LifeWatch INBO

A tutorial on visualizing bird tracking data with CartoDB

We have been using CartoDB for bird tracking data for a while now and are very happy to see that we have inspired others to do the same, including for other species. To introduce even more people to this great tool for animal tracking data, I was invited to give a hands-on course at two workshops1. Rather than handing the course material to the participants of these workshops only, I decided to publish it here on this blog, so anyone can use it.

Introduction

CartoDB is a tool to explore, analyze and visualize geospatial data online. In my opinion, it's like Gmail or GitHub: one of the best software tools ever. CartoDB is used in a wide area of domains and has great documentation, but in this tutorial I'll focus on how it can be used for exploring and visualizing animal tracking data. Since we are tracking birds, I'll use our open data of Lesser Black-backed Gulls in the examples, but the methods can be applied to other animal tracking data as well (I hope). This tutorial is by no means meant to be exhaustive: it's a step by step guide to get you started and hopefully inspire you to do cool things with your own data.

Note: If you want to follow along with this tutorial, you'll at least need to do the actions in bold, all the rest in optional.

Create an account

Go to https://cartodb.com/signup to create an account, if you haven't got one already. Free accounts allow you to upload 50MB of data, but keep in mind that all your data and maps will be public2.

Login

  1. Once logged in, you see your private dashboard. This is where you (and only you) can upload data, create maps and manage your account.
  2. CartoDB will display contextual help messages to get you to know the tool. For an overview, see the documentation on the CartoDB editor.
  3. At the top, you can toggle between your Maps and Datasets.
  4. You also have a public profile (https://user.cartodb.com/maps). All datasets you upload and maps you create, will be visible there.

Upload data

For this tutorial, well use our open bird tracking data. To make it easier to follow along with a free CartoDB account, you can download a subset of the data (2.1MB), containing migration data for three gulls. If you want to know how that subset was created, here's the SQL query I used:

SELECT
    t.the_geom_webmercator,
    t.altitude,
    t.date_time,
    t.device_info_serial,
    t.direction,
    t.latitude,
    t.longitude,
    |/(t.x_speed^2 + t.y_speed^2) AS speed_2d,
    d.bird_name
FROM bird_tracking t
    LEFT JOIN bird_tracking_devices d
    ON t.device_info_serial = d.device_info_serial
WHERE
    t.userflag IS FALSE
    AND t.date_time >= '2013-08-15'
    AND t.date_time < '2014-05-01'
    AND d.bird_name IN (
        'Eric',
        'Nico',
        'Sanne'
    )
ORDER BY
    d.bird_name,
    t.date_time
  1. Download this zipped bird tracking csv file.
  2. Go to your datasets dashboard.
  3. Upload the file by dragging it to your browser window. CartoDB recognizes multiple files formats.

Data view

  1. CartoDB is powered by PostgreSQL & PostGIS and has created a database table from your file and done some automatic interpretation of the data types. Some additional columns have been created as well, such as cartodb_id.
  2. Geospatial data are interpreted automatically in the_geom. This interpretation assumes the geodetic datum to be WGS84. the_geom supports points, lines and polygons, but only one type per dataset.
  3. Click the arrow next to field name to manipulate columns, such as sorting, renaming, deleting or changing data types.
  4. Most of the functionality is in the collapsed toolbar on the right, such as merging datasets, adding rows or columns, and filters.
  5. Filters are great for exploring the data. Try out the filter for altitude.

    Filters

  6. Filters are actually just SQL, a much more powerful language to select, aggregate or update your data. CartoDB supports all PostgreSQL and PostGIS SQL functions.

  7. Click SQL in the toolbar and try this SQL to get some statistics about the scope of the dataset:

    SELECT
        count(*) AS occurrences,
        min(date_time) AS min_date_time,
        max(date_time) AS max_date_time,
        count(distinct device_info_serial) AS individuals
    FROM bird_tracking
    
  8. From the Edit menu in the top right you can export any query you make, in multiple file formats3. This is useful if you want to convert geospatial data from one file format to another, but don't have the tools on your computer to do so.

  9. Click Clear view to remove any applied SQL.

Create your first map

  1. Click Visualize in the top right to create your first map.
  2. Once created, click the title bird_tracking1 and rename it to My first map3.
  3. Click Map view.
  4. You can change the background map by clicking Change basemap in the bottom right4. Positron is a good default basemap, but there are many other options available and even more via Yours (including daily cloud cover maps from NASA). Note that for the Positron and Dark matter basemaps, city labels will be positioned on top of your data, making them more readable. Choose Positron (labels below) to turn this off or Positron (lite) to have no labels at all.
  5. Click Options in the bottom right to select the map interaction options you want to provide to the visitors of your map, such as Zoom controls or a Fullscreen button.
  6. The map view also provides a toolbar on the right, where you'll recognize the same SQL and Filters features from the data view.
  7. Click Wizards in the toolbar to see a plethora of visualization options. These are all explained in the CartoDB documentation.
  8. Try Intensity with the following options to get a sense of the distribution of occurrences:

    Intensity map

  9. Try Choropleth with the following options to see the relative altitude distribution (see the documentation to learn more about the different quantification methods):

    Choropleth map

  10. Just like the filters are powered by SQL, the wizards are powered by CartoCSS, which you can use to fine-tune your map5. Click CSS in the toolbar to discover how the quantification buckets (in this case Quantile) are defined:

    /** choropleth visualization */
    
    #bird_tracking{
        marker-fill-opacity: 0.8;
        marker-line-color: #FFF;
        marker-line-width: 0.5;
        marker-line-opacity: 1;
        marker-width: 7;
        marker-fill: #F2D2D3;
        marker-allow-overlap: true;
    }
    #bird_tracking [ altitude <= 6965] {
        marker-fill: #C1373C;
    }
    #bird_tracking [ altitude <= 634] {
        marker-fill: #CC4E52;
    }
    #bird_tracking [ altitude <= 338.5] {
        marker-fill: #D4686C;
    }
    #bird_tracking [ altitude <= 66.5] {
        marker-fill: #EBB7B9;
    }
    #bird_tracking [ altitude <= -205.5] {
        marker-fill: #F2D2D3;
    }
    

Create a map of migration speed

  1. We want to save our previous work and create another map. Click Edit > Duplicate map and name it Where does gull Nico rest?.
  2. Add a WHERE clause to the SQL to only select gull Nico between specific dates:

    SELECT * 
    FROM bird_tracking
    WHERE
        bird_name = 'Nico'
        AND date_time >= '2013-08-15'
        AND date_time < '2014-01-01'
    
  3. We want to visualize the travel speed of gull Nico. The best way to start is to create a Choropleth map, with the following options:

    Start from a choropleth map

  4. Most of the dots are red and the story does not come across yet. Let's dive into the CSS to fine-tune the map. We basically set all dots to green, except where the speed is below 2m/s, which we show larger and in red:

    /** choropleth visualization */
    
    #bird_tracking{
        marker-fill-opacity: 0.8;
        marker-line-color: #FFF;
        marker-line-width: 0.5;
        marker-line-opacity: 1;
        marker-width: 6;
        marker-fill: #1a9850;
        marker-allow-overlap: true;
    }
    #bird_tracking [ speed_2d < 2] {
        marker-fill: #d73027;
        marker-width: 10;
        marker-line-width: 1;
    }
    
  5. Click Legends in the toolbar to manually set what to be shown in the legend (using template Custom):

    Update the legend

  6. Click a point and chose Select fields to create an info window.

    Define info windows

  7. Describe your map by clicking Edit metadata... in the top left.

  8. Share your map by clicking Publish in the top right. The dialog box provides you with a link to the map or the code to embed it in a web page. CartoDB.js is for advanced use in apps.
  9. Copy the link and paste it in a new browser tab to verify the info windows are working and the bounding box makes sense, i.e. are the interesting part of the data visible? Anything you update in your map (including zoom level and bounding box) will affect the public map (reload the page to see the changes).
  10. Researchers often ask if they can export the map6. That's not the goal of CartoDB (which is creating online, interactive maps), but you can create a screenshot by clicking Export Image in the top left. Unedited, it's probably not fit for publication in a journal (e.g. the scale and indication of north are missing, which you could add manually), but luckily the default basemaps are already open data (required by some journals). You just need to credit OpenStreetMap.

The final map:

Create a map of tracks per month

  1. Duplicate your map and name it Tracks per month.
  2. This time we want to string the occurrences together as lines: one line per individual (with the occurrences sorted by date), per month. This can be done in the SQL. See the PostgreSQL documentation for date functions. the_geom_webmercator is a geospatial field that is calculated by CartoDB in the background based on the_geom and is used for the actual display on the map. Since we're defining a new geospatial field (i.e. a line), we have to explicitly include it.

    SELECT
        ST_MakeLine(the_geom_webmercator ORDER BY date_time ASC) AS the_geom_webmercator,
        extract(month from date_time) AS month,
        bird_name
    FROM bird_tracking
    WHERE
        date_time > '2013-08-15'
        AND date_time < '2014-01-01'
    GROUP BY
        bird_name,
        month
    
  3. We want to display each month in a different colour, so start with a Choropleth map, with the following options:

    Start from a choropleth map

  4. We will also include labels (start doing this in the Choropleth options), so you can still see which track belongs to which individual. Fine-tune the map in the CSS (note that I've changed the months to integers):

    /** choropleth visualization */
    
    #bird_tracking{
      polygon-opacity: 0;
      line-color: #FFFFCC;
      line-width: 1.5;
      line-opacity: 0.8;
    }
    
    #bird_tracking::labels {
      text-name: [bird_name];
      text-face-name: 'Lato Bold';
      text-size: 12;
      text-label-position-tolerance: 10;
      text-fill: #000;
      text-halo-fill: #FFF;
      text-halo-radius: 2;
      text-dy: -10;
      text-allow-overlap: false;
      text-placement: line;
      text-placement-type: simple;
    }
    
    #bird_tracking [ month <= 12] {
       line-color: #253494;
    }
    #bird_tracking [ month <= 11] {
       line-color: #2C7FB8;
    }
    #bird_tracking [ month <= 10] {
       line-color: #41B6C4;
    }
    #bird_tracking [ month <= 9] {
       line-color: #A1DAB4;
    }
    #bird_tracking [ month <= 8] {
       line-color: #FFFFCC;
    }
    
  5. Update the legend:

    Update the legend

  6. To provide some more context, let's annotate the map. In the top right, click Add Element > Add annotation item and indicate summer and winter locations. The position of an annotation element is linked to a location on the map (though placement can be a bit difficult) and you can define between which zoom levels to show it, to avoid cluttering:

    Add annotations

  7. Finally, update the description in Edit metadata... and publish your map.

The final map:

Create an animated map

  1. Duplicate your map and name it Migration in time.
  2. This time, we'll add a map on top of the previous one. Click + on the right hand side to add a new layer and choose the same table bird_tracking.
  3. Apply the same time constraints in the SQL:

    SELECT * 
    FROM bird_tracking
    WHERE
        date_time > '2013-08-15'
        AND date_time < '2014-01-01'
    
  4. From the Wizards, choose Torque cat7, with the following options. The Time Column should always be your date.

    Torque category options

    Torque category options

  5. The final CSS looks like this:

    /** torque_cat visualization */
    
    Map {
    -torque-frame-count:256;
    -torque-animation-duration:30;
    -torque-time-attribute:"date_time";
    -torque-aggregation-function:"CDB_Math_Mode(torque_category)";
    -torque-resolution:1;
    -torque-data-aggregation:linear;
    }
    
    #bird_tracking{
        comp-op: source-over;
        marker-fill-opacity: 0.9;
        marker-line-color: #FFF;
        marker-line-width: 0;
        marker-line-opacity: 1;
        marker-type: ellipse;
        marker-width: 3;
        marker-fill: #FF6600;
    }
    #bird_tracking[frame-offset=1] {
        marker-width:5;
        marker-fill-opacity:0.45; 
    }
    #bird_tracking[frame-offset=2] {
        marker-width:7;
        marker-fill-opacity:0.225; 
    }
    #bird_tracking[value=1] {
        marker-fill: #B81609;
    }
    #bird_tracking[value=2] {
        marker-fill: #FFA300;
    }
    #bird_tracking[value=3] {
        marker-fill: #A53ED5;
    }
    
  6. Update the legend, remove the bird_name labels from the other layer (they are no longer required) and publish your map.

The final map:

Go forth and start mapping

And there you have it. I hope this tutorial helped you to get a better idea of what you can do with CartoDB and that you're inspired to use it for your own tracking data. Please share your maps or any feedback you have regarding this tutorial in the comments below.

For inspiration and tutorials, see:


  1. The Animal Movement Analysis Summer Course organized by the Institute for Biodiversity and Ecosystem Dynamics on July 10 and the LifeWatch GIS and WebGis workshop organized by the Universit√© catholique de Louvain and the INBO on September 16. 

  2. They are public in the sense that they can be discovered on your public profile, for which one needs to know your user name. 

  3. Maps can have spaces and punctuation in their name, dataset names (which are actually PostgreSQL database tables) use lowercase and underscores. 

  4. You'll have to dismiss the cool, but somewhat obtrusive Analyzing dataset pop-up. 

  5. If you want to edit the CSS, it's best to always start from a wizard and set most of the options there first. Once you start editing the CSS, changes to the wizard options are no longer applied. You can only reset this by choosing another visualization from the wizard, which will override all CSS changes. 

  6. In addition to the data, which you can export from the Edit menu in the top right (see also step 8 of the Data view section of this tutorial). 

  7. You can add many layers to a map, but only one Torque layer (= one animated layer). That is because CartoDB cannot guarantee that multiple Torque layers will use the same time scale and speed (which is something the user defines), so it wouldn't make sense to play those at the same time. If you want to animate the same data, but with different colours for a certain attribute (e.g. individual), use the Torque cat like we did here. This works best if you don't use too many categories. 

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