Tag Archives: ArcGIS

New Book – ‘GIS For Biologists: A Practical Introduction For Undergraduates’

24 Jan

GIS For Biologists - CoverGIS For Biologists: A Practical Introduction For Undergraduates is a new book by GIS In Ecology‘s founder Colin D. MacLeod.

It provides background information on using GIS in biological research as well as six practical exercises specifically created to help biologists learn how to use GIS in daily lives.

The instructions for these practical exercises are provided for both ESRI’s ArcGIS For Desktop 10.3 (the most widely used commercial GIS software package) and QGIS 2.8.3 – the leading open source, and so freely available, GIS software.

As well as providing the perfect practical exercises for any biologist interested in learning how to use GIS, this book is also well-suited for those who wish to teach GIS, but who do not have the time to develop their own course content.

This book is supported by a dedicated GIS For Biologists webpage which provides helpful information on where to get your preferred GIS software, how to download and install it, and how to download the data used in the practical exercises in the book, as well as links to free short videos which have been created to accompany the book’s contents.

GIS For Biologists is available to purchase as a paperback or as a kindle ebook (although due to its fixed page format, it is only available on devices and Kindle apps with ‘pinch and zoom’ capabilities). Free previews of the contents can be downloaded from the book’s homepage.

From The Back Of The book:

This book provides a user-friendly and practical introduction for undergraduates to the use of Geographic Information Systems (GIS) in biological research. Unlike most other books about using GIS, this information is specifically presented in a biological context and it is divided into two sections.

The first section provides just enough background information to allow the novice biological GIS user to get started with GIS without getting too bogged down in the theory behind it or making some of the most common mistakes made by beginners. It covers areas such as what GIS is, why GIS is useful in biology, the basics of GIS, common concepts and terms in GIS, how data are contained in a GIS, useful information about what to think about before starting a GIS project and how to break down and translate biological tasks into the language of GIS. This information is all provided in easy-to-read and non-technical language, with specific reference to its application in biological research.

The second section, which constitutes the main body of the book, consists of six practical exercises accompanied by detailed instruction sets. The first four exercises introduce the novice biological GIS user to basic, but important, GIS skills, such as making a map, creating new feature data layers, creating raster data layers and joining together data from different data layers. The final two consist of case studies of how GIS can be used to answer real biological research questions. Each of these exercises represents a stand-alone GIS lesson which can be completed either on its own or as part of a practical session for an undergraduate class. In addition, each exercise focuses on a different area of biology, such as tropical ornithology, epidemiology, marine biology and rainforest ecology, and on a different part of the world, including the Amazon rainforest, a Scottish field station, Mount Mabu in northern Mozambique, the North Atlantic Ocean and the USA. Instructions for each exercise are provided for both the leading commercial GIS package (ESRI’s ArcGIS® 10.3 software) and the leading freely available open-source GIS software (QGIS 2.8.3, also known as Quantum GIS), meaning that this book can be used to learn, or teach, how to use GIS in biological research, regardless of the availability of commercial software licences.

Taken together, the two sections of this book provide the perfect primer to show undergraduates, and other novice GIS users, how useful GIS can be in biological research, why it is rapidly becoming a key skill in many areas of biology, and how to start using it.

The PSLS series of books uses Task-Oriented Learning (TOL) to teach the practical application of research skills to the life sciences. This involves demonstrating how these skills can be used in the specific circumstances in which they are likely to be required, rather than concentrating on teaching theoretical frameworks or on teaching skills in a generic or abstract manner. By seeing how the similar processes are used to achieve a variety of different goals within a specific field, it becomes easier for the reader to identify the general rules behind the practical application of these processes and, therefore, to transfer them to novel situations they may encounter in the future.

***Please Note: Links to the Amazon listing provided in this post are affiliate links. This means that I will receive a small percentage of any purchases made after following these links. This helps support the existence of this blog. If you do not wish this to happen, click here to go to the Amazon listing directly.***

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GIS For Biologists: Tip #16 – The ‘Shapefile Approach’ Vs The ‘Geodatabase Approach’ To GIS

10 Dec

There are two basic ways to do structure and store your GIS data. These are the ‘Shapefile Approach’ and the Geodatabase Approach’.

The Shapefile Approach uses the almost-universally accessible shapefile format for vector data layers (and similarly widely used formats for raster data layers) to store data layers in a single folder, usually on the C: drive of your computer (if you are running a Windows operating system). This information can then be accessed with almost any GIS software package.

In contrast, the Geodatabase Approach is specific to ESRI’s ArcGIS software package. In it, all the data layers in a GIS project are stored in a single, specially formatted geodatabase file on your computer and can only be accessed with ArcGIS.

This video discusses the advantages and disadvantages of these two approaches for those who want to use GIS in biological research.

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 #15 – ArcGIS Vs QGIS: Which Is Better For Biologists?

26 Jun

When selecting GIS software, there are two main choices for biologists. These are the commercial package ArcGIS and the open-source, freely available package QGIS. This video provides a brief comparison of some of the key benefits and limitations of these two alternatives, and provides advice on which is best for biologists.

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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What’s New In GIS And Biological Research: 26 May 2015

26 May

This week’s summary contains a variety of very different posts which cover topics ranging from how-to tips, to why you don’t get pineapples in the Antarctic. So, without further ado, I’ll begin.

The first post I want to highlight is a tutorial from Saara Pakarinen on creating a PostGIS database for QGIS. While not everyone who does GIS will use the database management systems, for those who do find that they need to use them, then this tutorial will help get you started.

Secondly, and while still on the subject of QGIS, there’s a really nice post from GIS Digest about qquality control, and how you can use the QGIS topology checker to help deal with any quality control problems you come across with your GIS data layers. This is something which is really important to know how to do, not only because it can help you work out why a specific data layer isn’t working properly, but also because, as with all analysis, in biological research, your results will only be as good as the quality of data which goes into your analysis in the first place.

Next, I want to consider a post from Geospatial Wanderings on extracting data layers from OpenStreetMap. For those of you who don’t know, OpenStreetMap can be a great source of spatial information, but sometimes it can be a little tricky to extract exactly the information you need. Geospatial Wanderings’ post provides instructions on how to do this in two different ways. They’re both command-based, rather than graphic user interface-based, but the flexibility that they provided in extracting just the data you want more than pays off the fact that they are a bit difficult to get to grips with the first time you use them.

Fourthly, I want to draw your attention to Volunteered Geographic Information (VGI), and how it can be used to help fill in spatial information where little is currently available. VGI (and the above mentioned OpenStreetMap is an example of this) does exactly what it says on the tin, and uses volunteered information to increase the amount of spatial data available. In ecology and conservation, this can involve things like looking for evidence of changes in forest cover from satellite images, or other similar changes in land use, but the example I’m going to point you towards today is humanitarian in nature and about how VGI is being used to help those caught up in the recent earthquakes in Nepal. It’s a nice case study of how communities of people from around the globe can come together to help others with the skills that they have.

To return to advice about using GIS, MaybeItsAMap has a great post for ArcGIS users which looks at how to select data points or features from a data layer based on their spatial locations, or the spatial locations of features in another data layer. The example they use is selecting features from a line data layer of streams based on things like polygons of management or political areas, and it provides detailed information about how to use this tool effectively to select exactly the subset of data that you want to select.

Still on the advice for using GIS, but going back to QGIS, if you’re interested in making really nice terrain maps complete with shaded elevations and contours, then check out this post by Anita Graser titled How to create illuminated contours, Tanaka-style. This isn’t something I’ve done before, but I could see it being a nice skill to have for creating really smart-looking maps for reports and presentations, especially when overlaid with biological data, such as sampling locations.

The last four posts I’m going to mention this week are brought together under the banner of things that made be stop and think. They are all loosely GIS-based (some, admittedly, more loosely than others), and all connected to various aspects of biology.

The first of these posts comes from Hamilton Ecology Lab, and is about a study of genetic diversity in an invasive species. In this case, it is European stoats in New Zealand. As invasive species often start with a small number of individuals, you’d usually expect their genetics to go through a bottleneck, but this doesn’t seem to be the case in this example. Or rather, it seems, the original source population in Britain has, for various reasons, gone through a greater bottleneck than the introduced one in New Zealand. Where’s the spatial element in all this? Well, it just goes to show that you shouldn’t make assumptions about your samples based on where the came from. Instead, you need to approach them without such preconceived spatial prejudices.

Over at Mashables, in tribute to the recent International Day for Biological Diversity, they put together a post to highlight the five greatest threats that biodiversity faces: Climate change, habitat loss, overexploitation, invasive species and pollution. This list will be nothing new to most biologists, but it strikes me how important spatial analyses are for studying, and managing, all these threats. In fact, without a decent spatial knowledge to underpin our management strategies, it’s unlikely we’d be able to control any of these impacts effectively.

HominidLikeMe has an interesting post on non-infectious epidemics, and while they are rather bizarre examples, they all have one thing in common: spatial clustering of people suffering from unusual symptoms that might, at first, appear to be caused by infections of some kind. However, further exploration results in the identification on non-infectious causes. As with one of the first ever studies that integrated spatial analysis and epidemiology, these examples show how spatial information can help us understand the causes behind human diseases, and how they are spread.

The final post comes from Scientiflix, and is aimed at kids. It’s about why certain types of plants are only found in some places and not others. In other words, it provides a kid-friendly introduction to the idea that there are spatial patterns in where different species occur, and that is a great introduction to one of the reasons why GIS is such an important tool for studying spatial patterns in ecology.  Without GIS, we wouldn’t be able to explore and test the hypothesis we generate to explain such patterns, and if we couldn’t do that, then we’re not doing science. And of course, it’s never too early to get kids interested in GIS!

So these are the GIS-related things that have caught my eye this week, but, as always, I’m sure there’s a lot of other good stuff out there as well.

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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.

When Storing Your Spatial Data, Which Approach Is Better, Shapefiles Or Geodatabases? There’s Only One Way To Find Out….FIGHT!!

28 Oct

Apologies to Harry Hill for plagiarising one of his catchphrases, but I think this is an interesting question and one that is worthy of discussion.  From ArcGIS 9 onwards, there was a shift away from storing spatial data using individual shapefiles and raster grids (what I’ll call the ‘shapefile approach’) and towards storing all spatial data for a GIS project in a single Geodatabase (the ‘geodatabase approach’).  Most GIS textbooks, instructional information and, indeed, training courses, for ArcGIS now seem to recommend the use of Geodatabases, but these generally seem to be aimed at large organisation with very big and complex GISs that are accessed by many different people for many different purposes. The situation in ecological research is often very different, and it is much more likely to be one person and a laptop with a relatively small and simple GIS. So when using GIS for ecological research, is there actually any advantage of using one approach over the other?

Here’s my thoughts:

1. Geodatabases contain all the information in a single file, while using shapefiles and rasters requires that all the data layers are stored as separate files: This can be seen either as a benefit of using geodatabases or as a disadvantage.  With a single file, it’s much easier to keep track of all the data layers and to back up or transfer your data between computers.  It also means that its easier to ensure that working on the same files (this can be a problem with shapefiles that have a nasty habit of multiplying!).  However, it also means that if something goes wrong with that single file, you are completely screwed.  At least if you’re using shapefiles and your project crashes, you can easily re-build it from the individual shapefiles themselves as they are stored separately from the project file.

2. Geodatabases are specifically designed to work with ArcGIS – Part one:  This is not a problem as long as you continue to have access to ArcGIS. However, what happens when the ArcGIS licence for your project runs, or you have to move institutions and no longer have a licence?  If you’ve used the geodatabase approach, you may find that cannot access all your GIS data any more.  If you use the shapefile approach, there are many alternative, and often free, GIS software packages out there that you can use to access, explore, plot and manipulate your data layers.  Therefore, if you are unsure where your next ArcGIS licence might come from (and I am sure this is true for many ecologists), using the shapefile approach means that you will always be able to access your data no matter what.  This may not always be the case if you use the geodatabase approach.

3. Geodatabases are specifically designed to work with ArcGIS – Part two: Because geodatabases are specifically designed to work with ArcGIS, you can take full advantage of all the whistles and bells of the ArcGIS software.  However, it also means that you cannot easily access your data layers using different GIS software packages.   While this might not always be an issue, there are often instances in ecological research where ArcGIS just can’t do what you want it to and you find that you wish to use a different software package (e.g. doing a viewshed analysis in GRASS so that you don’t have to pay for the expensive spatial analyst tools extension to the basic ArcGIS software package just to do one thing).  If you use the geodatabase approach you may find that you can’t easily do this, whereas it’s much easier to seamlessly move between different software packages if you use the shapefile approach.

4. Geodatabases are specifically designed to work with ArcGIS – Part three:  If you are working with people from different organisations/research groups and not everyone has an ArcGIS licence, you may find sharing your data difficult if you use the geodatabase approach.  However, with the shapefile approach sharing your data layers with people using other GIS software packages is much easier.

5. Geodatabases are specifically designed to work with ArcGIS – Part four:  If you learn all your GIS using ArcGIS and geodatabases, you may find that you cannot as easily transfer this knowledge to other GIS software, and especially to free, open source GIS software.  This is not a problem if you can guarantee that you will always have access to ArcGIS for the rest of your research career, but if you think you might one day have to rely on using different GIS software, you may find it much easier to transfer your skills if you are at least familiar with the shapefile approach.  This also means that if you start with GIS career using the shapefile approach even if you’re doing it with ArcGIS, you can then choose whether to specialise in this software and move onto geodatabases, or whether to move on to other GIS software.

6. Geodatabases are more difficult to learn to use for complete beginners:  One of the main limitations for encouraging ecologists to use GIS in their research is that they get put off by over-complicated explanations of what GIS is and how it can be used. I’ve found that if I can get people playing around with real data layers as soon as possible they see how useful a tool GIS can be for their research, and they will persist with it.  If they don’t see this within the first few hours of using GIS, they will often abandon it, after all there are a lot of other key research skills out there that they can spend their time learning that will also benefit their research. One of the main reason that I tend to teach people GIS using the shapefile approach, is that it gets them up and running, working with real data, as quickly as possible (often within minutes if I’m sitting with them and using their own data in a one-on-one session).  If they become sufficiently interested, they can explore whether they would prefer using the geodatabase approach for their own work.  If I start by teaching the geodatabase approach, I have to spend those first precious minutes explaining how geodatabases are structured, how they work, the terminology, and so on. I will then quickly see their eyes glaze over and know that they’ll be lost from GIS forever.

From the above, you will clearly see that I favour the shapefile approach, I think it is more flexible and it means that you are much less chained to using ArcGIS whether you like it or not.  However, it is worth emphasising here that the bottom line is that you should use the approach that is best suited you and your own circumstances. If you like the geodatabase approach, go with it, if you like the shapefile approach, why not use it? In the end, GIS is just a tool to help you do your research.  As long as you succeed in do what you need to, it doesn’t really matter which approach you take, and don’t let anyone tell you anything different.

This article was originally posted on the GIS In Ecology forum at https://groups.google.com/forum/?fromgroups#!topic/gis-in-ecology-forum/piG6OzJEKAY.