- Author: Shane Feirer
Normally at this time of Year, I am getting ready to travel to San Diego for the ESRI User Conference. At the user conference 20,000 people from all over the world gather to hear about what new GIS tools and functionality ESRI is building into their GIS products. The participants also attend hundreds of technical sessions and workshops to improve their GIS Skills and they also network and discuss how they are using GIS in their fields of interests.
This year with COVID-19 the in-person user conference is not occurring, and the User Conference is going to be presented as a virtual conference (see agenda) with plenary sessions, technical sessions, and technical support. This is unfortunate, but it provides for a broader community to attend the plenary and learn about how GIS is currently being used and what GIS can be used for.
The plenary session is always an eye-opener! It typically has examples of impactful ways in which GIS is changing the world - examples from education, environment, planning, health, and so much more! It is really a great experience, and I recommend it.
If you are curious about what GIS can do or to get ideas about how else GIS could be used in our Organization please register and attend the plenary sessions of the ESRI Virtual User Conference. If you want to talk about GIS or about what you saw at the Virtual User Conference, please email me at email@example.com.
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The Problem: An Outdated and Unwieldy Site
The Informatics and GIS (IGIS) Statewide Program was established in 2012 to meet UCANR's growing need for geospatial research and technical training. We created our website using ANR's Site Builder content management system, which was state of the art at the time. Like many programs, our website grew organically over the years, until we woke up one day and discovered we had over 70 subpages!!
The size of our site made it not only unwieldy to navigate, it was also difficult to maintain and keep relevant. You know the drill: multiple subpages that you forgot about; no one updating; a general sprawl of information that only a few knew how to navigate. With feedback from UCANR Strategic Communications, we came to realize that our site was highly focused on our own needs and that of an internal (UCANR) audience. Clearly, we needed to redesign the website with a more external focus, and make it easier to navigate and get information. We did a collective “Sprint” during the COVID-19 shutdown, and revamped the site.
Goals for the New Site
Rather than merely do a superficial makeover, we decided to reorganize our site from the ground-up. We started out thinking about our communication goals, and the needs and interests of our clientele. Some people come looking for a specific resource, such as a software license or Tech Note. Others come looking for info about our upcoming training programs, or to learn more about our GIS and Drone Services. Still others just want to see what we do, and how we fit into ANR's overarching program umbrella.
Our new site is organized around four themes: Research, Services, Training, and Resources. To convey the breadth of what we do, we decided to develop “cards”, or nuggets of information about our work. A common thread in everything we do is connecting-the-dots, so we decided to make heavy use of tags and hyperlinks that connect our work to ANR's Strategic Goals, Public Value Statements, and our collaborators around the state.
Solution: Customization via Site Builder
Results: Dynamic and Focused Content
Custom Section Dividers
To help visitors navigate the home page and find the content they're looking for quickly, we developed attractive page dividers that split the landing page into sections. Under the hood these are simple DIV tags with custom background and color attributes, and are super-easy to make.
Another visual enhancement that makes a web page look less generic is achieved by using custom icons as buttons. We modified some standard clipart images to use as links on the ‘Client Services' toolbar which take users to different parts of our site. For a little branding flourish, we used colors that match the ANR palette, and created an ‘inverse' version of each images which appears when you hover over it. This is all very standard HTML and easy to implement.
Integration with Google Sheets
Over the past couple years, we've migrated the bulk of our program planning and tracking into Google Sheets. Nearly everything we do - workshop offerings, drone flights, service projects, publications, surveys - are recorded in a collection of easy-to-update Google Sheets. For this project, we created a new sheet to hold content specifically for certain parts of our website - including the project cards, metrics about our training and GIS services, and even quotes from our clientele.
Keeping Things Fresh through Randomization
To avoid stale content, we built in some randomization. Every time you come back to the home page, or refresh it, the video loop, project cards, and other content changes. As we add more content on the backend, the selection will be even more varied, making every visit seem new and fresh.
We've been looking for a way to show off some of our drone video for a long time, but the standard embedded YouTube player just wasn't cutting it. After creating a custom space for a video loop on the homepage, we used a command line utility called
ffmpeg to clip, resize, fade, and encode some of our favorite drone video clips at a low bandwidth (see if you can guess which RECs they come from!). Adding the videos to the page was super easy using the standard HTML5 video tag, and getting them to auto-play and loop simply involved a couple of extra arguments. The video files live on our server, and the file names are randomized, so every time you refresh the page a new video starts playing.
Encoding video for webpages is standard practice these days, so to make life easier for others (and ourselves!) we typed up this workflow in a new TechNote entitled Encoding Drone Video for the Web. In it. you'll find a link to a Google Sheet that reduces the pain of using ffmpeg by generating the command line for you. Simply substitute your own video file name, start & stop times, and crop parameters, and the command is generated for you ready to copy-paste into a command window.
Modularizing Content for Flexible Placement
Good site design starts with thinking about your visitors, your content, and your communication goals. Transitioning to the new Site Builder template was a good excuse for us to jettison eight years and 70 pages of accumulated web content, and think about what really matters. We really like the new Site Builder template, and managed to get the look and feel we were hoping for with a modest amount of HTML customization and Google Sheets integration. Web pages are never ‘done', but future development will be a lot easier now that we have the building blocks in place. And we'd love feedback! Check out our new site if you're interested, and contact us if you have thoughts or would like to learn more.
Interested in knowing how people are using their geospatial skills in the era of COVID-19?
Last week, Harvard hosted a 10-panelist webinar (Center for Geographic Analysis Virtual Forum: Responding to the COVID-19 Pandemic with Geospatial Research and Applications) in which experts explored real-time datasets, displayed transmission models, and discussed data ethics of the current pandemic.
Innovative uses of datasets (such as mobile phone data and social media Tweets) exemplified how we can instantaneously map the spread of this disease at very high temporal and spatial scales. Yet, as many geospatial fanatics and drone pilots know, with high resolution comes high risk (of privacy concerns, in this case).
Data privacy emerged as a recurring theme throughout this webinar. Several panelists discussed confidentiality issues of pandemic mapping, which involve the spatial resolution at which data are analyzed – at the individual level or aggregated to a larger and more anonymized level: a scale at which houses, faces, and identities cannot be recognized in detail.
Dr. Caroline Buckee (Harvard), who has been building a research network in collaboration with data companies to aggregate, anonymize, and analyze COVID-19 cellular phone data, explained why the data she analyzes are disseminated at the county level, instead of at the house or neighborhood level. One reason for this is that we would not want punitive action to take place against specific neighborhoods or households if they are not following mandates such as the shelter-in-place policy, because we don't know if these individuals are attending work or are performing essential tasks. It is important that the data we share does not result in discrimination.
Dr. Doug Richardson (Harvard) echoed these sentiments and provided information on a platform he is developing to promote data security and confidentiality: Geospatial Virtual Data Enclave (GVDE). Ethical and security standards embedded into this portal can help ameliorate issues of data confidentiality.
Another theme that was brought to light in this webinar was how narratives can become lost in COVID-19 geospatial data. Dr. Mei-Po Kwan (Chinese University of Hong Kong) mentioned how every dot on the map has a story – and these stories are steeped in inequity and inequality. Dr. Buckee reminded us that each transmission has important geographic context, and considering different risk factors (such as age and socioeconomic status) and covariates (such as population density) are key to interpreting these data. Finally, Dr. Este Geraghty (Esri) introduced several resources that Esri provides to incorporate and honor the stories of those who have battled against the virus (https://coronavirus-resources.esri.com/pages/resources).
Below are notes on some of the methodologies and resources discussed in the webinar.
Twitter COVID-19 Hot Spots (April 7-14, 2020) created using the Twitter geo-search API (spatial query, no semantic query), and the Getis Ord Gi* function (hot spot analysis) on the attribute: #relevantTweets/#allTweets (per cell). The methodology (semantic machine learning) is described in this publication: https://www.tandfonline.com/doi/full/10.1080/15230406.2017.1356242.
A location / allocation model in Esri's ArcGIS Pro for finding optimal testing sites, treatment sites, and food distribution sites during the pandemic in San Bernardino County. This model determines the population demand by creating a risk surface (including transmission, personal susceptibility, exposure, socioeconomic factors), and then calculates optimal locations (layers: road network data, risk surfaces, supply chain constraints for staffing facilities / administering tests).
- Esri COVID-19 resources: https://coronavirus-resources.esri.com/pages/resources
- ArcGIS implementation of the University of Pennsylvania's COVID-19 Hospital Impact Model for Epidemics (CHIME): https://www.arcgis.com/home/item.html?id=37ad6eb0d1034cd58844314a9b305de2
- COVID-19 Spatiotemporal Rapid Response Gateway: https://covid-19.stcenter.net/
- COVID-19-related big-data analytics demo by Todd Mostak of OmniSci Technologies portraying interactive exploration of 16 billion rows of location data from mobile phones, from their cell phone partner X-Mode: https://youtu.be/Oeg3jF5xs6o?t=147
In summary, this was a very informative seminar that acknowledged several critical topics in geospatial data analysis, highlighting strengths of data sources and methodologies, along with concerns and shortcomings in the current state of pandemic mapping.
Got the Coronavirus blues? Stuck at home staring at that stubborn dataset that's been on the back-burner for a year or more?
The IGIS Team is pleased to announce an exciting expansion to our Online Office Hours. In addition to quadrupling our time slots, we are also introducing dedicated Office Hour appointments for consultations in the statistical programming language R. We are also lengthening the time slots from 20 minutes to 30 minutes.
IGIS's Online Office Hours are one of ANR's best kept secrets. Since 2018, the IGIS team has availed itself for free online consultations to all ANR employees in a range of technical and data analysis topics including:
- using GIS for research, needs assessment, communication, planning, evaluation, etc.
- where to find spatial data
- how to go from a question to a GIS analysis
- software recommendations
- ArcGIS questions and workflows
- WebGIS and Story Maps
- tools for mobile data collection
- how to store & share spatial data
- working with climate data from Cal-Adapt
- spatial stats
- data analysis with R
- R Shiny
- drone equipment, regulations and best practices
- analyzing drone data with Pix4D
- MS Access
- Google Apps
- proposal consultations
Who does what, you might ask? Sean Hogan is guru in all things related to drones and remote sensing. Shane Feirer and Robert Johnson are professional GIS developers and programmers, have deep expertise in the ESRI suite of GIS tools, and work with Python and Django on a daily basis. Andy Lyons is highly experienced in R, and has a background in GIS and remote sensing. Director Maggi Kelly has supervised hundreds of student projects and has a commanding view of the entire geospatial sciences. Lyons and Feirer also have strong backgrounds in MS Access, data modeling, advanced Google Apps, and are working together on a project to make climate data from Cal-Adapt easier to access and work with. While we certainly can't answer every question, we enjoy discussing all things related to GIS and informatics, and can probably point you in the right direction.
General Office Hours (all topics) are offered Mondays and Tuesdays from 3-4. R consultations Office Hours are available Monday and Tuesday from 4-5. To sign up for a 30-minute slot, please go the sign-up page. The Zoom link will be sent to you in the confirmation email.
Hope to see you in Office Hours!
Welcome to the final IGIS year-in-review of the decade! 2019 was another productive and satisfying year, full of innovation, outreach, and collaboration. Our work this year has been guided by ANR Strategic Goals and contributed to the Public Value Statements. In this Part I, we highlight our impact toward ANR's Strategic Goal framework. In Part II, we discuss our contributions toward UC ANR's Public Value Statements.
Strategic Goal #1. Strengthen Research and Extension Partnerships
Our work as a technology unit puts us in an enviable position to collaborate widely both within UC ANR as well other UC units, state agencies, and beyond. Our expertise in geospatial technology, combined with the domain knowledge our ANR academics, multiplies the impact and efficiency research efforts. Some of our key UC ANR collaborators in 2019 included:
- Adina Merenlender, California Naturalist Program. We assessed climate literacy by analyzing what is taught in climate change courses in higher education around the country.
- Ali Montazar, UCCE Imperial & Riverside Counties. Assessment of alternative crops and irrigation practices for water conservation in the Imperial Valley.
- Beth Grafton-Cardwell, UC Riverside and Lindcove Research and Extension Center. Web map of distribution of Asian Citrus Psyllid and huanglongbing disease in California. App for growers and homeowners to determine location in relation to HLB detections.
- Brady Holder, Kearney Research and Extension Center. Acquired and processed UAV imagery for use in the evaluation of the potential use of aerial imagery in detecting weedy rice in California rice fields.
- Daniele Zaccaria, UC Davis. Helped update Information on Evapotranspiration of Mature Micro-irrigated Citrus Orchards in the San Joaquin Valley using uavs.
- Dohee Kim, UCCE Los Angeles County. County program distribution maps.
- James Schaeffer, UCCE Fresno County. Alkaliweed reporting tool in Survey 123.
- Jeremy James, Sierra Foothill Research and Extension Center. Online calculator for the financial returns of invasive species management, siting infrastructure for experimental plots.
- Jenny Sowerwine, UC Berkeley. Story Map training for youth, development of mobile data collection tools and drone mapping for agro-ecological resilience.
- John Bailey, Hopland Research and Extension Center. Acquired and processed UAV imagery following the 2018 River Fire.
- Lenya Quinn-Davidson, UCCE Humboldt County. Analyzed historic and current aerial imagery to assess Douglas Fir encroachment in Oak woodlands the Humboldt County.
- Leslie Roche, UC Davis. Acquired and processed UAV imagery for work related to the UC ANR - Rustici Grant, that monitored Post-fire plant succession in Lassen and Modoc Counties, for adaptive management of working rangelands.
- Maurice Pitesky, UC Davis. Developed an app for tracking high density waterfowl and potential avian flu.
- Rick Satomi, UCCE Shasta County. Woody Biomass database, Pond Volume Calculator, GIS training for Foresters.
- Rob Bennaton, UCCE Alameda and Contra Costa County. Bay Area Urban Ag Map.
- Ruth Dahlquist-Willard, UCCE Fresno & Tulare Counties. Mapped Southeast Asian Farms in relation to Disadvantaged Communities.
- Stephanie Castle, UC Davis. Acquired and processed UAV imagery for Tecopa Marsh data to assess endangered vole habitats
- Tapan Pathak, UC Merced. Agro-climatic decision support tools.
- Whitney Brim-DeForest, UCCE Sutter and Yuba Counties. Evaluated the potential for aerial imagery in detecting weedy rice in California rice fields.
Stepping it up a notch, we developed and strengthened several major Institutional Collaborations in 2019. Institutional collaborations start with individuals, but to enable significant amounts of resource sharing add another layer involving sub-awards, MOUs, and laborious project management and reporting systems. There's more overhead to be sure, but the results are worth it!
In 2019 we had the good fortune to continue our collaboration with the UC Natural Reserve System on the California Heartbeat Initiative. This ambitious project is centered around collecting longitudinal multispectral drone images at 10 UC reserves across CA. In 2019 we flew 1300 acres at 7 reserves for the CHI project, and provided additional support training UC NRS employees and helping them develop a data management system for the long-term.
Monterey Bay DART, Cal State Monterey Bay (CSUMB), and UCSC Fort Ord Natural Reserve were our primary partners in putting on our third annual DroneCamp. DroneCamp is our flagship training event, and if you haven't been to one in a while it's continued to get bigger, more comprehensive, and with a more polished curriculum. Monterey Bay DART is a non-profit spearheading technology focused regional development in the Monterey Peninsula, including an industry UAS symposium that we scheduled to align with DroneCamp. CSUMB provided amazing logistic support and modern facilities for the data processing sessions (e.g., imagine a computer lab with 40 high-powered Alienwares!). Our flight practice sessions were held at the beautiful nearby UCSC Fort Ord Natural Reserve. Although it took a lot of effort to coordinate all the pieces, the joint program went brilliantly and we're getting the band back together for 2020.
Our long-term collaboration with the UC Berkeley Geospatial Innovation Facility (GIF) ramped up this year with the launch of a new three-year project funded by the Strategic Growth Council. The goal of the project is to develop new ways to access complex climate data from California's official portal for climate data, Cal-Adapt, also managed by the GIF. Under the new project, we are conducting climate needs assessments for climate data in agriculture and natural resources, and developing new software tools to make it easier to access and analyze both historic and forecast climate data. Maggi, Sean and Andy also continue to be regular instructors at the GIF's GIS workshop series.
We maintain collaborations with the State agencies through a number of projects. We continue to be the lead unit developing the California Adaptation Clearinghouse, with funding by the Governor's Office of Planning and Research and technical work done by the GIF. We are a members of the California Natural Resources Agency UAS Work Group, along with Dr. Brandon Stark from the UC Center of Excellence on UAS Safety. This has led to some valuable collaborations, including the participation of the California Dept of Fish and Wildlife in our drone workshops at Hastings Reserve. Sean is also a regular at the Ag Day at the State Capital, where he talks about applications of GIS and drone data in agriculture.
Strategic Goal #10. Generate Revenue and Optimize Resource Deployment
IGIS was instrumental in assisting ANR and UC partners secure external grants. Some highlights in 2019 include our work with Tapan Parthik (UC - Merced), who received grant support from the USDA Climate Hub to build a Climate App for clientele, and our work with the Geospatial Innovation Facility (UC Berkeley), who received grants from the California Strategic Growth Council and the Governor's Office of Planning and Research for climate change planning. A key part of why these grants were successful was the partnership between the GIF and IGIS, in which IGIS provides content, networking and technical innovation in web mapping. Our drone services program has helped a number of ANR partners secure external funding to complete their mapping missions: Of the 10 drone projects we flew in 2019, mapping nearly 6,000 acres of croplands, rangelands and forests in California, 90% of the support came from external funding sources.
Strategic Goal #12. Modernize Technology and Facilities Infrastructure
IGIS has always had a close connection with the REC system. We've maintained and hosted spatial data for the RECs for years, because making data discoverable and accessible is essential for planning, administration, and coordinating science on field stations. However finding REC data was clunky. In 2019, we used a new data sharing platform from ESRI called OpenData to build a new user-friendly REC System Data Portal. Some of the layers are public, and some of them are restricted to ANR employees, but all of them are documented and discoverable.
Internally, we made a good bit of progress cracking the holy grail of data sharing and discoverability - drone data! Drone data are massive and diverse. Unlike satellite imagery, which is decades old, there are no industry standards for drone metadata, platforms to submit data, or government heavyweights like NASA or USGS to create the incentives to develop and adopt standards to make data findable, accessible, interoperable, and reusable (i.e., FAIR). However this is changing rapidly, and we are trying to be at the front of the wave. In 2019, we finally got all our drone data in one place, and are working to catalog it, archive it, and make it discoverable for future researchers.
RECs are also some of our biggest collaborators for GIS projects. In 2019 we conducted a solar radiation analysis to help Sierra Foothill REC (SFREC) locate experimental warming plots for an exciting study on climate change impacts on forage production. In a similar manner we analyzed the topography on SFREC to help them plan deployment of wireless mesh relay stations.
Building upon what we learned organizing our collection of drone imagery, we built the data architecture for the massive drone mapping mission we flew for Hopland REC after the 2018 River fire. Those data are now available for fire ecology researchers in the coming years in a well-organized and documented platform.
Our network of Cooperative Extension offices are also unfortunately vulnerable to fire, as we came to learn again in 2019. Working closely with David Alamillo (UC ANR EH&S), we did a GIS analysis of the wildfire risk for each of our 54 offices throughout the state and published the results as a web map. The results will be used to help keep our facilities and staff safe by planning risk reduction strategies as well as examine wildfire response plans to.
Strategic Goal #13. Streamline Administrative Functions
The versatility of the GIS and data management technologies we use enables us to help other ANR units plan, evaluate, and communicate their programs more effectively. An example of this is the map we built this year for LA County UCCE (PI Dohee Kim), showing the distribution of their programs and impact. We've done similar projects for the Master Gardener program in Marin County, and hope to do more of this next year to help counties who are feeling increasing pressure to convey their programmatic value to local and regional partners. While we can't take credit for it, we were also thrilled to see the California Naturalist program use what they learned in one of our Story Map workshops to create a Story Map of CalNat Volunteer Profiles and Impact, and provided support to other units in our online Office Hours to create story map versions of annual reports.
At the Division level, we built the UC ANR Footprint web app to visualize the academic footprint of CE Advisors and Specialists. Initially designed as a general planning tool, we then enhanced the map and underlying to support the position call process. Tools like this can help make diverse types of information more manageable, and help leadership direct resources where it will have the most impact.
Strategic Goal #15. Tell UC ANR's Story
Maps and data visualizations are powerful tools for telling stories, and the majority of our web app projects help tell UC ANR's story through our clients. In 2019, we also gave over 25 public presentations reaching over 2300 people. Not included in this number are the dozens of people we met at the World Ag Expo. The 2019 World Ag Expo was notable not only for the rainy weather, but for our on-camera interview with a local TV outfit on applications of drone imaging in agriculture. Over the year we also passed out dozens of copies of the UC ANR Map we designed in 2018, and made plans for an updated version in 2020.
Next: continue reading about IGIS's 2019 contributions toward ANR's Public Value Statements in Part II.