Tag Archives: QGIS

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).

 

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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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!

QGIS 3.4 Released!

On November 2nd QGIS 3.4 ‘Madeira’ was released. It is the first long-term release in the new 3.x platform.  To install it you can visit the QGIS Download page. Installers are ready for Windows, Max OSX and Linux.

QGIS VERSIONS
Remember QGIS always has two main versions available. There is the long-term release, which is the most stable because it is supported for one calendar year. In addition there is always a latest release. QGIS 3.4 falls into this former category.

QGIS 3.4
This is a great time to update your version of QGIS. Especially if you are still using the 2.x line. QGIS 3.x is fast, stable and feature rich. If you are still a 2.x user there is a huge list of new features and useful changes. At this point most of the popular plugins have been migrated over from 2.x to 3.x. The chart below shows the steady migration and growth of 3.x plugins. You can review the visual changelog for this version here. You can also find the changelogs for versions 3.0 and 3.2.

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CHM Frequently Asked Questions (FAQ’s)

There are some questions I am asked regularly when teaching CHM workshops. This blog post addresses those common questions, many of which deal with data security.

Can more than one person collect data at the same time with Fulcrum?

Yes it is possible add users to your Fulcrum Organization for team based data collection. You set this up from your Fulcrum Settings page. When adding users you can give them a Role as a Standard User, Manager or Owner. You can also grant member access to your individual data collection apps. At that point those users have the access you granted them via their Role in your organization.

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Is there an organizational account for Fulcrum?

Not really. An organization can have a single account, but that account needs to be associated with a single email address. So the user name and password would then need to be shared with anyone in the organization. This isn’t the way Fulcrum is set up to work and they prefer users not do this. A better way is to create an account and add users to your organization.

The exception to this is Fulcrum Community This is a version of Fulcrum for use in humanitarian relief and disaster situations. You need to apply for a Community license. If granted you can invite any number of data collectors via their email address and they don’t have to have accounts. The Community license is free and lasts one year. We used this in Miami last fall and the project is features on the Community flood page  (Post-Irma Environment Reporting)!

When does Fulcrum record the point?

The point is taken when you click “Save”. You may have backed up to take a photo. However, when you are ready to save the record, you should have your device as close to the object you want to map as possible.

Why do I end up with two datasets from Fulcrum?

Photos you take with your mobile device are geotagged. When you download your data from your Fulcrum account you may end up with two datasets. One is based on your data collection app. The other is based on the coordinates embedded in the photos you took. For example, if you backed up to take a photo of a bench and then saved your point standing over the bench, you will be able to see both where the photo was taken and where the bench is located.

How accurate are the points collected with my mobile device?

There are a number of things that can affect data accuracy such as the quality of the GPS receiver, current satellite configuration, limited sky view, proximity to large buildings, tree cover etc. There is a two part blog post about this you can read here.

One thing to keep in mind is that when you are using Fulcrum to collect field data, the point is taken when you click “Save”. You may have backed up to take a photo. However, when you are ready to save the record you should have your device as close to the object you are mapping as possible. It is also possible to edit and correct point locations after the fact via Fulcrum, Carto or QGIS.

Is my data secure on QGIS?

QGIS is simply a piece of desktop software, not a platform for data storage. With QGIS you can map and analyze your spatial data. Data security has more to do with the security of your computer network and your system for backing data up. QGIS has no more bearing on data security than any other piece of desktop software such as ArcGIS or Microsoft Excel.

Does Fulcrum have HIPAA compliant security?

No. Fulcrum does employ 256-bit SSL connections to keep data safe as it travels to and from your cloud account. As they say, this is the same level of security provided by online banking and e-commerce sites. However, The HIPAA Security Rule requires implementation of three types of safeguards: 1) administrative, 2) physical and 3) technical. So Fulcrum is not HIPAA compliant. However, if they hear from enough users that this is a crucial feature they will likely work on it!

What is open source?

It is both a software license and a way to create software. There are two main types of software licenses: proprietary and open source. Proprietary licenses tend to restrict your usage of the software in some way:

  • number of computers you can install the software on
  • the number of features available
  • the time period you can use the software (e.g., a year)

On the other hand open sources licenses tend to grant users rights and freedoms around using the software. For example with QGIS, the license grants you the freedom to install the software on any number of computers and access to all the features forever. The software also has no monetary cost, it’s free.

Open source is also a software development strategy. The developers work in an open and collaborative way. Many developers feel this is a more efficient way to create software. In an open source project all the source code is available. This last point may not be a hugely important consideration for many. However, access to the source code means that if you have the capability, you can study how the software works and improve it. Because of this feature open source software is not a “black box.” Additionally, even if you cannot program a new feature yourself, you can hire someone who can. Since you are not paying any licensing fees this is often a very viable option.


If you have any other questions about Community Health Maps email them to Kurt Menke and he will try to answer them and add them to this post!

QGIS 3 Released!


On February 23rd QGIS 3 was formally released. Since then the developers have been working on completing installers for Windows, Mac and Linux. As of yesterday the software is ready to be installed on every operating system! To install it you can visit the QGIS Download page.

QGIS VERSIONS
QGIS always has two main versions available. There is the long-term release, which is the most stable because it is supported for one calendar year. In addition there is always a latest release. QGIS 3 falls into this latter category, it is the latest release. At the moment the long-term release is version 2.18. The latest release is still considered stable, but a new one comes out every 4 months.

WHICH VERSION TO CHOOSE?
If you want to have one version of QGIS without having to worry about updates, use the long-term release (2.18). If you want to experience all the new features that come with version 3 you will want the latest release (3.0). As mentioned last month, version 3 is a major new release with a lot of changes and new features.

On Windows machines you can have both. You can easily install both versions of QGIS side by side with no conflicts by using the OSGeo4W Network Installer. On Mac and Linux machines you can only have one version, so you need to choose.

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QGIS 3 is fast, stable and feature rich. The main issue for many users is that not all Plugins have yet  to be ported to QGIS 3. This is because this responsibility falls onto the individual plugin authors. With that said, at last count there were already 117 plugins available for version 3.

 

QGIS 3.0 To Be Released in February!

It’s an exciting month for QGIS. On February 23rd there will be a major new release of QGIS: QGIS 3.0. We haven’t had a major new release since 2013 when 2.0 came out. The development team has been working on this for a solid year. This version will be faster and have a lot of new features. Kurt Menke has been closely following the development of QGIS3. Over the last few months he has been experimenting with the pre-release version (v2.99). This post will cover some of the highlights that will be useful to Community Health Mappers. In general QGIS is going to be faster, more powerful and more efficient to work with. First off QGIS 3.0 comes with a new logo!qgis-logo_anita02

Overall the look of QGIS is very similar.  There are  the Layers and Browser panels to the left, a Map Canvas and lots of buttons and menus above. However, upon closer inspection there are a lot of very useful changes. For example, instead of there being a row of add data buttons down the left side, there is now a Unified Data Source Manager button which opens up a browser.

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The Unified Data Source Manager can be used to access the myriad of data formats QGIS supports and add them to QGIS. This includes vector, raster, database, web services etc. You can even browse within Esri File Geodatabases. Any GIS layer you are interested in, can then be added to QGIS by dragging and dropping it onto the map. DataSourceManager.gif

 

The Processing toolbox was completely redesigned and many tools were rewritten. This means many are now faster, more flexible and stable. There are also many new tools that didn’t exist in QGIS v2.x. Additionally processing tasks also now run in the background. This means  you don’t have to stop working while a tool runs! Yet another new processing feature is that layers in different projections will automatically be reprojected, so there is no need to reproject beforehand.

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Map Labels: It now much easier to edit labels. Previously you had to set up attribute columns and set those as data defined overrides. If you don’t know what all that means, it’s OK. Now all you have to do is simply put the layer into edit mode and edit labels with tools on the Label toolbar. Maps also now redraw more quickly due to cached label renderers.

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There is now a Search bar in the lower left corner that can be used to search for map layers, features and processing tools. This makes finding things in QGIS quick and easy.

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The QGIS print composer was completely redesigned. They are now referred to as Layouts. Map insets can now be in a different map projection than the main map. There is a new and improved system of guides which include settings in any unit of measurement you could want (mm, cm, m, in, ft, pt, pica, pix). There are new controls for choosing fonts which include recently used fonts. When you export a map, a link to the folder shows up making it easy to track down the exported map.2018-01-31_163437.jpg

 

Other notable enhancements include:

  • A fully integrated 3D environment
  • Editing improvements including: a) widgets for layer attributes, b) CAD style digitizing tools that allow you to create perfect rectangles, circles, ellipses etc. and c) a new node editing tool with a lot of behavior improvements
  • Previews of where each map projection can be used. This will be a big help for beginners!2018-01-31_170602.jpg
  • User profiles that allow you to set up QGIS with different panels, plugins and toolbars for different projects or uses.
  • Improved hidpi/retina support

 

Where do you go from here?

  • 2.18 will be considered the supported long-term release (LTR) through June.
  • When 3.0 is released in a few weeks it will be considered the latest stable version.
  • 3.2 will become the LTR in June when it is released.
  • Starting on February 23rd you will be able to download and install it. Remember you can have multiple versions installed with no conflicts. I encourage  you to install it in a few weeks and begin to explore it! You won’t want to go back.

NOTE: QGIS 3 projects won’t be entirely backwards compatible with QGIS 2.x. So if you are going to open an existing project in QGIS 3, be sure to click Project –>Save As and save a new verion of the project for use in QGIS3.

A Busy Summer with a QGIS Conference in Denmark and FOSS4G in Boston

This summer Kurt Menke first attended the 3rd Annual QGIS User Conference, Hackfest and Developer meeting in Denmark. From there he traveled to Boston to attend the Free and Open Source for Geospatial (FOSS4G) International Conference. 

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Trip Map Created in QGIS using Live Layer Effects

The QGIS conference was small and intimate and a lot of new information was shared by the developers about the future of QGIS.

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QGIS Conference

There was so much presented that this will be a separate future blog post. While there Kurt conducted a full day workshop on Data Visualization and Cartography in QGIS.

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Kurt Menke teaching about Data Visualization & Cartography in QGIS

He shared many of the new sophisticated and powerful data styling tools now found in QGIS including: 2.5D, 3D, Live Layer Effects, Inverted Polygon Shapeburst Fills, Blending Modes, and some plugins such as Time Manager. Perhaps this could be a workshop shared with CHM partners at a future date? Some examples are shown below:

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Use of Blending Modes to highlight road density

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Lower Manhattan displayed in 3D via the QGIS2ThreeJS plugin

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Cyclones Annually from 1950 – 2015 in QGIS with the Time Manager plugin

In Boston Kurt presented the Community Health Maps project. The talk was well attended and there was a lot of interest. Fulcrum was a sponsor of the conference, and Kurt was able to meet with several of the Fulcrum representatives. While there he learned about Fulcrum Community. This is a new initiative designed to help humanitarian agencies, non-profits, NGOs, or Government entities. To begin you need to request a Fulcrum Community account. One important caveat is that data collected via a Fulcrum Community account is anonymized, free, and open to all by default. It is essentially an initiative that will help in larger crowd sourcing efforts. More details will be forthcoming as Kurt explores this and how it may apply to Community Health Mappers.

This month (September), Community Health Maps will be travelling to the University of Connecticut (Community Medicine and Health Care) and to Miami to teach workshops. The workshop at the University of Connecticut will be to a large diverse audience. The Miami workshops will be focused on showing community members how to map damage and issues related to King Tides.

Stay tuned for blog posts on: 1) the future of QGIS, 2) Fulcrum Community, 3) experiences in Connecticut and 4) Miami.

CHM Lab Exercises Updated!

One of the most valuable resources for Community Health Mappers remains the series of lab exercises created two years ago. Our workshops, while effective, are short and only scratch the surface of what you can do with mapping tools. They are basically a quick start guide to Community Health Mapping. The labs however, can be used as a resource to help you build your skills once you’ve taken the first steps towards mapping your community.

The technology changes rapidly. QGIS produces a new stable version every 4 months. Annually QGIS also produces a long-term release. Carto and Fulcrum also update their tools on a regular basis. This mean the lab exercises need to be updated to keep pace.

The good news is that this spring the labs were all updated and expanded. There is some foundational knowledge needed to really take the next step after a workshop. The current revised set of labs includes Lab 0: A Community Health Map Introduction and Reference. This lab has background on the Community Health Maps project and the workflow. It also contains a Glossary of GIS terms, and several appendices covering: A) available software, B) data sources and C) everything you need to know to better understand coordinate systems and projection.

The remaining labs are as follows:

Lab 1 covers field data collection and has been updated to work with Fulcrum. This has allowed us to unify the exercise into one document for both iOS and Android users.

Lab 2 shows you how to bring your field data into QGIS. This includes a tour of the QGIS interface, and how to map coordinate data stored in a spreadsheet.

Lab 3 is named Combining Field Data with other Organizational Data. It shows you how to work with coordinate systems in QGIS. It also covers how to join tabular data to the attribute table of a GIS layer. This is a step that often has to be done to merge socioeconomic data from the U.S. Census to census geography such as tracts or block groups. It concludes with a lesson on address geocoding. This is the process you use to produce points from addresses.

Lab 4 shows you how to do some basic spatial analysis. You learn how to clip data to your study area, measure proximity, query your data to select features and calculate areas/ density.

In Lab 5 you learn how to use some of the great data visualization techniques found in only in QGIS. The lab then walks you through how to compose a map. Along the way you learn some data styling tricks and how to use the Print Composer.

The series concludes with Lab 6 Data Visualization with Carto. Carto underwent a major update and rebranding since the first edition of these labs were created. You can use this exercise to see how to work with the new Carto Builder interface and tools to create an online map of your results. It covers uploading your data, styling and sharing your map with others.

The four labs that deal with QGIS have been updated to include some exciting new features that have been added to QGIS in the last year. Links to the lab data are included. So head to the Resources page and build your Community Health Mapping skills!