infrastructure: '''David Vieglais''' DataOne Director of Development and Operations, will support access to existing infrastructure to publish data with appropriate metadata annotations that support discovery and access. Dr. Gil participates in the DataOne Provenance Working Group, which is extending the W3C PROV standard to science workflows.

* Towards a Shared Data Infrastructure across NSF Science Domains: '''Emily Stanley''' will support access to a vast array of data from lakes in northern Wisconsin, including limnological, hydrological, meteorological, and land use land cover. Stanley will help integrate the proposed work into the scientific agenda of NTL, providing additional collaboration opportunities and broader impact. Futhermore, hydrologists currently working within NTL LTER will provide invaluable insights into regional hydrology, greatly expediting the model calibration needed in the proposed work.

* ETV infrastructure for high resolution precipitation isoscape (CONUS): '''Kei Yoshimura''': climate scientist and lead scientists for global and regional scale simulation of stable isotopes in precipitation will contribute hourly, daily and weekly and gridded time series for North America which will serve to extend the measurement record at Shale Hills Trout lake to the climate reanalysis record 1979-present and provide an important new data resource for catchment isoscapes globally.

* Sharing USGS Federal Data and Modeling Assets For Catchment-Lake Modeling: '''Jordan Read''', USGS, physical limnologist and lake modeler who has extensive experience in developing and implementing numerical simulations for lakes. His recent use of GLM, lake numerical simulation software, models lake temperatures in hundreds of Wisconsin lakes.

==Meeting Summary==

Attending: Brian Wee, David Vieglas, Rick Hooper, Kei Yoshimura, Hilary Dugan, Jordan Read, David Tarboton,
Christopher Duffy, Yolanda Gil, and Paul Hanson



{{#set:
Owner=Chris_Duffy|
Participants=Yolanda_Gil|
Participants=Paul_Hanson|
Progress=100|
StartDate=2014-10-01|
TargetDate=2014-11-24|
Type=Low}}

Collect relative humidity data for North Temperate lakes

2014-12-01T18:47:26Z

Jordan: Set PropertyValue: Progress = 90

[[Category:Task]]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
Progress=90|
StartDate=2014-10-01|
TargetDate=2014-12-01|
Type=Low}}

Collect relative humidity data for North Temperate lakes

2014-12-01T18:33:07Z

Jordan: Set PropertyValue: Type = low

[[Category:Task]]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
StartDate=2014-10-01|
TargetDate=2014-12-01|
Type=Low}}

Collect air temperature data for North Temperate lakes

2014-12-01T18:32:43Z

Jordan: Set PropertyValue: Progress = 90

Collect air temperature data for North Temperate lakes

2014-12-01T18:32:36Z

Jordan: Set PropertyValue: Type = low

[[Category:Task]]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
StartDate=2014-10-01|
TargetDate=2014-12-01|
Type=Low}}

Collect wind speed data for North Temperate lakes

2014-12-01T18:07:47Z

Jordan: Set PropertyValue: Progress = 60

[[Category:Task]]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
Progress=60|
StartDate=2014-10-01|
TargetDate=2014-12-01|
Type=Low}}

Collect wind speed data for North Temperate lakes

2014-12-01T18:07:40Z

Jordan: Set PropertyValue: Type = low

[[Category:Task]]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
StartDate=2014-10-01|
TargetDate=2014-12-01|
Type=Low}}

Format meteorological data for model input

2014-12-01T18:07:08Z

Jordan: Set PropertyValue: Progress = 100

[[Category:Task]]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
Progress=100|
StartDate=2014-10-01|
TargetDate=2014-12-01|
Type=Low}}

Format meteorological data for model input

2014-12-01T18:07:00Z

Jordan: Set PropertyValue: Type = low

[[Category:Task]]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
StartDate=2014-10-01|
TargetDate=2014-12-01|
Type=Low}}

Collect Downwelling longwave radiation data for North Temperate lakes

2014-12-01T18:06:39Z

Jordan: Set PropertyValue: Progress = 90

Collect Downwelling longwave radiation data for North Temperate lakes

2014-12-01T18:06:27Z

Jordan: Set PropertyValue: Type = low

[[Category:Task]]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
StartDate=2014-10-01|
TargetDate=2014-12-01|
Type=Low}}

Obtain meteorological data for North Temperate Lakes

2014-11-19T18:01:19Z

Jordan:

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model. Working on this as part of [https://github.com/USGS-R/mda.lakes/issues/40 github tasks]


{{#set:
Expertise=Hydrodynamic_modeling|
Owner=Jordan_Read|
Participants=Paul_Hanson|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
StartDate=2014-10-01|
SubTask=Collect_Downwelling_shortwave_radiation_data_for_North_Temperate_lakes|
SubTask=Format_meteorological_data_for_model_input|
SubTask=QAQC_meteorological_data|
SubTask=Collect_Downwelling_longwave_radiation_data_for_North_Temperate_lakes|
SubTask=Collect_air_temperature_data_for_North_Temperate_lakes|
SubTask=Collect_relative_humidity_data_for_North_Temperate_lakes|
SubTask=Collect_wind_speed_data_for_North_Temperate_lakes|
SubTask=Collect_rainfall_data_for_North_Temperate_lakes|
SubTask=Collect_snowfall_data_for_North_Temperate_lakes|
TargetDate=2014-12-01|
Type=Medium}}

Set up R by Jordan Read

2014-10-27T15:03:31Z

Jordan: Set PropertyValue: Progress = 100

[[Category:Task]]
 
What this task is about: Install the R programming language and the RStudio software. These tools will be used to prep GLM models, run GLM models, and analyze the results 
Details on how to do this task: [[Installing_R]] 


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-19|
TargetDate=2014-10-26|
Type=Low}}

Run GLM demo by Jordan Read

2014-10-27T15:02:19Z

Jordan: Set PropertyValue: Progress = 100

[[Category:Task]]
 
What this task is about: Follow the task instructions to install the GLM model and run the model demo in R 
Details on how to do this task: [[Run_GLM_demo]] 


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-21|
TargetDate=2014-10-26|
Type=Low}}

Download PIHMgis tutorial and documents by Jordan Read

2014-10-27T15:00:32Z

Jordan: Set PropertyValue: Progress = 100

[[Category:Task]]
 
What this task is about: You may also download archive of relevant PIHM/PIHMgis documents. 
Details on how to do this task: [[Download_PIHMgis_tutorial_and_documents]] 


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-18|
TargetDate=2014-10-26|
Type=Low}}

Download PIHMgis input data by Jordan Read

2014-10-27T13:52:00Z

Jordan: Set PropertyValue: Progress = 100

[[Category:Task]]
 
What this task is about: Download input geo-spatial datasets that we will be using to develop a prototype catchment simulation using PIHMgis. Please have the dataset specific to software version you installed downloaded on your laptop at an easily identifiable and accessible folder e.g., "PIHMWorkshop" in your users home directory. 
Details on how to do this task: [[Download_PIHMgis_input_data]] 


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-17|
TargetDate=2014-10-26|
Type=Low}}

Download and install PIHMgis software by Jordan Read

2014-10-27T13:51:38Z

Jordan: Set PropertyValue: Progress = 100

[[Category:Task]]
 
What this task is about: Download PIHMgis, and select appropriate version of PIHMgis based on the operating system that you are running on your computer. Version 3.0 is not available for Windows yet. 
Details on how to do this task: [[Download_and_install_PIHMgis_software]] 


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-16|
TargetDate=2014-10-26|
Type=Low}}

Install R packages by Jordan Read

2014-10-27T03:15:40Z

Jordan: Set PropertyValue: Progress = 100

[[Category:Task]]
 
What this task is about: Install the R packages 
Details on how to do this task: [[R_Packages]] 


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-20|
TargetDate=2014-10-26|
Type=Low}}

Run GLM demo

2014-10-26T14:16:08Z

Jordan: /* Installing required packages */

[[Category:Task]]


===Installing required packages===

For '''windows, OSX, or Linux''' use use the following command in R:
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.io/", "http://cran.us.r-project.org"),
dependencies = TRUE,
type = "both")</pre></code>

You now have GLM (<code>GLMr</code>), R tools for GLM (<code>glmtools</code>), NetCDF file handlers (<code>ncdf</code>), and <code>rLakeAnalyzer</code> installed!!

If you installed glmtools a while ago, it would be best to update it:
<code><pre> update.packages(repos = "http://gleon.github.io/",
type = "source")</pre></code>

===Run GLM demo===
<code><pre>library(GLMr)
demo(glm)</pre></code>

If you get a success message, your task is complete!

===Troubleshooting===
Only supported for OSX 10.9 (Mavericks) and newer.

Package has been updated, so the following should not arise.
Mac Users: If you get a 'permission denied error' when running demo(glm), you must change the permission setting on the sim folder in terminal.
 Example error:
<code><pre> sh: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/GLMr/extbin/macGLM/bin/glm: Permission denied </pre></code>

'''Steps'''
* Open TERMINAL
* Change directory folder to that listed in the error. (copy bold text, and change to match your personal file path)
example:
''MyLovley-MacBook-Pro:~ user$'' '''cd /Library/Frameworks/R.framework/Versions/3.0/Resources/library/GLMr/extbin/macGLM/bin'''
** If you type '''ls''', you should see 10 files, one of which is titled 'glm'
* Type
<code><pre> chmod 755 glm </pre></code>
* You should now be able to run demo(glm)


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-26T14:15:28Z

Jordan: /* Installing required packages */ update instructions

[[Category:Task]]


===Installing required packages===

For '''windows, OSX, or Linux''' use use the following command in R:
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.io/", "http://cran.us.r-project.org"),
dependencies = TRUE,
type = "both")</pre></code>

You now have GLM (<code>GLMr</code>), R tools for GLM (<code>glmtools</code>), NetCDF file handlers (<code>ncdf</code>), and <code>rLakeAnalyzer</code> installed!!

If you installed glmtools a while ago, it would be best to update it:
<code><pre> update.packages(repos = "http://gleon.github.io/"),
type = "source")</pre></code>

===Run GLM demo===
<code><pre>library(GLMr)
demo(glm)</pre></code>

If you get a success message, your task is complete!

===Troubleshooting===
Only supported for OSX 10.9 (Mavericks) and newer.

Package has been updated, so the following should not arise.
Mac Users: If you get a 'permission denied error' when running demo(glm), you must change the permission setting on the sim folder in terminal.
 Example error:
<code><pre> sh: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/GLMr/extbin/macGLM/bin/glm: Permission denied </pre></code>

'''Steps'''
* Open TERMINAL
* Change directory folder to that listed in the error. (copy bold text, and change to match your personal file path)
example:
''MyLovley-MacBook-Pro:~ user$'' '''cd /Library/Frameworks/R.framework/Versions/3.0/Resources/library/GLMr/extbin/macGLM/bin'''
** If you type '''ls''', you should see 10 files, one of which is titled 'glm'
* Type
<code><pre> chmod 755 glm </pre></code>
* You should now be able to run demo(glm)


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-26T14:13:41Z

Jordan: /* Installing required packages */ simpler install instructions

[[Category:Task]]


===Installing required packages===

For '''windows, OSX, or Linux''' use use the following command in R:
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.io/", "http://cran.us.r-project.org"),
dependencies = TRUE,
type = "both")</pre></code>

You now have GLM (<code>GLMr</code>), R tools for GLM (<code>glmtools</code>), NetCDF file handlers (<code>ncdf</code>), and <code>rLakeAnalyzer</code> installed!!

===Run GLM demo===
<code><pre>library(GLMr)
demo(glm)</pre></code>

If you get a success message, your task is complete!

===Troubleshooting===
Only supported for OSX 10.9 (Mavericks) and newer.

Package has been updated, so the following should not arise.
Mac Users: If you get a 'permission denied error' when running demo(glm), you must change the permission setting on the sim folder in terminal.
 Example error:
<code><pre> sh: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/GLMr/extbin/macGLM/bin/glm: Permission denied </pre></code>

'''Steps'''
* Open TERMINAL
* Change directory folder to that listed in the error. (copy bold text, and change to match your personal file path)
example:
''MyLovley-MacBook-Pro:~ user$'' '''cd /Library/Frameworks/R.framework/Versions/3.0/Resources/library/GLMr/extbin/macGLM/bin'''
** If you type '''ls''', you should see 10 files, one of which is titled 'glm'
* Type
<code><pre> chmod 755 glm </pre></code>
* You should now be able to run demo(glm)


{{#set:
Owner=Jordan_Read|
Progress=100|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-21T15:45:10Z

Jordan: /* Installing required packages */

Run GLM demo

2014-10-20T21:54:04Z

Jordan: /* Run GLM demo */

[[Category:Task]]


===Installing required packages===

For '''windows''' use use the following command in R:
In R, type:
<code><pre> install.packages("ncdf4",
repos = "http://gleon.github.com/",
type = "win.binary") </pre></code>

then
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both",
INSTALL_opts = "--no-multiarch") </pre></code>

For '''OSX or Linux''' use the following command in R:
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both")</pre></code>

You now have GLM (<code>GLMr</code>), R tools for GLM (<code>glmtools</code>), NetCDF file handlers (<code>ncdf4</code>), and <code>rLakeAnalyzer</code> installed!!

===Run GLM demo===
<code><pre>library(GLMr)
demo(glm)</pre></code>

If you get a success message, your task is complete!

{{#set:
Owner=Jordan_Read|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-20T21:45:52Z

Jordan: /* Run GLM demo */

[[Category:Task]]


===Installing required packages===

For '''windows''' use use the following command in R:
In R, type:
<code><pre> install.packages("ncdf4",
repos = "http://gleon.github.com/",
type = "win.binary") </pre></code>

then
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both",
INSTALL_opts = "--no-multiarch") </pre></code>

For '''OSX or Linux''' use the following command in R:
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both")</pre></code>

You now have GLM (<code>GLMr</code>), R tools for GLM (<code>glmtools</code>), NetCDF file handlers (<code>ncdf4</code>), and <code>rLakeAnalyzer</code> installed!!

===Run GLM demo===
<code><pre>library(glmtools)
sim_folder <- system.file('extdata/sim/', package = 'GLMr')
if (run_glm(sim_folder)==0){cat('congratulations on setting up and running GLM!')}else{cat('setup failed, contact jread@usgs.gov with questions')}</pre></code>

{{#set:
Owner=Jordan_Read|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-20T21:35:42Z

Jordan: /* Installing required packages */

[[Category:Task]]


===Installing required packages===

For '''windows''' use use the following command in R:
In R, type:
<code><pre> install.packages("ncdf4",
repos = "http://gleon.github.com/",
type = "win.binary") </pre></code>

then
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both",
INSTALL_opts = "--no-multiarch") </pre></code>

For '''OSX or Linux''' use the following command in R:
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both")</pre></code>

You now have GLM (<code>GLMr</code>), R tools for GLM (<code>glmtools</code>), NetCDF file handlers (<code>ncdf4</code>), and <code>rLakeAnalyzer</code> installed!!

===Run GLM demo===

{{#set:
Owner=Jordan_Read|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-20T21:34:19Z

Jordan: /* Installing required packages */

[[Category:Task]]


===Installing required packages===

For '''windows''' use use the following command in R:
In R, type:
<code><pre> install.packages("ncdf4",
repos = "http://gleon.github.com/",
type = "win.binary") </pre></code>

then
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both",
INSTALL_opts = "--no-multiarch") </pre></code>

For '''OSX or Linux''' use the following command in R:
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both")</pre></code>

You now have GLM, R tools for GLM (glmtools), NetCDF file handlers (ncdf4), and rLakeAnalyzer installed!!

===Run GLM demo===

{{#set:
Owner=Jordan_Read|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-20T21:32:51Z

Jordan: /* Installing required packages */

[[Category:Task]]


===Installing required packages===

For '''windows''' use use the following command in R:
In R, type:
<code><pre> install.packages("ncdf4",
repos = "http://gleon.github.com/",
type = "win.binary") </pre></code>

then
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both",
INSTALL_opts = "--no-multiarch") </pre></code>

For '''OSX or Linux''' use the following command in R:
install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both")

You now have GLM, R tools for GLM (glmtools), NetCDF file handlers (ncdf4), and rLakeAnalyzer installed!!

{{#set:
Owner=Jordan_Read|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-20T21:29:58Z

Jordan: /* Installing required packages */

[[Category:Task]]


===Installing required packages===

For '''windows''' use use the following command in R:
'''Lake Analyzer''' 
In R, type:
<code><pre> install.packages("ncdf4",
repos = "http://gleon.github.com/",
type = "win.binary") </pre></code>

then
<code><pre> install.packages("glmtools",
repos = c("http://gleon.github.com/", "http://cran.us.r-project.org", "http://usgs-r.github.com/"),
dependencies = TRUE,
type = "both",
INSTALL_opts = "--no-multiarch") </pre></code>


{{#set:
Owner=Jordan_Read|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-20T21:21:48Z

Jordan: fleshing out text. will be modifying

[[Category:Task]]


===Installing required packages===

'''Lake Analyzer''' 
In R, type:
<code><pre> install.packages('rLakeAnalyzer') </pre></code>
To use package, type:
<code><pre> library(LakeAnalyzer) </pre></code>
see [http://cran.r-project.org/web/packages/rLakeAnalyzer/rLakeAnalyzer.pdf Lake Analyzer pdf] for help

'''Lake Metabolizer''' 
In R, type:
<code><pre> install.packages('LakeMetabolizer') </pre></code>
To use package, type:
<code><pre> library(LakeMetabolizer) </pre></code>
see [http://cran.r-project.org/web/packages/LakeMetabolizer/LakeMetabolizer.pdf Lake Metabolizer pdf] for help

To see which packages are currently loaded into your R session, type:
<code><pre> search() </pre></code>

'''GLMtools''' (Not on CRAN) 
instructions from [https://github.com/USGS-R/glmtools USGS github]

''For windows use the following command in R:''
<code><pre> install.packages("ncdf4",repos = "http://gleon.github.com/",type = "win.binary") </pre></code>
''then''
<code><pre> install.packages("glmtools",repos = c("http://gleon.github.com/","http://usgs-r.github.io",
"http://cran.us.r-project.org"), dependencies = TRUE,type = "both",
INSTALL_opts = "--no-multiarch") </pre></code>

''For OSX or Linux use the following command in R:''
<code> <pre>install.packages("glmtools",repos = c('http://gleon.github.com/',"http://usgs-r.github.io",
'http://cran.us.r-project.org'), dependencies = TRUE,type = "both")</pre></code>


{{#set:
Owner=Jordan_Read|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-18T13:11:02Z

Jordan: Set PropertyValue: Owner = Jordan Read

[[Category:Task]]


{{#set:
Owner=Jordan_Read|
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-18T13:10:50Z

Jordan: Set PropertyValue: StartDate = 2014-10-18

[[Category:Task]]


{{#set:
StartDate=2014-10-18|
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-18T13:10:46Z

Jordan: Set PropertyValue: TargetDate = 2014-10-24

[[Category:Task]]


{{#set:
TargetDate=2014-10-24|
Type=Low}}

Run GLM demo

2014-10-18T13:10:30Z

Jordan: Set PropertyValue: Type = low

[[Category:Task]]


{{#set:|
Type=Low}}

Run GLM demo

2014-10-18T13:10:18Z

Jordan: Creating new page with Category: Task

[[Category:Task]]

G16 Age of Water workshop preparation materials

2014-10-18T13:10:18Z

Jordan: Added PropertyValue: SubTask = Run GLM demo

[[Category:Task]]


====Pre-workshop Survey====
Participants are asked to fill out a short [https://www.surveymonkey.com/s/WDVKDN3 survey] to allow us to better coordinate workshop activities


{{#set:
Owner=Hilary_Dugan|
Participants=Gopal_Bhatt|
Participants=Jordan_Read|
Participants=Craig_Snortheim|
Progress=25|
StartDate=2014-09-20|
SubTask=Run_GLM_demo|
SubTask=Installing_R|
SubTask=R_Packages|
SubTask=Install_PIHM|
SubTask=Install_GLM|
TargetDate=2014-10-24|
Type=Low}}

Participant list

2014-10-13T18:20:56Z

Jordan:

[[Category:Task]]

{| class="wikitable"
! Last
! First
! Institution
! Career Stage
! Country
|-
| Hipsey
| Matt
| UWA
| Faculty
| Australia
|-
| Motta Marques
| David
| UFRGS
| Faculty
| Brazil
|-
| Cavalcanti
| Rafael
| Federal University of Rio Grande do Sul
| Student
| Brazil
|-
| Rusak
| Jim
| Dorset
| Faculty
| Canada
|-
| Lavender
| Mike
| U. Saskatchewan
| Student
| Canada
|-
| del Giorgio
| Paul
| UQAM
| Faculty
| Canada
|-
| Vachon
| Dominic
| UQAM
| Student
| Canada
|-
| LaPierre
| Jean-François
| UQAM
| Student
| Canada
|-
| Prairie
| Yves
| UQAM
| Faculty
| Canada
|-
| Arnott
| Shelley
| Queen's University
| Faculty
| Canada
|-
| Jennings
| Eleanor
| Dundalk Institute of Technology
| Faculty
| Ireland
|-
| Santoso
| Arianto
| Waikato
| Student
| New Zealand
|-
| Kpodonu
| Theodore
| Waikato
| Student
| New Zealand
|-
| Kim
| Bomchul
| Kangwon Nat'l Univ.
| Faculty
| South Korea
|-
| Weathers
| Kathie
| Cary Institute
| Faculty
| USA
|-
| Hetherington
| Amy
| Cornell
| Student
| USA
|-
| Pollard
| Amina
| EPA
| Faculty
| USA
|-
| Soranno
| Soranno
| MSU
| Faculty
| USA
|-
| Pierson
| Don
| NYCDEP
| Faculty
| USA
|-
| Janus
| Lorraine
| NYCDEP
| Faculty
| USA
|-
| Nihar
| Samal
| NYCDEP
| Faculty
| USA
|-
| Harmon
| Tom
| UC Merced
| Faculty
| USA
|-
| Jones
| Stuart
| UND
| Faculty
| USA
|-
| West
| Will
| UND
| Student
| USA
|-
| Beard
| Doug
| USGS
| Faculty
| USA
|-
| Wemple
| Beverly
| UVM
| Faculty
| USA
|-
| Isles
| Peter
| UVM
| Student
| USA
|-
| Perillo
| Venesa
| UVM
| Student
| USA
|-
| Oliver
| Sam
| UW
| Student
| USA
|-
| Carey
| Cayelan
| Virg. Tech
| Faculty
| USA
|-
| Doubek
| Jon
| Virg. Tech
| Student
| USA
|-
| Gerling
| Alex
| Virg. Tech
| Student
| USA
|-
| Hamre
| Kate
| Virg. Tech
| Student
| USA
|-
| Klug
| Jen
| Fairfield University
| Faculty
| USA
|-
| Hargreaves
| Bruce
| Lehigh University
| Faculty
| USA
|-
| Bruesewitz
| Denise
| Colby College
| Faculty
| USA
|}



{{#set:
Owner=Paul_Hanson|
Progress=100|
StartDate=2014-09-01|
TargetDate=2014-09-12|
Type=Low}}

G16 Age of Water workshop preparation materials

2014-09-12T17:12:14Z

Jordan: Added PropertyValue: Participants = Craig Snortheim

[[Category:Task]]


The workshop material for downloading the geospatial data will be available by the first week of October. Gopal will notify Hillary as soon as available.


{{#set:
Owner=Hilary_Dugan|
Participants=Craig_Snortheim|
Participants=Gopal_Bhatt|
Participants=Jordan_Read|
StartDate=2014-09-20|
TargetDate=2014-10-10|
Type=Medium}}

G16 Age of Water workshop preparation materials

2014-09-12T17:11:58Z

Jordan: Added PropertyValue: Participants = Jordan Read

[[Category:Task]]


The workshop material for downloading the geospatial data will be available by the first week of October. Gopal will notify Hillary as soon as available.


{{#set:
Owner=Hilary_Dugan|
Participants=Jordan_Read|
Participants=Gopal_Bhatt|
StartDate=2014-09-20|
TargetDate=2014-10-10|
Type=Medium}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:16:51Z

Jordan: Deleted PropertyValue: Answer = Wind speed

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model.


{{#set:
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=Format_meteorological_data_for_model_input|
SubTask=QAQC_meteorological_data|
SubTask=Collect_Downwelling_shortwave_radiation_data_for_North_Temperate_lakes|
SubTask=Collect_Downwelling_longwave_radiation_data_for_North_Temperate_lakes}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:16:49Z

Jordan: Deleted PropertyValue: Answer = Relative humidity

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model.


{{#set:
Answer=Wind_speed|
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=Format_meteorological_data_for_model_input|
SubTask=QAQC_meteorological_data|
SubTask=Collect_Downwelling_shortwave_radiation_data_for_North_Temperate_lakes|
SubTask=Collect_Downwelling_longwave_radiation_data_for_North_Temperate_lakes}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:16:48Z

Jordan: Deleted PropertyValue: Answer = Air temperature

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model.


{{#set:
Answer=Relative_humidity|
Answer=Wind_speed|
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=Format_meteorological_data_for_model_input|
SubTask=QAQC_meteorological_data|
SubTask=Collect_Downwelling_shortwave_radiation_data_for_North_Temperate_lakes|
SubTask=Collect_Downwelling_longwave_radiation_data_for_North_Temperate_lakes}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:16:27Z

Jordan: Deleted PropertyValue: Answer = Downwelling longwave radiation

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model.


{{#set:
Answer=Air_temperature|
Answer=Relative_humidity|
Answer=Wind_speed|
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=Format_meteorological_data_for_model_input|
SubTask=QAQC_meteorological_data|
SubTask=Collect_Downwelling_shortwave_radiation_data_for_North_Temperate_lakes|
SubTask=Collect_Downwelling_longwave_radiation_data_for_North_Temperate_lakes}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:16:26Z

Jordan: Deleted PropertyValue: Answer = Downwelling shortwave radiation

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model.


{{#set:
Answer=Downwelling_longwave_radiation|
Answer=Air_temperature|
Answer=Relative_humidity|
Answer=Wind_speed|
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=Format_meteorological_data_for_model_input|
SubTask=QAQC_meteorological_data|
SubTask=Collect_Downwelling_shortwave_radiation_data_for_North_Temperate_lakes|
SubTask=Collect_Downwelling_longwave_radiation_data_for_North_Temperate_lakes}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:16:19Z

Jordan: Added PropertyValue: SubTask = Collect Downwelling longwave radiation data for North Temperate lakes

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model.


{{#set:
Answer=Downwelling_shortwave_radiation|
Answer=Downwelling_longwave_radiation|
Answer=Air_temperature|
Answer=Relative_humidity|
Answer=Wind_speed|
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=Collect_Downwelling_longwave_radiation_data_for_North_Temperate_lakes|
SubTask=Format_meteorological_data_for_model_input|
SubTask=QAQC_meteorological_data|
SubTask=Collect_Downwelling_shortwave_radiation_data_for_North_Temperate_lakes}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:16:02Z

Jordan: Added PropertyValue: SubTask = Collect Downwelling shortwave radiation data for North Temperate lakes

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model.


{{#set:
Answer=Downwelling_shortwave_radiation|
Answer=Downwelling_longwave_radiation|
Answer=Air_temperature|
Answer=Relative_humidity|
Answer=Wind_speed|
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=Collect_Downwelling_shortwave_radiation_data_for_North_Temperate_lakes|
SubTask=Format_meteorological_data_for_model_input|
SubTask=QAQC_meteorological_data}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:15:33Z

Jordan:

[[Category:Task]]
Collect meteorological driver data for modeling North Temperate lakes. These data will need to be time series drivers according to the needs of the hydrodynamic model.


{{#set:
Answer=Downwelling_shortwave_radiation|
Answer=Downwelling_longwave_radiation|
Answer=Air_temperature|
Answer=Relative_humidity|
Answer=Wind_speed|
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=QAQC_meteorological_data|
SubTask=Format_meteorological_data_for_model_input}}

Obtain meteorological data for North Temperate Lakes

2014-06-09T19:14:15Z

Jordan: Jordan moved page Obtain meteorological data to Obtain meteorological data for North Temperate Lakes

[[Category:Task]]
placeholder text for description.


{{#set:
Answer=Downwelling_shortwave_radiation|
Answer=Downwelling_longwave_radiation|
Answer=Air_temperature|
Answer=Relative_humidity|
Answer=Wind_speed|
Participant=Paul_Hanson|
Participant=Jordan_Read|
SubTask=QAQC_meteorological_data|
SubTask=Format_meteorological_data_for_model_input}}

Obtain meteorological data

2014-06-09T19:14:15Z

Jordan: Jordan moved page Obtain meteorological data to Obtain meteorological data for North Temperate Lakes

#REDIRECT [[Obtain meteorological data for North Temperate Lakes]]

Hydrology

2014-06-09T18:51:51Z

Jordan: Added PropertyValue: Is a = Expertise

[[Category:Object]]


{{#set:|
Is a=Expertise}}

Hydrology

2014-06-09T18:51:36Z

Jordan: Creating new page with Category: Object

[[Category:Object]]

Hydrodynamic modeling

2014-06-09T18:50:18Z

Jordan:

[[Category:Object]]
Hydrodynamic modeling involves simulating the temporally-resolved mixing and fluxes of various scalars that are important to water researches or managers. These scalars include heat, dissolved constituents (including ions and dissolved organic carbon), particulate matter, and others. Hydrodynamic models can take the form of resolved layers, grids, cubes, etc in 0, 1, 2, or 3 dimensions (0D, 1D, 2D, or 3D). For example, most 1D models (e.g., [[GLM_Software|GLM]]) are built using a vertically resolved layer structure, while 0D models simulate a single water volume which evolves over time.