Input on iOS!

The previous post covered a promising new tool named Input for data collection. As a reminder, this tool involves setting up a QGIS project and using the Mergin plugin to transfer the project and data to and from your computer and smartphone. It is also a free app. Another aspect of Input is that until now it has only been available for Android.

Yesterday Lutra Consulting announced the release of the beta version for iOS. It is available via an app named TestFlight!

From there is can be used just as was described in the previous post where setting up a project, using Mergin and collected data with Input was described. Once I have had a chance to experiment with it I will follow up with a summary on that. In the meantime, if you are an Apple iOS user, download the app and follow the previous post to give it a trial run.

Using Input/Mergin and QGIS for Field Data Collection

This post will show the basic steps for working with an alternative to Fulcrum for community data collection with a smartphone. The app is named Input. It’s a mobile app developed by Lutra Consulting. The app is free. Until now it was only available on Android. However, Lutra Consulting is working on a version for iOS! The Input workflow is based in QGIS. This means you set up your data layers in QGIS, along with the logic for your data collection. (This will mean a steeper learning curve for those not already familiar with QGIS. But don’t let that discourage you, it is not that much steeper!)

You then use their Mergin  cloud service to synchronize your QGIS project and data between your desktop and phone. There is a Mergin QGIS plugin making this quite simple. All the symbology you set up with your data in QGIS will be honored by the Input mobile app. With the combination of QGIS and Input/Mergin you can mimic all the field data collection functionality covered in a typical Community Health Maps workshop!

Getting started

Here I will walk through the steps in setting up the same type of data collection in CHM workshops. (Note: this post was inspired by the well done video by Dr. Hans van der Kwast on using Input). To get started:

  • Create a folder for your project
  • Open QGIS (in this example I’m using v 3.8).
  • Install the QuickMapServices plugin and add the OSM Standard and Google Satellite basemaps.
  • Zoom in to your study area.

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This step is optional but helpful. You will set up a layer as the study area boundary.  From the QGIS menu bar choose: Layer | Create layer | New Geopackage Layer.

  • Save the Database  (*.gpkg) into your folder.
  • Table name = study_area
  • Geometry typePolygon 
  • Click OK.

Now that the study area has been created, the polygon for the study area can be digitized and then styled. Right-click on the layer and choose Toggle Editing from the context menu. Use the Add Polygon Feature tool on the Digitizing toolbar to trace your study area. 

Styling the Study Area

Clicked F7 to open the Layer Styling Panel.  Here I gave the polygon a Fill Style of No Brush, a Stroke Color of bright red and a Stroke Width of 1.26. This study area covers a school and park near my office.

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Creating the Infrastructure Points Layer

This is more important. Create a second layer into which you will record points out in the field. Repeat the above steps to create a point layer and save it into the same GeoPackage. Name the Table infrastructure and set the Geometry type to point. Before clicking OK you will add columns to record the data you will collect. For each new column, enter the name, set the Type , Maximum length and click the Add to Fields list button. (Although not in the screenshot below you can also choose to add a date column – type = DateTime.) When you have added each field click OK to create the layer. 

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When saving, choose Add New Layer so the layer is added to the existing GeoPackage.

Now symbolize the points. Here I have used to Simple markers to create a purple target icon.

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Save your QGIS project as a QGS file into the same folder. (At the moment Input does not support the zipped default QGZ project file format.)

Creating Offline Basemaps

If you have a cellular connection the basemaps will work fine. However, if you anticipate losing cellular connection out in the field, you can use the Generate XYZ Tiles (MBTiles) processing tool to create offline versions of each basemap. You can set the extent to that of your study area layer. You will need to experiment with the zoom level settings. When they have been created you can use the Browser Panel to add these to your map. 

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Working with Map Themes

You can also set up Map Themes. These allow you to have different views of your map. Clicking the eye icon at the top of the Layers Panel will open the Map Themes menu. For example, to set up a map theme for just the Offline Satellite layer the study area and your point layer, you would just turn those three layers on. Then choose Add Theme and name it Offline Satellite from the Map Themes menu. Here I have set up several themes. With these I can easily toggle between these different views while in the field. 

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Setting Up Field Widgets for the Points Layer

The next steps are key for mimicking the data form functionality in Fulcrum. You will open the Layer Properties for the point layer, and switch to the Attributes Form tab. Here you can select each Field, and set up custom widgets which will control the editing behavior in the field. Below are the fields typically used in a CHM workshop.

  • fid – you don’t need to see this field, so select it and choose a Widget type of Hidden.
  • Infrastructure type – Select a Widget type of Value map. Here you can enter a series of choices with 1-x values. Under Constraints check Not Null which makes this required data.

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  • Bike rack capacity –  Select a Widget type of Text Edit. This allows the data collector to type the number for this. Since this only needs to be answered if the infrastructure type = Bike rack you can enter that as an expression in the Constraints section.

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  • Num bikes – set this up the same as the bike rack capacity.
  • Tree type  Widget type = Text Edit and you can set up the appropriate Constraint expression for this.
  • Sign type – Widget type = Text Edit and again set up the appropriate Constraint expression.
  • PhotographWidget type = Attachment. In the Path section click Relative paths. Then scroll down to find the Integrated Document Viewer section. Set the Type to Image.
  • Date – Set the Field Format to Date. Uncheck Calendar popup. Under Constraint check Not Null. Then in the Defaults section enter $now which will default to today’s date. 

Close Layer Properties and save your project. 

Project Properties

Now there is just one more setting to create. From the Project menu choose Properties and switch to the Data Sources tab.  Here check the box making the study_area Read only. This layer is just for reference and will not be edited in the field.

Save your project.

You are done with the set up and will now use the Mergin plugin to migrate your data to the server. In QGIS install the Mergin plugin.

Setting Up Mergin

Visit the Mergin web page (https://public.cloudmergin.com) and set up an account. With the free account you get 100Mb of data storage. (You can inquire with Lutra Consulting about getting additional cloud storage space.) 

In the QGIS Browser panel you will see a new Mergin data provider. Click on it and when prompted enter your credentials.

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In the Browser panel again right-click on the Mergin icon and choose New Project. Fill in the details and click OK. The data will upload to your cloud account.

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Collecting Data with Input

Now that the project is uploaded to the Mergin server you can switch to your smartphone. Install the Input app. Log in with your credentials and you will be able to access your project from the Projects list. You can then use the More option to switch between different map themes.

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When you are ready to collect a point, click the Record button and then the Add Point button. The form will open allowing you to collect all the data for that feature including a photograph. The points which have a condition preventing them from being entered will be unavailable and red. For example, the animation below shows a Stop sign being collected. The fields related to other things (bike racks and trees) are unavailable because a condition has been set within QGIS. Once the information has been entered simple click Save and move to the next data collection point.

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Downloading/Synchronizing the Data

When you are ready to download the data you can either 1) Use the Mergin data provider via the QGIS Browser panel to Synchronize your data, or 2) Synchronize the data via the Mergin website.

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You can then open the updated project from the same Mergin provider and begin to work with your data!

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This is still a very new app but shows immense promise for Community Health Mappers. I encourage Android users to try it out. iOS users stay tuned for future developments.

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!