Tag Archives: Ecology

GIS For Biologists: Tip #9 – How To Add A Google Earth Or Bing Maps Image To A GIS Project

15 May

This video is the ninth in a series of helpful hints and handy tips for biologists who want to use Geographic Information Systems (GIS) in their research. It demonstrates how to add an image from Google Earth or Bing maps to a GIS project using QGIS, the leading freely available open source GIS software. For those working in the commercial ArcGIS software package, a similar end can be achieved by adding the World Imagery basemap from ESRI to a GIS project.

If you are wondering why you would want to add such images to a GIS project, they open up some very interesting and useful possibilities. Firstly, and most basically, they provide a nice background to help put any data you are displaying in your GIS project in a wider context. For example, you can see areas of woodland, or lakes, or see their proximity to other features, such as rivers, houses and roads.

Secondly, and this is where things get interesting, once you have such images in your GIS project, you can create new data layers and trace features from the image into them. Through this process, you can create high-resolution data layers of features within your study area, such as the above mentioned areas of woodland and lakes. In fact, this is one of the quickest and best ways to generate high-resolution data layers of features in your local environment, especially for small study areas and parts of the world where there are few sources of suitable existing data layers.

While this video only covers the adding of Google Earth and Bing maps images to your GIS project in QGIS, you can find information on how to make new data layers here.  Similarly, the QGIS OpenLayers Plugin, which is used to import these images, can also be used to import images from OpenStreetMap, MapQuest and other potential source of GIS data that are likely to be useful to biologists, so it is really useful to know how to use this plugin.

If you have any questions or queries about this video, feel free to comment on this post and I’ll do my best to answer them.

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Dr Colin D. MacLeod,
Founder, GIS In Ecology
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GIS For Biologists: Tip #8 – How To Change How A Data Layer Is Displayed In A GIS Project

24 Apr

This video is the eighth in a series of helpful hints and handy tips for biologists who want to use Geographic Information Systems (GIS) in their research. It provides a brief introduction on how to change how data layers are displayed in A GIS project using QGIS.

While it is often tempting to stay with the default display option selected by your GIS software when you add a new data layer to a GIS project, by changing the way that your data layers are displayed, you can greatly enhance both the contents of your GIS project, and any maps that you create from it. This video takes you through some of the different options which are available for displaying different types of data layers, including point data layers, polygon data layers and raster data layers. While these are demonstrated in QGIS, the same options are available in other GIS software packages.

If you have any questions or queries about this video, feel free to comment on this post and I’ll do my best to answer them.

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Dr Colin D. MacLeod,
Founder, GIS In Ecology
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GIS For Biologists: Tip #5 – Adding An Existing Data Layer To A GIS Project

1 Apr

Once you have set the projection/coordinate system of your GIS project, you can think about adding data layers to it. Almost all GIS software packages allow you to add data layers in a similar way, but for this video, QGIS is used to show how to add an existing data layer to your GIS project. As part of this video, you will learn not just how to load the data layer into your GIS project, but how to check what projection/coordinate system it is based on, and how to change the way that it is displayed. These are the standard procedures which you should follow whenever you add an existing data layer to a GIS project, regardless of the GIS software which you are using.

If you have any questions or queries about this video, feel free to comment on this post and I’ll do my best to answer them.

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Dr Colin D. MacLeod,
Founder, GIS In Ecology
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GIS For Biologists: Tip #4 – Setting A Projection / Coordinate System For Your GIS Project

27 Mar

Whenever you start a new GIS project, the first thing that you should always do is set its projection/coordinate system. This may also be known as the coordinate reference system, or CRS, depending on the GIS software that you are using. Setting a projection/coordinate system is easy to do, and is done in a similar way in most GIS software packages.

This video provides easy to follow instructions on how to set the projection/coordinate system of a GIS project in QGIS, the leading open source and freely available GIS software package. As you see, it’s not difficult to do, however, you do need to remember to do it each and every time you start a new GIS project. If you want to find out more about projections in general, you can find a video which explains what they are here.

If you have any questions or queries about this video, feel free to comment on this post and I’ll do my best to answer them.

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Dr Colin D. MacLeod,
Founder, GIS In Ecology
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GIS For Biologists: Tip #3 – What Are Projections And Why Are They Important In GIS?

16 Mar

One of the most important concepts that biologists need to get their head round to successfully use GIS in their research is that of projections. Projections are mathematical transformations that allow the curved surface of the Earth to be displayed on the flat two-dimensional surface of a map or screen. All projections produce distortions of some kind, and this means that you need to make sure you select the correct projection for any given GIS project. However, the very idea of what projections do is something that biologists often struggle to get their heads around.

This video uses the Google Earth interface to provide an easy to follow introduction to projections and why they are important in GIS. By looking at things from a global perspective, It shows how distortions increase the further you get form the centre of a projection and why it is important to make sure you select one that is appropriate for the size, shape and location of your specific study area.

If you have any questions or queries about this video, feel free to comment on this post and I’ll do my best to answer them.

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Dr Colin D. MacLeod,
Founder, GIS In Ecology
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A New Custom Home Range Toolbox For ArcGIS Users

12 Mar

As a result of discussions during a recent course run by GIS In Ecology, I finally sat down and put together a custom toolbox for ArcGIS users for automatically running home range analyses. These tools are based on the processes which I outline in An Introduction To Using GIS in Marine Biology: Supplementary Workbook Four – Investigating The Home Ranges Of Individual Animals, and include the ability to create kernel density estimates (KDE) in environments with barriers to movements. Currently, there are few other ways of doing this, and none that I know of which allow you to take into account complex barriers to movements (such as coastlines). These tools can be used with both marine and terrestrial data sets.

In addition, it provides tools for extracting percentage volume contours (PVCs) from KDEs using the approach I developed for Supplementary Workbook Four, as well as tools to allow you to generate multiple 95% PVCs from KDEs from the same data set each with a different h value (also known as the smoothing parameter, bandwidth or search radius) to help with selecting the optimal value for this using the ad hoc approach from Kie 2013 (Animal Telemetry 1: 13), which is the approach I recommend for doing this.

If you are interested in using this toolbox, you can download it from http://www.gisinecology.com/Home_Range_Tools.zip. There’s a Readme file in the compressed folder which provides information about how to install it on your computer and how to import it into your version of ArcGIS. This toolbox is free to use, customise and distribute (although you will need the usual ArcGIS licences to use it), and is provided on an ‘as is’ basis. That means while it works for me, I can’t guarantee that it’ll work for you, or in every possible circumstance. Nor can I guarantee that it’s completely error free.

Any feed back you have is welcome, while any questions about using it should be directed to the GIS In Ecology Forum

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Dr Colin D. MacLeod,
Founder, GIS In Ecology.
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Why We Need To Change The Way We Teach GIS To Ecologists

11 Nov

The use of Geographic Information Systems (GIS) has exploded in the last decade and it is now an important skill for many ecological research projects, as well as being an ever-more common requirement in job adverts.  However, the way GIS is taught to ecologists, both at undergraduate and postgraduate levels, hasn’t developed in consort with this explosion in its use. Instead, it remains stuck in its roots as a tool for geographers, cartographers and businesses. This means GIS tends to be taught as a series of more or less abstract exercises that demonstrate how to use specific tools within GIS software packages rather than as an integrated skill-set. As a result, while students may learn how to do individual tasks, they often fail to grasp how to apply what they learn to their own research. It doesn’t help that the classes as often taught by geographers who have little understanding of ecology and use standard examples that have no relevance to those working in biological sciences (a standard one involves working out where best to site a new shop based on information about population densities and road networks, and this leaves most ecologists scratching their heads as they try to work out why on earth they’d ever need to know such a thing). In short, the way that GIS is currently taught to ecologists manages to confuse and alienate them, and many simply give up on ever trying to get to grips with this increasingly important skill, to the detriment of both their research and their job prospects.

In this respect, GIS currently finds itself in much the same position that statistics was twenty years ago. Now, we recognise that in order to teach students how to use statistics properly, we need to teach them not just the mechanics of a specific test, but that we need to also teach them everything from survey design, through data collection to test selection and on to how to write up the results.

If the use of GIS in ecological research is to develop in the way that statistical analysis has in recent years, we need to completely change the way it is taught.  We need to stop trying to teach by showing how to use individual tools within GIS software in a more or less abstract manner, and instead teach it as a connected and integrated skill set. This needs to include instructions on how to collect data in a manner that it is GIS-compatible (including how to set up and use GPS receivers properly), how import these data into GIS projects, how to link data from different sources together, and most importantly, how to integrate any work carried out within a GIS framework into other related frameworks, such as statistics. This needs to be taught in a manner and a language that ecologists can easily understand, and this means that it needs to be taught by other ecologists and not members of the nearest Geography faculty.

Students on a GIS In Ecology course learning how to collect GIS-compatible data not in a lecture theatre or in a computer classroom, but in the field as they would do as part of their own research projects.

This is the approach that GIS In Ecology was set up to both pioneer and promote.  It has been developed through more than a decade of use of GIS within my own research projects, training my own graduate students and also teaching various classes. This has culminated in our first course aimed specifically at terrestrial ecologists that GIS In Ecology ran for graduate students at a field station near Glasgow last week.  Over the three-day block, it took students with little or no knowledge of GIS and taught them everything from making a map through collecting data in the field using a GPS and how to build a GIS project that could be used to answer a specific research question.  While some of the course consisted of lectures, most of it involved students working through practical exercises, both in the classroom and out in the field.  All examples and data sets used came from real ecological research projects, meaning that the student were learning their skills in a manner that would be similar to how they would need to be able to apply them.  Similarly, since the course was being taught by someone who was both an ecologist and a GIS specialist, any questions they had could be answered in an ecological framework. 

While the true measure of the success of this approach will only really come once these students start using GIS in their own research projects, the immediate feedback was extremely positive.  By lunchtime on the first day, they’d already made their first map, and at least one said she’d learned more in those three hours than on a dedicated  twelve week undergraduate GIS module. By the end of the course, almost all were eager to start using their newly acquired skills to their own ecological research.  This compares to the large numbers that leave traditional courses vowing to never use GIS again for as long as they live.

However, unlike many modules taught by geographers, the GIS In Ecology approach does not stop there.  By providing a dedicated GIS forum for ecologists, we provide a place where those who take part in our courses (or anyone else who is interested) can ask for help from the GIS In Ecology instructors, and indeed from each other.  Through this, we aim to provide a more integrated and complete training environment that provides ecologists with a way to learn how to actually use GIS in an ecologically meaningful manner and apply it to their own research projects. Our experiences so far have suggested that if this approach was adopted more widely, we would quickly see a sea-change in the use of GIS in ecological research that would greatly benefit both those wishing to make ecology their career and the quality of ecological research as a whole. If, however, GIS continues to be taught in the same piece-meal manner that is, unfortunately, so common at this current time, it is likely to stagnate to the detriment all involved in ecology.