Author Archives: Geomenke

About Geomenke

FOSS4G user/advocate/trainer | Conservation GIS specialist for hire | Co-author 'Mastering QGIS' | 14ers | Good coffee | Paleo | Fitness | Vinyl

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 with funding provided by the Association of State and Territorial Health Officials (ASTHO) as well as 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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The Basics of Using MapBox Studio for Web Mapping

MapBox is a very popular web mapping platform used by many social networking apps and news outlets. It includes a very powerful set of tools and comes with a modest pricing scheme.  The amount you pay depends on the web traffic your site receives, for many this will be next to free. As such this can be a great alternative way to publish interactive maps.

Uploading Data

If you have collected data using Fulcrum you will want to export that as a GeoJSON file.

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To start you can create a free account at https://www.mapbox.com/.  Once logged in click on the Products menu, choose Studio. From there click the Get started link.  From your Studio dashboard click on Datasets.

  • Click the New Dataset button
  • Select Upload  
  • Drag your GeoJSON file onto the form and click Confirm and Create
  • After it has finished uploading click Start editing. The data editor will open and your points will be displayed on a dark basemap. Next you will export your data to something called a tileset. Web maps are composed of tiles for each zoom level. During this next step MapBox will generate all the map tiles for your dataset.
  • Click the Export button and select Export to a new tileset.
  • Name your tileset and click Export.
  • It will process your data. When it has finished click on the dataset name to return to your Datasets on your Studio dashboard.

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Creating a Style

Now that you have uploaded your data you will learn about map Styles. Click on the Styles link on the top row of your dashboard.

  • Click the New style button
  • Choose an existing style such as Basic Template and click the Create button.
  • The style template will open. You can rename it from Basic Template to something more meaningful. Here the style has been renamed to Demo.
  • Next search for your area of interest in the white box to the right. In the example below I have searched for Ann Arbor, Michigan and then zoomed in a little closer to the data collection area.
  • You can customize the styling for any and all of the layers that make up this template. Here I am darkening the brown used for buildings a bit. To do this I clicked on Buildings and changed the color with the color widget.
  • Once you have made the changes you desire click the Publish button. Click Publish again and you have created your own basemap style.

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Adding a Layer to Your Map

Now you can add your tileset to your map style. Click the Add Layer button and choose the tileset you created.

 

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Styling Points

Once the layer has been added click on the Style tab of the layer. Next you will learn to give each type of Infrastructure it’s own point color.

  • Select the Color component
  • Click on Style with data conditions
  • The popup box for Choose a data field window opens. In this case the field is named Infrastructure so I begin typing Inf to more quickly locate the field. When you have found the field containing the categories for mapping, select it.
  • A Set values for box window opens. Select the first value e.g., Bench. The Data field will now read: Data field Infrastructure is Bench. Select the color for that item.
  • In the Set values for box window select the next item e.g., Sign and assign a color.
  • Continue until you have assigned colors to each value.

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Creating pop up windows takes a little more work. You can read the MapBox tutorial for that here.

Publishing a Map

  • When you are ready to share your map click the Publish button.
  • In the window that opens click Publish again and you Style will be published again and a url to your map will be provided.
  • You can also change the permissions here, and if you do you will receive a Success message.
  • When finished close the window.
  • Then click the Share button. You are given a url on the Share tab and a code snippet on the Use tab. The code snippet can be copied and pasted into a website to embed your map.

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This is just a basic primer for getting started with MapBox Studio. There is a lot you can do with this platform. You can find more tutorials here.

Community Health Maps in Michigan: Four Workshops in Four Days in Four Cities!

This past week Kurt Menke traveled to Michigan and taught four Community Health Maps workshops for the University of Michigan. These were organized by the University of Michigan Libraries and were done in four days on four different campuses: Ann Arbor, Flint, Detroit Center and Dearborn. These workshops were part of the Community Health Maps project and were funded by the National Library of Medicine (funding for the workshops was provided under a sub-award from the National Library of Medicine to ICF International)

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A map showing the four workshops and the route taken between them.

Due to great outreach by the University of Michigan team of – Tyler Nix, Marisa Conte, Alexa Rivera, Justin Schell, Sara McDonnell, Troy Rosencrants, Kui-Bin Im and Claudia Walters – the workshops had great attendance and ran like clockwork.

The first was held at the University of Michigan – Ann Arbor at the Hatcher Graduate Library.  Twenty eight people attended. The audience was mainly a mix of faculty and representatives of local public health/community organizations with a few students. The final hour was reserved for group discussion and Justin Schell did a fantastic job moderating. Ideas for mapping park safety and identifying underserved populations were discussed as projects where mapping could help.

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Participants at the Ann Arbor workshop

The second was held the following day at the UM Flint. We started in the University Center Happenings Room and moved to Thompson Library for the afternoon QGIS session. Forty five people came out for this second training, quite a bit more than we expected. This included some walk-ins and late registrants. In addition to faculty and students there were quite a few representatives from local county health departments and non-profits.

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UM – Flint workshop participants working on QGIS.

The third was held at the UM Detroit Center on April 4th. Thirty people registered for this workshop. This was probably the most diverse group including some UM faculty, plus Wayne State faculty, county public health staff (including some as far away as Saginaw County) and non-profit public health workers.

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Kurt Menke describing Help Resources at the Detroit Center

The fourth was held at UM Dearborn on April 5th. This was the smallest of the four with 20 registrants. However, this allowed us to get a little farther into the capabilities of QGIS.

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Data collection at the UM Dearborn campus.

One of the most helpful components was a web page Marisa Conte set up for the workshops. It initially had all the important details for each workshop, including driving directions, links to the slides and workshop data. This alone set a new standard for workshop outreach and organization. During the discussion on the first day she began adding url’s for sites containing useful data and other resources identified during the afternoon discussion. During the week this  evolved into what is now a fantastic resource for everyone who attended. This will be helpful to anyone implementing CHM related projects or those who weren’t able to attend.

For the week  123 people were trained in Community Health Maps! This is a record that may never be broken. However what came out of the week more than the numbers, is the incredible potential for projects that can make a real difference in these communities. I’m looking forward to working more with everyone I met. Thanks again to UM Michigan for organizing such a successful series of workshops.

QGIS 3.6 Noosa Released!

This past weekend QGIS 3.6 Noosa was released as the next stable release. You can visit the QGIS download site to find installers for Windows, Mac and Linux.

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At the same time QGIS 3.4 Madeira became the latest long-term release. This means that version 3.4 will be supported for a calendar year with bug fixes. This is now the version you should install and  work with for the next year.

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If you have not yet worked with the new 3.x line you can look at the visual changelogs here: Version 3.0 – Version 3.2 – Version 3.4. In general the QGIS 3.x line is a major upgrade from 2.x. I encourage you to install it and make a map!