Tag Archives: Community Health Mapping

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)

Q & A with Kurt Menke, CHM Moderator

By Jenny Rewolinski

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Kurt Menke, GISP

The following is a question and answer interview with the moderator of the with Community Health Maps (CHM) blog, Kurt Menke, GISP (Certified geographic information systems (GIS) professional). Kurt has worked with CHM since its inception in 2014 and is a valuable resource for users of CHM.

What is your background?

Kurt: I started out as an archaeologist. I spent 8 years in the desert southwest working on Anasazi pueblo archaeology. I went on to receive a Masters in Geography from the University of New Mexico in 2000. While in graduate school I began working at the UNM’s Earth Data Analysis Center (EDAC). That’s where I really learned about GIS. I worked there for 11 years as a GIS Analyst/Programmer.

When did you being using open source GIS?

It was at EDAC, about 15 years ago, when I was first exposed to open source mapping software. We began using Mapserver for web mapping applications, because it was faster and more stable than the Esri alternative. I realized there was a whole ecosystem of open source tools out there.

How did you first come to work with NLM?

Kurt: John Scott, President of the Center for Public Service Communications and I have collaborated on health related projects with NLM for over 10 years. We first met while I was working at EDAC on a project with the National Indian Council on Aging (NICOA). I had developed an app named the Interactive Health Atlas. That project eventually ended and I left the university to create my business Bird’s Eye View. John thought we should take the best parts of the NICOA project to the National Library of Medicine (NLM). It evolved into what we called the Health Equity Atlas. This was custom software we developed, which was really time consuming. It worked great, but wasn’t widely adopted. We learned a valuable lesson, for something like this to be successful, it needs to be something organizations are asking for. No matter how useful it may be, if people don’t have time for it, it will just sit on the shelf.

How did CHM begin?

Kurt: In 2012, John asked me to look at existing smart phone apps. His idea was, rather than developing a completely new application, we could use existing low cost software. Plus we would work with organizations who had mapping as a defined need. I ended up completing a thorough survey of smartphone data collection tools and some of them were perfect. I identified what I thought were the two or three best. We realized we could stitch together a series of low cost intuitive tools that collectively address everyone’s mapping needs.

We settled on Fulcrum, QGIS, and Carto as our core CHM workflow tools. We started with pilot projects at the University of Hawaii and the Urban Indian Health Institute in Seattle. Showing people how to use these tools via a train-the-trainer approach ended up working really well.

You are a QGIS expert. When did you first begin using QGIS?

Kurt: QGIS was started in 2002 and I began playing with it in 2005. I just discovered it fromDiscoverQGISCover a listserv. At first it was very limited, being little more than a data viewer. But I was really curious to see how it might evolve, so I started following it. It really started becoming a useful alternative in 2010. I gradually migrated to it with my business. I also started teaching GIS classes with it. I used to keep a list of things you could do with ArcGIS that you couldn’t in QGIS. Now it’s come so far that I have a list of things you can do in QGIS that you can’t in ArcGIS!

How has CHM evolved?

Kurt:  Once we realized we had something that would be useful to people, we began looking for partner organizations. These are organizations who work with data and can benefit from mapping, but lack the resources to get started. We conduct workshops and webinars to get people started down the mapping path.

Along the way I thought a blog would be a really helpful tool to keep people up to date with new technology. These tools are constantly improving and I thought this would be a way to share these enhancements with everyone. Later we realized we needed additional resources for people to continue to build their skills after the initial workshops. I developed a series of six labs covering the mapping tools in more detail. These labs were inspired from a separate project I worked on called the GeoAcademy. This is a complete college curriculum for teaching GIS using open source tools. It even won an award!geoacademy_logo_col_5

Our primary goal for CHM has always been to provide tools that are helpful to users. After years of trying to build something from scratch, we are now finally gaining some traction with CHM. It feels like a snowball, rolling downhill and gaining speed. I believe it is both because the tools are powerful and intuitive, plus we are getting better at identifying potential users.

Would you recount one experience with CHM that felt especially influential for CHM’s progress so far?

Kurt: Yes the first thing that comes to mind is the work with the Medical University of

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St. Johns HS students learning CHM

South Carolina (MUSC). In early 2015 I taught a CHM workshop to 8 people. The training went well. No one in attendance had ever worked with any type of mapping software before. Yet I was able to show them how to make a data collection form, collect points, and map the data in Carto. The next day I went to a high school on John’s Island and taught several students over their lunch break how to collect data. They picked up on it immediately and spent the semester mapping food and water locations on the island.

Months later, the MUSC participants were so excited by the possibilities that they asked me to come back. This second training had 25 people. Later that year we came back for a third workshop, and 80 people from across MUSC attended! That I could show such a large group, how to work with these tools in a half day was a real proof of concept!

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The third workshop at MUSC with 80 particpants

Several projects were inspired these MUSC workshops. Of particular note is Dr. Bryan Heckman’s smoking cessation research project. I must point out that Dr. Deb Williamson and Dana Burshell worked to organize and plan the MUSC trainings and deserve most of the credit for the turnout.

Our successful trainings with MUSC have served as a model for teaching bigger groups such as those at the CHM Symposium at the National Library of Medicine in June, 2016 and recent trainings in Seattle.

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The most recent workshop in Seattle

The most gratifying aspect of these workshops was seeing people shed their technological insecurities. It’s common for people to show up and admit they’re scared of the technology. To then see in a few short hours, they are getting it all to work, and actually getting excited about the possibilities, is a beautiful thing.

 What are your plans for the future of CHM?

Kurt: The work that people are doing right now with CHM barely scratches the surface in terms of the potential. I would like to get more community members involved. I envision a scenario where there is an organization can really engage with citizens to map the community. The data could be managed by a central data manager in the organization. It would be such a great way to involve the community in a project directly related to their healthcare.

I’d also like to see someone get past the initial data gathering and map making phase. QGIS has a lot of spatial analysis capabilities. I’d like to see someone push beyond the CHM labs and do some interesting analyses in QGIS or use some of the cool data visualization techniques in Carto.

What advice you would give to new CHM users?

Kurt: Don’t be afraid to dive in and use the tools. Be adventurous and creative with your projects. Don’t be afraid to mess up. That’s how you learn. There is no limit to the kinds of things you can accomplish with mapping and spatial analysis tools. If you can imagine it, it can be done.

Field Data Collection with Fulcrum

Fulcrum was reviewed in our initial survey of field data collection apps in 2012, and almost made the top three. In the last 3 years Fulcrum has improved and has become perhaps the most intuitive and useful data collection app we’ve evaluated period.

It is available for both iOS and Android. It isn’t free, but the subscription fee is affordable. It costs anywhere from $18 – $25 per month. The three pricing plans give you 10 – 30Gb of online storage, which is substantial. Fulcrum offers a free 30 day trial which includes all the functionality. You can use this option to test Fulcrum for your projects. In the following example, I will be using a health care facility data collection form to show how Fulcrum works.

Fulcrum has the most intuitive data collection form builder of any app we’ve seen. When you design a form Fulcrum calls it an ‘app’. Simply drag and drop from the Add Fields section to your ‘app’ to add questions (see figure below). Available data input types include text, numbers, date, single or multiple choice, photos, videos, and audio.  There are no tricks to collecting GPS locations as with iForm. Fulcrum collects locations automatically.

A health care facility data collection form in Fulcrum.

A health care facility data collection form in Fulcrum.

Once a field has been added simply set you parameters. The figure below shows the facility type question being edited. To do this simply click on a field, and fill out the details. It’s so easy a 50 year old can do it!

The health care facility type question parameters.

The health care facility type question parameters.

The companion mobile app can be downloaded for free from the Apple Store or the Google Play Store. Once installed, login and your data collection app(s) will sync with your mobile device. The figure below shows the health care facilities data collection app on an iPhone. Answering the questions is intuitive. Once collected your data will be synced with your cloud account.

Health Care Facilities data collection form on an iPhone

Health Care Facilities data collection form on an iPhone

Once back in the office, login to your account, select your data collection app, and choose Start Export Wizard. You will be taken to the page below. Choose your file format. A complete array of GIS formats is available including: shapefiles, geodatabases, KML, PostGIS and Spatialite.  Choose any other appropriate options and click Next to download your data.

Fulcrum Data Export Options

Fulcrum Data Export Options

I highly recommend that everyone involved in Community Health Mapping evaluate Fulcrum. Along with iForm and ODK Collect is a CHM recommended data collection tool. There is a monthly subscription fee but it is low. It is the easiest and most flexible tool we’ve found. You can use the free 30 day trial period to see if it works for you.

Tableau Public for Data Visualizations

Tableau Public is free software that can help users publish interactive data visualizations to the internet. This software is another great option for data visualization along with GIS Cloud or CartoDB. It has powerful charting and graphing tools, and also allows you to map data and display that data against several online datasets and basemaps.

No plug-ins or programming skills are required, just a browser with JavaScript enabled. Tableau Public uses a simple drag and drop process that anyone can learn. You can work with either the free Tableau Desktop app, or Tableau Online the free cloud based server. Either way you can save your work to the Tableau Public Web servers, which are accessible by everyone on the Internet. One important note about this is that any data you publish is accessible to everyone on the internet.

People see and understand data, reports and dashboards faster with visual analytics technology, which can help uncover key trends, relationships, patterns, and outliers that might otherwise be a challenge to find. Tableau Public can be used to pare down information to its simplest form by stripping away the less important data.

The software can connect to Microsoft Excel, Microsoft Access, and multiple text file formats. It has a limit of 1,000,000 rows of data allowed in any single file. Your organization may use up to 50 megabytes of space.

Tableau Public projects can be shared by emailing a link or by embedding the work in a blog, wiki, or website. Clicking on an emailed link will open a browser page with the view loaded. If embedded onto a page, anyone who visits the page will see the live interactive view.  The following shows the use of Tableau Public in two health related studies.

Public Health Case Studies

To visualize the specific social problem of teen pregnancy over time, Tableau Public was used by the Wisconsin Council on Children and Families to show the decline in births to teen mothers in Wisconsin over recent years. The data depicts racial disparities in teen births in Wisconsin as well as differences in birth rates between older and younger teens. The online link to the data visualizations created with Tableau Public for this study can be found here: http://tblsft.com/public/gallery/teen-pregnancy-declines

The figure below is a screenshot of one of the data visualizations from this study. Data visualizations are interactive. Here the white popup window is showing data from a specific place on the line graph.

Teen Pregnancy Data Visualization

Teen Pregnancy Data Visualization

Such visualizations may help communities address and manage such issues as health problems associated with prematurity and poor academic performance of children of teen parents.

Data can also be mapped by geographic coordinates, city, state, county, and zip code. The visualization below deals with Medicare Costs and combines a map with a chart showing trends in the data.

Tableau Public Desktop - Medicare Cost Data Visualization

Tableau Public Desktop – Medicare Cost Data Visualization

Other data visualization examples created with Tableau Public can be found in the Gallery:

http://www.tableausoftware.com/public/gallery

Other Tableau Public Resources can be found here:

https://public.tableau.com/s/resources

 

 

Community Health Maps Presentation and Training at the Medical University of South Carolina

In May Kurt Menke presented the Community Health Maps project, and conducted a training at the Medical University of South Carolina College of Nursing. The presentation was recorded and is now available online. The presentation was about 45 minutes and includes the powerpoint slides, audio and visual. This is a great way for you to learn more about the project from the comfort of your own office!

Community Health Map Presentation at MUSC

Community Health Map Presentation at MUSC

Using CartoDB for Beautiful Online Maps

CartoDB is an online cloud based platform for storing and visualizing spatial data. It is the perfect tool for the third part of the workflow (outlined in the Introduction). You can sign up for a free account, which gives you 50Mb of storage space. Data can be collected with a smart phone or tablet with iForm, and brought directly into CartoDB.  It is a very intuitive platform. You can literally drag and drop a spreadsheet onto the CartoDB page and have the data upload to your account.  It will accept the most common geospatial file formats including: spreadsheets and comma delimited text files with addresses or coordinates, KML/KMZ, GPX, and shapefiles. Below is an example of a spreadsheet of Baltimore Dialysis Centers in CartoDB. This shows the spreadsheet in Data View .

CartoDB Data View

CartoDB Data View

After telling CartoDB which columns contain the latitude and longitude values, the data can be viewed in Map View (below). Here the default Positron basemap is being used. There are a variety of basemaps to choose from including imagery, Stamen maps and Nokia maps.

CartoDB Map View

CartoDB Map View

Once multiple data layers have been uploaded you can create a visualization. Below is a map focusing on Balitmore Diabetes. It includes Baltimore neighborhoods classified by the number of diabetics, food deserts and dialysis centers.  CartoDB provides wizards and other tools for styling your data. The dynamic map can be accessed here: http://cdb.io/1G4xP7j

CartoDB Visualization

CartoDB Visualization

Visualizations can be shared via hyperlinks and embedded into webpages.  CartoDB also has great documentation including:

Sign up for a free account and take it for a spin. On a related note Community Health Maps is almost done with a complete curriculum for community health mapping. It consists of six labs. The final lab shows you how to work with CartoDB from setting up an account to sharing a visualization. Stay tuned!

Community Health Maps Presenting at FOSS4G in Portland – September 2014

Kurt Menke will be presenting the Community Health Mapping project in Portland next month at FOSS4G. FOSS4G stands for Free and Open Source for Geospatial. It is the international open source GIS conference.

FOSS4G

Free and Open Source for Geospatial – PDX 2014

If you are nearby, or able to travel, it will be a great opportunity to learn more about the project including the workflow and how several groups have implemented it. The conference has eight concurrent tracks beginning Wednesday September 10th and ending on Friday September 12th. Conference talks will cover both new mapping technology and applications. The mapping technology will cover data collection, desktop analysis, cartography and web mapping. Over 1,000 attendees are expected. Mr. Menke’s talk is scheduled for 1:00pm on Wednesday September 10th. Hope to see you there.