Category Archives: Data Visualization

Vector Borne Disease Surveillance Workshop for State Based Health Officials

The Second Vector Borne Disease Surveillance Workshop

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On June 18 & 19, 2019, eight state based health officials took the second Vector Borne Disease Surveillance workshop in Providence, Rhode Island. This was the second of two 2-day workshops aimed specifically at tackling the spread of diseases like Dengue fever, West Nile and Zika viruses. As with the first one, this was a Community Health Maps training specifically designed to demonstrate how to collect and work with geographic data related to vector borne diseases, i.e. those that are transmitted to humans via other animals such as mosquitoes. Attendees represented health departments in: Colorado, Georgia, Kansas, Louisiana, Mississippi, New Mexico, Virginia and Guam.

Again this workshop was a team effort. The training was organized by the Association of State and Territorial Health Officials (ASTHO). Participants attendance was funded by CDC’s National Center for Emerging and Zoonotic Infectious Diseases. Travel for the trainers was funded by the National Library of Medicine, (funding for the workshop is provided under a sub-award from the National Library of Medicine to ICF International). This particular CHM workshop was taught in conjunction with ASTHO’s State Environmental Health Directors (SEHD) Peer Network Annual Meeting.

After an introduction to the Community Health Maps project – it’s origins, workflow and examples of past projects – participants learned to create a data collection form and use their smartphones to map features (trees, signs, benches etc…) around the conference site using Fulcrum.

For the remainder of the first day, the group took the data they collected earlier and imported into QGIS. In this section they became familiar with QGIS and how to symbolize layers and make a print map.

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Attendees working through GIS vector surveillance exercise

In addition to the data collected on site, we worked with mosquito data acquired courtesy of Dr. Chris Barker  covering Madera County, CA. The data included mosquito trap results over five years, virus testing, mosquito biting complaints, storm drains, parcel boundaries, roads and a hypothetical case of Dengue fever.

The second day focused on generating vector borne disease surveillance products. The participants:

A) generated trend graphs of mosquito populations through time via the QGIS Data Plotly plugin,

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B) generated heatmaps of mosquito populations,

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C) calculated the minimum infection rate per year for West Nile and St. Louis Encephalitis viruses,

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D) identified potential mosquito sources to be inspected (storm drains) using a combination of a buffer operation (done against mosquito complaints with the distance  the species is known to be able to travel) and select by location against storm drains,

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E) identified parcels at risk due to their proximity to a fictional outbreak of Dengue Fever,

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and F) learned to animate temporal data using the QGIS Time Manager plugin. Here the mosquito population (heatmap) is being animated weekly for the year 2018 with mosquito management zones be displayed.

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All participants received official QGIS certificates for their participation.

These workshop materials will part of the suite of https://communityhealthmaps.nlm.nih.gov/resources/ available through the Community Health Maps program in the near future.

If you are interested in having this taught for you or your colleagues contact Kurt Menke (kurt@birdseyeviewgis.com)

Pacific islanders Dive Deep into Community Health Maps Workflow

The First Vector Borne Disease Surveillance Workshop

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On June 8 & 9, 2019, twelve pacific island public health professionals met in Honolulu, HI to participate in a Community Health Maps training specifically designed to demonstrate how to collect and work with geographic data related to vector borne diseases, i.e. those that are transmitted to humans via other animals such as mosquitoes. Attendees represented: American Samoa, the Federated States of Micronesia, Guam, the Commonwealth of the Northern Mariana Islands, the Republic of the Marshall Islands and the Republic of Palau.

This was the first of two, two-day, workshops aimed specifically at tackling the spread of diseases like Dengue fever, West Nile and Zika viruses. It was a team effort. The training was organized by the Association of State and Territorial Health Officials (ASTHO). Participants attendance was funded by CDC’s National Center for Environmental Health. Travel for the trainers was funded by the National Library of Medicine, (funding for the workshop is provided under a sub-award from the National Library of Medicine to ICF International). This particular CHM workshop was taught in conjunction with ASTHO’s Insular Area Climate and Health Summit.

After an introduction to the Community Health Maps project – it’s origins, workflow and examples of past projects – participants learned to create a data collection form and use their smartphones to map features (trees, signs, benches etc…) around the IMG_20190610_214340_314_1_previewconference site using Fulcrum

Participants saw how this particular part of the workflow could be applied in their home regions to digitally locate areas of standing water and/ or sand pits that are some examples of breeding habitat for mosquitoes. Others anticipated mapping salt water resistant taro, households where infections have occurred and other geographic factors that contribute to the spread of vector borne diseases.

For the remainder of the first day the group took the data they created earlier and imported into QGIS, a sophisticated geographic visualization desktop software. In this section they became familiar with QGIS and how to symbolize layers and make a print map.

In addition to the data collected on site, we worked with mosquito data acquired courtesy of Dr. Chris Barker  covering Madera County, CA. The data included mosquito trap results over five years, virus testing, mosquito biting complaints, storm drains, parcel boundaries, roads and a hypothetical case of Dengue fever.

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The second day focused on generating vector borne disease surveillance products. Kurt Menke developed a curriculum to demonstrate how a GIS can create maps and statistical charts that transform simple text and numbers in a database into intuitive graphics that communicate information quickly and accurately. The previous blog post has more detail about the specific vector borne disease surveillance products participants learn to create.

20190607_114226(0)_1_previewThe attendees had a wide range of GIS skills from introductory to advanced capabilities. We experienced many of the common technical difficulties when working in a hotel conference room, older and newer computers and variations with different operating systems (Windows and Macs) as well. Despite all the differences, all of the participants: A) collected data with their smartphones, B) exported their data to a desktop GIS, C) used prepared data to create geographically accurate statistics, D) generated heatmaps of mosquito populations, E) calculated the minimum infection rate per year for West Nile and St. Louis Encephalitis viruses, F) identified potential sources using buffer operations with distances specific species are know to be able to travel, G) identified parcels at risk due to their proximity to a fictional outbreak of Dengue Fever and H) generated trend graphs of mosquito populations through time via the QGIS Data Plotly plugin. All participants received official QGIS certificates.

The skills required to complete these tasks are not always simple and straight forward. The participants of this workshop expressed great enthusiasm and persistence in figuring it all out… making mistakes and trying again. Many expressed a need for more training and a desire to have more specialized trainings on site specifically related to projects they are already working on.

The second workshop in the series will be taught next week in Providence, RI at the GIS Surveillance Workshop. This will be attended by State based health officials.

This vector borne disease surveillance version of the Community Health Maps workflow showcases the analysis and data visualization capabilities of QGIS, as well as, the data collection capabilities of Fulcrum. It represents perhaps the greatest potential for applied use of Community Health Maps to date.

These workshop materials will part of the suite of https://communityhealthmaps.nlm.nih.gov/resources/ available through the Community Health Maps program in the near future.

If you are interested in having this taught for you or your colleagues contact Kurt Menke (kurt@birdseyeviewgis.com)

Vector Borne Disease Surveillance with QGIS – A Series of Two Day Workshops

This spring, with funding provided by the Association of State and Territorial Health Officials (ASTHO), Kurt Menke developed a two day workshop that combines elements of the standard Community Health Maps workflow with vector borne disease surveillance analyses.

The workshop begins with an introduction to Community Health Maps, and learning how to use Fulcrum to develop a data collection form and collect community GIS data with a smartphone. Participants will then be introduced to QGIS. They will learn how to add the field data just collected, and symbolize it. They will then download some open data and create a map.

The second day focuses on a suite of mosquito trap data acquired from Madera County, CA, by Dr. Chris Barker at UC Davis. There are 5 years of mosquito trap data and mosquito virus testing data. There are also anonymized data for mosquito biting complaints, mosquito management zones, storm drain locations, parcels and roads.

Collectively this provides a rich yet manageable dataset. With it participants will learn to use to create information such as:

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Trend graphs of mosquito populations through time via the QGIS Data Plotly plugin.

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Heatmaps of mosquito populations per species

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Calculations of the Minimum Infection Rate per year for West Nile virus (WNV) and St. Louis Encephalitis (SLEV) virus

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Identify parcels at risk due to their proximity to a fictional outbreak of Dengue Fever. This is done by buffering the outbreak location by the potential flight range of the mosquito species

This workshop represents applied real-world workflows. These are many of the standard products needed by public health officials and typically produced by researchers. Having this sort of analysis and data visualization available via an open source package means anyone willing to take a few days to learn can produce them! This is especially true as the needed input data can be collected via Fulcrum if they don’t already exist.

This workshop will be taught twice in June. Both workshops will be part of the Community Health Maps project and are partly funded by the National Library of Medicine (funding for the workshop is provided under a sub-award from the National Library of Medicine to ICF International). The first iteration will be taught in conjunction with the Insular Area Climate and Health Summit in Honolulu, HI. This will be attended by public health officials from many of the Pacific Territories.

The second workshop will be taught in Providence, RI at the GIS Surveillance Workshop. This will be attended by State based health officials.

This material really showcases the analysis and data visualization capabilities of QGIS.  It represents perhaps the greatest potential for applied use of Community Health Maps to date. This workshop will part of the suite of Resources available through the Community Health Maps program in the near future.

If you are interested in having this taught for you or your colleagues contact Kurt Menke (kurt@birdseyeviewgis.com).

 

Community Health Maps at Rising Voices 7

Last week Community Health Maps traveled to Boulder, Colorado to teach a pre-conference workshop at Rising Voices 7. The theme was Converging Voices: Building relationships and practices for intercultural science. The conference was hosted by the National Center for Atmospheric Research (NCAR). The workshop was well attended with about two dozen participants representing numerous AI/AN tribes and other organizations. These workshop was part of the Community Health Maps project and was funded by the National Library of Medicine (funding for the workshop was provided under a sub-award from the National Library of Medicine to ICF International).

The goal of Rising Voices is to “advance science through collaborations”. Participants learn how indigenous and western scientific knowledge systems can compliment one another and advance our understanding of important issues in our communities. The focus is on climate.

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A photo taken by Dr. Angel Garcia (https://www.jmu.edu/geology/people/all-people/garcia-angel.shtml) during the workshop

At three hours the workshop was slightly shorter than normal. This allowed us to focus on field data collection with Fulcrum and web mapping with Carto. With a few minutes to spare Kurt Menke shared QGIS. Since he didn’t have time to really demonstrate the use of QGIS he focused on the open source aspect. As an open source project, QGIS is both GIS software and a community. As such it aligns with the ethics many communities try to foster at Rising Voices.

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A field data collection selfie!

 

Discover QGIS 3.x – A Workbook for Classroom or Independent Study

Today Discover QGIS 3.x was published by Locate Press. Authored by Community Health Mapper Kurt Menke, this is an update of the original title, using QGIS v3.6 and covering spatial analysis, data management, and cartography. It is designed to teach mapping and GIS using QGIS. As such it begins with basics. It is a comprehensive up-to-date workbook built for both the classroom and professionals looking to build their skills.

It is designed to take advantage of the latest QGIS features, and will guide you in improving your maps and analysis.

The book is a complete resource and includes:

  • Lab exercises
  • Challenge exercises
  • All data, discussion questions, and solutions

What’s new in this edition:

  • Updated to QGIS 3.6
  • Fifteen new exercises
  • A new section, Advanced Data Visualization, covering:
    • Blending modes
    • Live layer effects
    • Geometry generators
    • Rendering Points
    • Time Manager
    • Native 3D
    • Mesh data
  • Appendices covering:
    • Keyboard shortcuts
    • Useful Plugins
    • Getting involved

To see what’s included in the book, download the Table of Contents (PDF). Discover QGIS 3.x is available in color as an ebook or paper back.

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Mapping Field Photos in QGIS

We are on the eve of another QGIS release. Version 3.6 will be released any day now. This will mark an important milestone in QGIS development. QGIS 3.4 will become the first long-term release for the 3.x line. With 3.6 will come one specific change pertinent to this topic: the Raster Image Marker. Consider this post a small preview of what you can expect with v3.6!

In the typical CHM workshop attendees are shown how to use Fulcrum to download data collection points. These include photos. It is also possible to quickly and easily map any geotagged photo from your smartphone using just QGIS. For this example, I am using some photos I took yesterday during a hike with my iPhone.

    1. Using the Processing Toolbox, search for and open the Import Geotagged Photos tool and set it up as shown in below, pointing the tool to the folder containing your photos and naming the output point file.ImportGeoTaggedPhotos
    2. The data are in geographic coordinates (latitude and longitude). It will be helpful to project the photopoints to a Cartesian coordinate system such as UTM or State Plane. To do this right-click on the photopoints layer in the Layers Panel and choose Export –> Save As from the context menu.
    3. In the Save Vector Layer As window save a new copy of the layer. If you need help determining which coordinate system to use feel free to reach out to Kurt Menke (kurt at birdseyeviewgis.com). He is happy to help!SaveVectorLayerAs
    4. Now you have a couple interesting ways to visualize these points. First you can generate something called a Wedge Buffer.  These are pie shaped polygons that you can set up to represent the field-of-view of the photograph.wedgebuffers
    5. Search the Processing Toolbox for the Create Wedge Buffers tool.  The Input Layer will be the reprojected photopoints. The Buffers output can be a shapefile in your photos folder. The real trick is using what is known as a Data Defined Override. In QGIS you can use values in attribute columns or expressions for tool inputs instead of putting in a single typed value. In the animation below, a Data Defined Override is being used for the Azimuth parameter. This determines which way the wedge will be pointed. The Import Geotagged Photos tool extracts more than just photo location. It also extracts direction, altitude etc. Here the Azimuth parameter is simply being pointed to the direction attribute column and this orients the wedge in the direction the photo was taken! The only other parameter to set is the Outer Radius. This determines how long the wedge will be. Here it is being set to 300 meters.wedgebuffers
    6. Now there are both photo locations as points, and wedge buffers showing the field-of-view! wedgebufferscreated

 

  1.  Next let’s improve the default symbology for the wedge buffers using a Shapeburst fill. You will open the Layer Styling Panel (F7) and set the wedge buffers as the target layer. Next select the Simple Fill component and switch the Symbol layer type from Simple fill to Shapeburst fill. You can then set the two colors to use. Here I am using red and transparent. You can then set a distance for the effect and play with other settings like Blur strength. shapeburst
  2. Finally you will learn a feature that will be released with QGIS 3.6: Raster Image Markers. Here the target layer is the photopoints layer. The Symbol layer type is being switched from Simple fill to Raster image marker. Then the Data Defined Override for the image is being set to the photo field, and the Rotation parameter is being set to the rotation field!rasterimagemarker
  3. Now the photos have been mapped. Their field-of-view is being represented by a wedge buffer, and the photo itself is added to the map with a Raster image marker!photosmapped

Stay tuned for more tips on mapping and updates about this latest QGIS release.

A Pair of Community Health Maps Workshops at the ASTHO Climate and Health Summit

During the last week of May the Community Health Maps team (Janice Kelly, John Scott and Kurt Menke) traveled to Honolulu to participate in the Association of State and Territorial Health Officials (ASTHO) Insular Area Climate and Health Summit. There were representatives from:

  • American Samoa
  • Commonwealth of the Northern Mariana Islands
  • Federated States of Micronesia
  • Guam
  • Palau
  • Puerto Rico
  • Marshall Islands
  • U.S. Virgin Islands
  • Hawaii Department of Health
  • Pacific Island Health Officers Association (PIHOA)
  • ASTHO
  • CDC
  • NOAA
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Insular Climate & Health Summit Group Photo

The first afternoon was focused on the impacts of climate change, preparedness and building resilience. There were great presentations on climate change (Capt. Barry Choy – NOAA), an overview of the tools and programs available from the CDC (Paul Schramm), and issues with vector-borne diseases and mosquitoes (Janet McAllister).  The ASTHO grantees then gave some some sobering presentations on current issues people are dealing with in the Mariana Islands, Micronesia and the U.S. Virgin Islands.

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The opening session

The second day focused more on tools and resources. There were more detailed talks given by the CDC on Technical Assistance for Vector Control and Tools and Resources for Climate and Water Safety. That afternoon we taught a 3.5 hour Community Health Maps Train-the-Trainers workshop to a group of health officials from each territory.  We went through the entire CHM workflow: A) how to design a data collection form, B) how to collect data, C) how to make a map in Carto and D) how to bring the data into QGIS.

The last morning we taught a second Community Health Maps workshop open to everyone. We had about 30 attendees and again went through the entire CHM workflow.

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John Scott addresses the attendees on the final morning

Most of the trainees had little to no GIS training yet instantly knew how mapping could apply to their work and lives. They want to map everything related to hurricane relief, salt water resistant taro farms, infrastructure related to mosquito outbreaks etc. A benefit of having the community do this is that they can be in charge of their own data and it helps build community relationships.

Over the three days I heard a lot of side discussions about the usefulness of the free/low cost/open source CHM approach. The cost of proprietary solutions is often a significant barrier to entry into the world of community data collection and mapping. We were gratified to hear some very positive feedback on the workshops and CHM overall during the closing session. There seems to be a lot of potential in CHM helping both U.S. Territories and ASTHO deal with the immediate and long-term health issues related to climate.