Invasive Species in Ontario: An Animated-Interactive Map Using CARTO

By Samantha Perry
Geovis Project Assignment @RyersonGeo, SA8905, Fall 2018

My goal was to create an animated time-series map using CARTO to visualize the spread of invasive species across Ontario. In Ontario there are dozens of invasive species posing a threat to the health of our lakes, rivers, and forests. These intruding species can spread quickly due to the absence of natural predators, often damaging native species and ecosystems, and resulting in negative effects on the economy and human health. Mapping the spread of these invasive species is beneficial for showing the extent of the affected areas which can potentially be used for research and remediation purposes, as well as awareness for the ongoing issue. For this project, five of the most problematic or wide-spread invasive species were included in an animated-interactive map to show their spatial and temporal distribution.

The final animated-interactive map can be found at: https://perrys14.carto.com/builder/7785166c-d0cf-41ac-8441-602f224b1ae8/embed

Data

  1. The first dataset used was collected from the Ontario Ministry of Natural Resources and Forestry and contained information on invasive species observed in the province from 1982 to 2012. The data was provided as a shapefile, with polygons representing the affected areas.
  2. The second dataset was downloaded from the Early Detection & Distribution Mapping System (EDDMapS) Ontario website. The dataset included information about invasive species identified between 2010 and 2018. I obtained this dataset to supplement the Ontario Ministry dataset in order to provide a more up-to-date distribution of the species.

Software
CARTO is a location-intelligence based website that offers easy to use mapping and analysis software, allowing you to create visually appealing maps and discover key insights from location data. Using CARTO, I was able to create an animated-interactive map displaying the invasive species data. CARTO’s Time-Series Widget can be used to display large numbers of points over time. This feature requires a map layer containing point geometries with a timestamp (date), which is included in the data collected for the invasive species.

CARTO also offers an interactive feature to their maps, allowing users control some aspects of how they want to view the data. The Time-Series Widget includes animation controls such as play, stop, and pause to view a selected range of time. In addition, a Layer Selector can be added to the map so the user is able to select which layer(s) they wish to view.

Limitations
In order to create the map, I created a free student account with CARTO. Limitations associated with a free student account include a limit on the amount of data that can be stored, as well as a maximum of 8 layers per map. This limits the amount of invasive species that can be mapped.

Additionally, only one Time-Series Widget can be included per map, meaning that I could not include a time-series animation for each species individually, as I originally intended to. Instead, I had to create one time-series animation layer that included all five of the species. Because this layer included thousands of points, the map looks dark and cluttered when zoomed out to the full extent of the province (Figure 1). However, when zoomed in to specific areas of the province, the points do not overlap as much and the overall animation looks cleaner.

Another limitation to consider is that not all the species’ ranges start at the same time. As can be seen in Figure 1 below, the time slider on the map shows that there is a large increase in species observations around 2004. While it is possible that this could simply be due to an increase in observations around that time, it is likely because some of the species’ ranges begin at that time.

Figure 1. Layer showing all five invasive species’ ranges.

Tutorial

Step 1: Downloading and reviewing the data
The Ontario Ministry of Natural Resources and Forestry data was downloaded as a polygon shapefile using Scholars GeoPortal, while the EDDMapS Ontario dataset was downloaded as a CSV file from their website.

Step 2: Selection of species to map
Since the datasets included dozens of different invasive species in the datasets, it was necessary to select a smaller number of species to map. Determining which species to include involved some brief research on the topic, identifying which species are most prevalent and problematic in the province. The five species selected were the Eurasian Water-Milfoil, Purple Loosestrife, Round Goby, Spiny Water Flea, and Zebra Mussel.

Step 3: Preparing the data for upload to CARTO
Since the time-series animation in CARTO is only available for point data, I had to convert the Ontario Ministry polygon data to points. To do this I used ArcMap’s “Feature to Point” tool which created a new point layer from the polygon centroids. I then used the “Add XY Coordinates” tool to get the latitude and longitude of each point. Finally, I used the “Table to Excel” conversion tool to export the layer’s attribute table as an excel file. This provided me with a table with all invasive species point data collected by the Ontario Ministry that could be uploaded to CARTO.

Next, I created a table that included the information for the five selected species from both sources. I selected only the necessary columns to include in the new table, including; Species Name, Observation Date, Year, Latitude, Longitude, and Observation Source. This combined table was then saved as an excel file to be uploaded to CARTO.

Finally, I created 5 additional tables for each of the species separately. These were later used to create map layers that show each species’ individual distribution.

Step 4: Uploading the datasets to CARTO
After creating a free student account with CARTO, I uploaded the six datasets as excel files. Once uploaded, I had to change the “Observation Date” column from a “string” to “date” data type for each dataset. A “date” data type is required for the time-series animation to run.

Step 5: Geocoding datasets
Each dataset added to the map as a layer had to be geocoded. Using the latitude and longitude columns previously added to the Excel file, I geocoded each of the five species’ layers.

Step 6: Create time-series widget to display temporal distribution of all species
After creating a blank map, I added the Excel file that included all the invasive species data as a layer. I then added a Time-Series Widget to allow for the temporal animation. I then selected Observation Date as the column to be displayed, meaning that the point data will be organized by observation date. I chose to organize the buckets, or groupings, for the corresponding time-slider by year.

Since “cumulative” was not an option for the Time-Series layer, I had to use CARTCSS to edit the code for the aggregation style. Changing the style from “linear” to “cumulative” allowed the points to remain on the screen for the duration of the animation, letting the user see the entire species’ range in the province. The updated CSS code can be seen in the screenshots below.

Step 7: Creating five additional layers for each species’ range
Since I could only add one Time-Series Widget per map, and the layer with the animation looks cluttered at some extents, I decided to create five additional layers that show each of the species’ individual observation data and range.

Step 8: Customizing layer styles
After adding all of the layers, a colour scheme was selected where each of the species’ was represented by a different colour to clearly differentiate between them. Colours that are generally associated with the species were selected. For example, the colour purple was selected to represent Purple Loosestrife, which is a purple flowering plant. The “multiply” style option was selected, meaning that areas with more or overlapping occurrences of invasive species are a darker shade of the selected colour.

A layer selector was included in the legend so that users can turn layers on or off. This allows them to clearly see one species’ distribution at a time.

Step 9: Publish map
Once all of the layers were configured correctly, the map was published so it could be seen by the public.

Visualizing Alaska’s Forest Damage in Twenty Years

Author: Anitha Muraleedharan
Geovis Project Assignment@RyersonGeo,
SA 8905, Fall 2018 (Rinner)

Forest Damage in Alaska

Alaska is a dynamic region and has a long history of changeable climate. Alaska has lost a lot of its forests due to insect infestation, fire, flood, landslides, and windthrow. Aerial surveys are conducted to monitor forest health for the State of Alaska and to identify insect and some disease pest trends. This time series map animation will visualize the forest damage in Kenai Peninsula, Tanana Region and Fort Yukon Region of Alaska during the years 1989 to 2010. This blog will cover the entire processes involved in creating this visualization.

Data

The spatial data of the forest damage survey conducted during the period from 1989 to 2010 by the Alaska Department of Natural Resources are readily available for download from AK State Geo-Spatial Data Clearinghouse (http://www.asgdc.state.ak.us/?#2952). The shapefiles are available individually for each year from 1989 to 2010 except for years from 2000 to 2007. These data were used for preparing this Time Series map animation.

Preparing Data for Animation in QGIS

QGIS 3.2.3 64bit was used to prepare the data for animated map visualization of Alaska’s forest damage. QGIS is a free and open-source cross-platform desktop geographic information system (GIS) application that supports viewing, editing, visualization and analysis of geospatial data. Since the data were available only as individual files, the first step in preparing the data was to merge this data together into one shapefile. For this task, I used the Merge Vector Layers Tool in QGIS which merged all the individual shapefiles into a single shapefile.

Steps to Merge multiple vector layers into one

  • Step1: Add all the vector layers, intended to be merged, into QGIS
  • Step2: Go to Vector →Data Management Tools → Merge Vector Layers in the menu
  • Step3: Click input layers button and select all the layers needed to be merged
  • Step4: Click Merged Layer button to give a name for the merged output layer
  • Step4: Click Run in Background button to create the merged layer and add it to QGIS

Fig. 1 Merge Vector Layer Tool in QGIS

The next task was to format the timestamp column to fit the QGIS Time Manager plugin tool that will be used to create the animated map visualization. The timestamp column for this data was “SURVEY_YR” which was in four-digit format. The QGIS Time Manager Plugin requires that the timestamp data be in YYYY-MM-DD format. For this, a new field was created with name “Damage_Yr” and type string and used the Field Calculator tool in Processing Toolbox of QGIS.

Fig. 2 Field Calculator Tool in QGIS

In the Field Calculator tool, the expression “tostring(SURVEY_YR) + ‘-01-01’ ” was used to concatenate data in the field “SURVEY_YR” and the “-01-01”  together to make the timestamp in YYYY-MM-DD format and copy the data to the new field “Damage_Yr”.

Fig. 3 Attribute table showing the Damge_Yr in YYYY-MM-DD format after update.

Visualizing the Time Series

The Time Manager plugin was downloaded and installed in QGIS. The forest damage data was then added as a layer in QGIS. The Google Terrain map was added as the base map for this time series animation. The following steps were performed to add the Google Terrain map to QGIS.

  • Step1: Add a new connection to XYZ Tiles in QGIS and give it a name, say “Google Terrain”
  • Step2: Use https://mt1.google.com/vt/lyrs=t&x={x}&y={y}&z={z} as the URL.
  • Step3. Click Ok and then double-click the created layer to add the “Google Terrain” as the layer.

After the data was added, it was time to apply symbology to the polygon data showing the forest damage in QGIS. The layer was styled using the attribute “Damage_Yr” and categorized with sequential symbology. Once the data was styled, the Time Manager plugin needed to be configured to visualize the time series animation.

In the Time Manager Settings window, the Forest damage layer which needs to be animated was added using the “Add layer” button. The Damage_Yr column was chosen for the Start and End time and “Accumulate features” option was selected to show the features accumulated on the map as the year changes during the animation. 500 milliseconds duration was set in the animation options to show each year for that many seconds in the animation before showing the next year. To display each year as a label in the map during the animation, time format was set as “%Y” and the font, font size, and text color were also set.

Fig. 4 Time manager settings window

Fig. 5 Time display options.

The time frame in the Time manager dock was set as years since the forest damage in each year will be animated and displayed. The time frame size for the animation was set as 1 since we have data for each year from 1989 to 2010. The animation can be played by clicking the play button and QGIS will show the forest damage of Alaska in each year from 1989 to 2010 on the map window for 500 milliseconds each.

Fig. 6 Time Manager dock showing settings for the animation in QGIS

Converting the Time Series into Video

The Time Manager allows exporting the animation to a video. However, there is no option to add a legend onto the rendered maps in the animation in QGIS. Therefore, the maps were exported as .PNG image files. The map frames were exported first with the full extent of the map and subsequently, two more times with map zoomed to areas Tanana and Fort Yukon respectively for showing different areas in one animation. The legend along with title and data source labels were then added for each exported map frame using photoshop.

Finally, VirtualDub software was used to convert the .PNG files to video for each series of maps. VirtualDub is a free and open-source video capture and video processing utility for Microsoft Windows written by Avery Lee.  The generated .PNG files were then renamed in ascending order sequence in the format “frameXXX.png” where XXX is the frame number. For example, frame000, frame001 and so on. This is required for VirtualDub to detect the files as a sequence of images and then combine it to a video. The steps followed to create the animated video is as given below.

  • Step1: Open VirtualDub software
  • Step2: Go to File → Open video file option in the menu and navigate to the images folder
  • Step3: Click the first image in the map image series and VirtualDub will automatically add all the other images that are in sequence
  • Step5: Go to Video → Frame rate and set fps as 0.5 to show each frame for 500 milliseconds in the video
  • Step6: Preview the video and save it using File → Save as AVI option in the menu

Fig. 7 Combining the png files in VirtualDub software

Results


Watch the visualization on YouTube