Category Archives: Data Collection

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)

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!

 

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.

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.

UMD Students Learn How to Map Health Issues

By Angela Kim & Colette Hochstein

On October 4, 2018, National Library of Medicine® (NLM) Research Assistant Julian Argoti and University of Maryland (UMD), School of Public Health intern Angela Kim spoke to the “Professional Preparation in Community Health” class at the University of Maryland, School of Public Health, College Park. The 75-minute class was attended by approximately 45 undergraduate students in the UMD Behavioral and Community Health (BCH) program. The presenters introduced NLM’s Community Health Maps (CHM) blog and facilitated a hands-on activity.

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UMD Fall 2018 “Professional Preparation in Community Health” Class

The presentation covered a basic introduction to the tools and workflow in CHM. The students were asked to use Fulcrum, a low-cost tool, to build a custom data collection form for the first step of the CHM workflow – data collection. They discovered first-hand how intuitive the tool is. After creating their own custom data collection form on the topic of their choice, the students left the classroom to collect data points around the School of Public Health building.

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Students testing functionality of water fountain.

On their return, the students explored maps of their data points on Fulcrum. Many noted that the process of collecting data points was easy and fun. UMD Professor James Butler mentioned that although drinking a good amount of water is emphasized at the School of Public Health, he had not previously noticed that there is no water fountain near the faculty lounge. His comment underscored that issues are often not observed until actively examined, as during the mapping process.

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Students collecting data points on water fountain locations

The class ended with Professor Butler concluding the class by reiterating how CHM can serve as a useful tool for visualizing many of the different health issues discussed in class.

The students were alerted to the free new online Community Health Maps online tutorial, a self-paced course from the NLM designed to help users gain the skills needed to use Community Health Maps.

QField – A QGIS Related App for Data Collection

QField is an application for collecting field data via an Android device. It was started 4-5 years ago by the Swiss company OPENGIS.ch LLC which also employs several core QGIS developers. QField has reached the point where it rivals most data collection apps. The only reason we have not been using it for Community Health Mapping workshops is that it is not available for iOS. This is simply because the open source license used by QField does not allow it to be wrapped into a proprietary software license like the one Apple employs for it’s store.  If however, you are a Community Health Mapper who uses Android it is a fantastic choice.

NOTE: It is possible to set up an app which is compatible with iOS but does not participate in the App Store. This solves the licensing issue. Setting up an app this way necessitates becoming part of the iOS Enterprise Program which costs money.  QField developers would like to make this happen, and it will likely involve iOS users donating to QField.

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QField Logo

Although QField is rooted in QGIS code it is not a miniature version of QGIS. Rather it is a streamlined data collection app. As they say, “the buttons are few and they are large,” so you can work with it out in the field. QField lets you create a map in QGIS and upload that map to your mobile device. From there you can collect data.

The workflow for QField looks like this. You begin by making a QGIS project on  your computer. Importantly this project will contain the point, line or polygon layer(s) you want to populate in the field. (NOTE that Fulcrum only allows the collection of points!) This means you think of your survey form and data to be collected in the office, and create fields in your GIS layer(s) for each question you want to answer. With a little bit of QGIS editing familiarity this isn’t any more difficult or time consuming than creating a form in Fulcrum.  You then upload the folder containing the QGIS project and data to your mobile device. The GeoPackage data format, which is the default for QGIS 3.x, works great with QField. There is even a QGIS Plugin named QFieldSync that facilitates migrating your project to your device. Once the data has been copied to your mobile device you can open your QGIS map file using QField.

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Screenshots showing (left to right) selecting Mode, setting the Mode to Digitize and choosing the active layer. Images from http://johnhickok.com/

QField uses the same rendering engine as QGIS so the map will look identical to how it did in the office.  Once the map is open you can select from one of two modes: Browse or Digitize. When collecting data you would choose Digitize. Then select the layer you want to work with.

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Screenshots (left to right) showing the map in QField, clicking the edit button, populating the attributes and the resulting point. Images from http://johnhickok.com/

For public health officials with security concerns QField is a great fit because there is no third party cloud platform involved. The data is not being streamed across the internet. All the data is stored locally on your mobile device. You can simply use the My Files app on your device to navigate to your GeoPackage file and email it to yourself. If it is too large you can connect your device to you computer to download it or use a data sharing app such as DropBox or Google Drive.

Since this is an open source project you can request new features and report any bugs you encounter by contacting the developers! Since QField doesn’t cost anything to download and use, you can also consider donating to the project to help it continue. Even small donations are helpful to projects like this. Doing this makes QField better for everyone. I encourage you to try it out.

Editing Points in Fulcrum

I am often asked if and how points can be edited in Fulcrum. Yes, you can edit points in Fulcrum! This short post will show you how. Fulcrum is not only a way to collect community data, it’s also a platform for showing that data on a map and a database you can edit. For this example, I will use the App I designed for the recent ASTHO workshop in Hawaii. We collected points around the conference facility at the Ala Moana Hotel. If a point isn’t located correctly I can go in and edit the location in Fulcrum.

To demonstrate this I have opened my ASTHO app. To see the data I will click on the records icon to open the data in map view. From here I simply click on a point I want to edit. The data form for that point opens. To put the data into Edit mode I click the pencil icon2018-08-16_120747. To change the location I click the Edit Location button. Then I click on the map at the location where the point should be moved. To save my edits I click the green Accept edits button 2018-08-16_120800.

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I can also edit the attributes of a point. It is a similar process. First I click on the point I need to edit. Then I click the pencil icon. I scroll down to find the attribute I need to edit and make the change. Once done click the green check mark button to accept the changes.

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I can also add new points from this interface in Fulcrum. To do this I simply click the green Add point button 2018-08-16_121106 and populate the attributes. If I have elements where were set to required in my App, I will have to populate them here, just as I did with my mobile device in the field.

So if you have collected some data and realize it needs some correction you can do that directly in Fulcrum prior to downloading it. Also note that the data can also be edited in QGIS and Carto. I’ll cover those procedures in future posts.

Happy mapping!