Tag Archives: GIS and Ecology

What’s New In GIS And Biological Research: 8 May 2015

8 Jun

The first article which I want to highlight in this week’s digest is an important one for those of us who are interested in open source GIS. Open source GIS software packages provide a free alternative to the more traditional commercial GIS software, and while the first generation of these packages could best be described as basic, they are now advancing to a level where they can provide their commercial rivals with some serious competition. One in particular, QGIS, seems to be leaping ahead with it’s development at an ever increasing pace. Indeed, it has now reached a point that many in government and ecological consultancy are starting to mutter about why on Earth they are still paying for commercial GIS licences when there are such good free alternatives available. This was borne out in my own experiences last week when I was invited to run a QGIS training day for one such business. While there was some scepticism at the start of the day from dedicated ArcGIS users, by the end of it, I was amazed at how well they’d taken to this free alternative.

So, on the open source GIS front, I was very interested to come across this post about the plans for the development of QGIS 3. QGIS 2 was the first version of QGIS which I felt could really provide biologists with a viable alternative to commercial GIS software, and hopefully with QGIS 3, we should see this revolution continue. By the sounds of it, the development of QGIS 3 is being taken slowly but steadily, and is being developed at a pace which will let all those who provide the plugins and other packages which make QGIS so useful keep up. Too often, new software packages are rushed out and the result is a rather poor mishmash of new and old features that don’t really work as they should (I’m writing this article on a Windows 8 computer, which is a classic case in point!), so it is good to see the QGIS community taking things slowly, and with plenty of warning, rather than rushing forwards. I have no doubt that in the longer term, which will make for a much better product.

Moving on from GIS software, I want to consider a more applied element of GIS and biological research. One aspect of biological GIS is using it to help identify the best sites protected areas for the conservation and management of our natural resources. However, simply identifying the best location for a protected area should not be the end of this process. Once it has been established, you need to make sure that people know where the boundaries are, especially if there are restrictions on what can be done in specific areas. As this post about MPAs in California, USA, points out, the best way to do this is by creating maps. These can be traditional paper ones, but now-a-days, they are just as likely to be online or interactive ones. Yet, regardless of how these maps are accessed, you need to ensure that they are both accurate, and easy to interpret, and that is where good GIS skills come in.

For my pick of the self-help advice out there in the last couple of weeks, I’ve selected a series of posts that all centre around one general topic: how to make your maps (such as ones showing the locations of protected areas) look good. One of the key skills when using GIS in biological research is learning how best to display your information so that it is as easy to interpret as possible. This means not cluttering up your maps with features you really don’t need to show, and selecting colour schemes for those you do need to show which won’t induce migraines in the brains of anyone who looks at them for more than a few seconds.

The first of these are actually a pair of posts from Maps Nigeria Inititive and provide a basic introduction to changing the ways that data layers are displayed in ArcGIS and in QGIS. Meanwhile, over at MaybeItsAMap, there’s a nice post about using colour ramps to show variations in a specific characteristic within a data layer, and how to make sure your colours shade in the correct manner in relation to increasing or decreasing values, and another about how to change the maximum number of sampled values when creating ranges for colour ramps. Taken together, the advice in these two posts will help ensure that you always manage to highlight exactly the right variations within your data.

Finally, on the subject of setting how data layers are displayed, there’s a new Terrain Tool box for ArcGIS which can be used to help improve the look of maps land elevation or water depths. However, it strikes me that biologists could also use it to make striking images of things like predicted distributions from species distribution models that, if done correctly, could be really eye catching.

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.

========================
Dr Colin D. MacLeod,
Founder, GIS In Ecology
========================

What’s New In GIS And Biological Research: 19 May 2015

19 May

From this week’s summary, you’ll see that there’s been little of the usual postings about the specifics of using GIS, so instead, I’ve concentrated more on selecting some nice examples of how GIS is actually used in a variety of areas of biology, including some you might not usually associated with GIS.

However, before introducing you to these examples, there are a few how-to posts which I’d like to highlight. First, there’s the usual outputs from the MapsNigeriaInititive blog who are continuing their series of tips for QGIS users. This includes a post on how to conduct a spatial join using the MMQGIS plugin and one on how to perform spatial queries on data layers. Both of these are useful things for biologists to know how to do.

For ArcGIS uses, MaybeItsAMap continues to produce some useful tips. The ones I’ve picked out this week are one on how to alter a tool’s Environmental Settings, and one on how to repeatedly run a tool with exactly the same settings as before. If you run into problems when running a GIS tool, there’s a good chance that it is because you haven’t changed one of the settings under the Environments section. This is where you usually set things like which projection/coordinate system the output of the tool will use, and what extent it will have. Sometimes in the rush to run a tool, the Environment settings can get overlooked, but, as MaybeItsAMAp points out in the above post, this is something you do at your own peril. If you do find you make a mistake, and forget to set your environmental settings correctly, then the chances are you’ll have to run your tool again. This can be tedious, especially if you have to enter all the setting again from scratch. This is where the second post from MaybeItsAMap comes in. This shows you how to use the results window in ArcGIS to re-open the tool window with all the same settings you used before. If you set these correctly, you can run the tool again right away, but if you got one of them wrong, you can change it without having to re-set every other setting at the same time. This is really useful, and can save a lot of time when you make one of those little mistakes that it is so easy to do when doing GIS.

So, that’s the GIS user tips for this week, and it’s time to move on to the examples of GIS in action in biological research. While it will be clear how GIS is used on some of these, in others it will be less so, but this is often the case with GIS. The first of these is about the accuracy of visual estimates of land cover by a given vegetation type for monitoring changes in land use over time. Such visual estimates of land cover and land use are critical in many aspects of environmental monitoring, and are widely used in GIS-based studies, so it is essential that they are correct. Thus, it is useful to have a paper which specifically examines how valid the methods are for doing this.

The second example also deals with changes in land cover, but this time caused by something much more catastrophic. As David Frantantoni points out on his blog, it’s 35 years since Mount St Helens erupted in the Pacific Northwest of the US, instantly changing vast swathes of the landscape around it. What I want to concentrate on here, from a GIS perspective, is the satellite image that accompanies David’s post. This is exactly the type of image that biologists can use in GIS analyses to both investigate the effects of such catastrophic events on the surrounding environment, but also monitor how it changes over time as the local ecosystems seek to recover. St Helens may be one of the first volcanic eruptions where we have an almost complete time-series of such images, from the immediate aftermath of the explosions to the present day, which could be used to do this, but now it should be possible for almost any catastrophic event anywhere on the planet.

Continuing the trend of looking at environmental changes over time using GIS, but this time looking into the future rather than the past, Mark Grant as an interesting post on using big data and modelling to predict where climate refuges may occur, and how bush fire hazards may change in the future as the effects of climate change really start to bite. While this type of analysis is really only possible through large-scale collaborations, and may be beyond the reach of individual researchers working in small research groups, it is still useful to see how such are put together and what they can achieve. Again, GIS will be an essential component of any such enterprise.

The final example of environmental monitoring over time which I want to highlight here is a post about Puget sound, which is in the same part of the world as Mount St Helens, and looks at how the structure of local marine ecosystems has shifted from a fish-based on to one based on jellyfish. This is something we are increasingly seeing all around the world, and it is something that GIS is being used to investigate throughout the many locations where it is occurring.

There’s a common strand running through all these examples of GIS in action: none of them would have been possible without long time series of data, and in many cases the data were initially collected either incidentally or without a clear idea of how they might be used in the future. In these days of austerity, the collection of many such long-term data sets has been sacrificed in the name of short-term governmental cost-cutting. It might not be for many years, but I suspect that at some point, we, as the scientific community, will look back with regret that we did not fight harder to stop this happening, because only then will be become clear exactly what we have lost in terms of our ability to monitor how the world around us is changing over time.

On a final note, I want to mention something that, at first, will seem completely unrelated to GIS. This is a piece of software called IPEZ which can be used to aid in the identification of fish species.  What does this have to do with GIS? Well, the program works, in part, by taking morphological measurements and using these to help map out the shape of an unknown fish, and compare it to those of different species. This type of morphological analysis uses many of the same computational tools as GIS, and indeed, you can actually use GIS software to run these exact types of morphological analyses. This means that, while they may seem like very different fields, morphological analyses and GIS share a common skill set, and ones that can be transferred between them. Who would have thought that a bit of GIS could help you identify fish species?.

So these are my pick of GIS-related posts for this week, but, as always, I’m sure there’s a lot of other good stuff out there as well.

========================
Dr Colin D. MacLeod,
Founder, GIS In Ecology
========================

What’s New In GIS And Biological Research: 11 May 2015

11 May

After having taken a couple of weeks off from producing this regular digest, there are plenty of new things to highlight which will be useful to those interested in using GIS in biological research.  So, without further ado, here’s my pick of them.

Firstly, Ur Geologist has a great post with some essential information for those wishing to use remote sensing in their GIS. Their post, which can be found here, provides two tables, one which gives the resolution of various remote sensing options, and a second which provides information about which sensors are well suited to which applications, such as working in the marine environment, looking at agricultural characteristics, or assessing the environment.

The second post I want to highlight is one which deals with the tricky issue of data quality assessment and control. This is something that all biologists should have a good handle on, but all too often it is ignored in the rush to analyse spatial relationships in their data. However, if the underlying data are not of sufficient quality, then the old adage of GIGO (Garbage In – Garbage Out) applies. Thus, I’d recommend reading this post on using ArcGIS Data Reviewer as it has some useful hints and tips to help make sure that your data are of as high a quality as possible.

As usual, MaybeItsAMap has been continuing to regularly publish their Quick Tips series, and I’m going to specifically point you towards two of them in this post. The first is about paramatizing components when using ArcGIS Modelbuilder to create your own custom GIS tools, while the second is about how to disable the background processing in ArcGIS. Both of these are great little tips, and in particular, disabling background processing is something that all ArcGIS users should do as it always leads to confusion if there are processes running in the background which you don’t realise are happening. There’s also a nice tip about how to fix shapefiles which have become corrupted, something that makes all of us break into a cold sweat when it happens, using Andrew Williamson’s ShapeChecker tool.

On the QGIS front, there have also been a number of useful posts published over the last couple of weeks. MapsNigeriaInitiative has a nice post on using DNR GPS to convert shapefiles from GIS into a GPS-compatible format and load them onto a GPS receiver. This is really useful thing to be able to do because you can use your GIS project to identify sampling locations and then use your GPS to help you navigate to them so they can be sampled. They also have a good post on how to query information in the attribute table of a shapefile in QGIS.  Meanwhile Cartoblography has a useful post on using custom Mapbox base layers in QGIS. Base layers provide you with background information from sources such as OpenOS, OpenMap, Bing Maps and Google Earth, and learning how to create you own customised versions based on some of these data sets, is always a good trick to know.

Moving away from dedicated GIS software packages, OpenGeolStudy have a post highlighting that Google Earth pro is now free to download. As someone to regularly uses, and recommends, Google Earth to other biologists for use in their research, it feels only right to highlight this development in the availability of this software package and its associated data sets.

On a related subject, users of Google Earth, and other online mapping products, might find this post titled ‘Why Do Internet Maps User Mercator?‘ both interesting and illuminating. Projection issues are one of the biggest and most frequent problems that biological GIS users encounter, and from this perspective alone it is useful to understand why the internet maps which we so regularly rely on use a projection which is not really compatible with most biological research projects.

Finally, and I’ll be considering this more in my next Paper of the Week post in a few days, I just want to flag up recent post on the Solitary Ecologist blog. This post is titled ‘How do correlations between climate and biodiversity arise?‘ and it is a really nice example of how GIS-based analyses can be used to answer biologically interesting research questions, but as I said before, more of that in a later post.

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.

========================
Dr Colin D. MacLeod,
Founder, GIS In Ecology
========================

What’s New In GIS And Biological Research: 20 April 2015

21 Apr

For this week’s summary, I’m going to start with a recent post from the MapsNigeriaInitiative blog, which points out something which is so obvious that it needs repeating. If those of us based in Europe and North America find ourselves struggling to deal with the licence costs for commercial GIS software packages, how on Earth do our colleagues in South America, Africa and Asia cope? The answer finally seems to be coming to the fore in the shape of the free, open source QGIS software. However, while it seems that QGIS has finally caught up with its commercial counterparts in the last year or so, there is still a knowledge gap which needs filling in order for QGIS to taken up and used as widely as possible, and this can only be filled by the widespread availability of good quality training and advice. The MapsNigeriaInitiative are aiming to help close this gap by providing advice on using QGIS, and here at GIS In Ecology, we are doing the same with our GIS For Biologists How To … series of videos.

Having just highlighted the potential benefits of QGIS vs commercial GIS software, it is slightly ironic that the next post I’m going to highlight is a tip for ArcGIS users. However, I think it is an important and useful tip for biologists. This is MaybeItsAMap’s tip on how to create a set of random sampling points within a specific study area. This is something that many biologists and ecologists will need to be able to do on a regular basis, especially when using GIS to plan their field research, so it is always useful to have some advice on how to do it.

The next post I want to mention is a nice example of GIS in action. This is a study which uses GIS to investigate how glaciers are changing over time. Given the importance that monitoring the effects of climate change has for our understanding of what is likely to happen in the future, this type of study is invaluable. However, similar GIS-based techniques could also be used to monitor land use changes, deforestation, desertification, and many other processes that are of interest to biologists, and that is why I chose to highlight this study in this week’s digest.

I’m going to end this summary of interesting GIS-related things with a post from Kitty Hurley’s Geospatial Response blog which highlights how lost you can sometimes feel when doing GIS, and particularly when you’re thrown in at the deep end by your boss or supervisor. This is certainly something everyone experiences from time to time, and it is good to hear from someone who is willing to admit to feeling this way (rather than keeping  it buried inside like the rest of us). However, with the help of hints and tips highlighted in these weekly summaries, and provided in other posts on this blog, as well as the provision specialist forums like the GIS In Ecology Forum, hopefully there is an ever-increasing number of resources out there to help out any and all biologists and ecologists who find themselves struggling with GIS from time to time. And that is something we here at GIS In Ecology are always happy to see.

========================
Dr Colin D. MacLeod,
Founder, GIS In Ecology
========================

What’s New In GIS And Biological Research: 13 April 2015

13 Apr

I’m going to start this week’s summary of what’s new in biological GIS with a case study which outlines how GIS has been used to help conserve the world’s most endangered canid, the Ethiopian wolf. This study is a nice reminder of just how useful GIS can be in conservation biology, and so why it is such an important tool in the modern biological toolbox.

For those who work in the Antarctic, or for those who are just interested in it, the Maps Mania blog has a brief article about Leafarctica. This is an interactive map which allows you to explore Modis satellite data for Antarctica. You can not only zoom in on specific areas you might be interested in, but you can also select the exact date you wish to examine images for. As a result, this is a great resource for working out what Modis data might be available for a specific study area and time.

A few weeks ago, I highlighted a post about creating shapefiles from street addresses in the US, and this week I want to highlight one which explores how to create point data layers from UK post codes. This will be particularly useful for those who work on Citizen Science projects and who want to plot the data collected in a GIS.

There are also a couple of nice tips from Maybe Its A Map for ArcGIS users. The first provides a brief introduction to using the ModelBuilder module of ArcGIS. ModelBuiler is something I’m a big fan of, and I think that it’s something  many more biologists  should learn how to use as it has the ability to help them streamline their GIs data processing and analysis. The second one provides a neat tip for editing the contents of attribute tables using Find and Replace functions. This is a function I was not aware of within ArcGIS, but now I am, it’s certainly something I’ll use on  a regular basis.

For QGIS users, there’s a new command bar plugin which makes it easier to initiate Python commands in QGIS. While Python coding is not necessarily for the uninitiated, for those who already know how to use it, this will be a useful addition to QGIS. There’s also a new development for expanding the ways in which data layers can be displayed in QGIS, which will be useful for those who wish to make really clear, but fancy, maps.

Finally, for this week, I want to highlight a post which considers the future of data analytics. While this is aimed at more traditional data analytics and statistical analysis, many of the points also apply to biological data analysis. In particular, towards the end of the article, it highlights how GIS will become increasingly more important as data analytics develops, and this will most certainly be true in biology.

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.

========================
Dr Colin D. MacLeod,
Founder, GIS In Ecology
========================

What’s New In GIS And Biological Research: 6 April 2015

6 Apr

Perhaps unsurprisingly, since it was the run up to Easter, there hasn’t been a huge amount going on in the last week. However, there have still been some useful posts and articles published, and this is this week’s summary.

Firstly, there’ s post from the Ecostudies blog outlining how of create a map of species richness from IUCN range polygons using QGIS. This isn’t the way I would normally do it (I would generally go down the raster data layer route and use the raster calculator tool), but it’s always nice to see how the sae thing can be done in a different way. This post also has useful links which provide access to IUCN range polygons for threatened species which will be of interest to some

Secondly, as always, there’s a couple of interesting posts on Jame’s GIS blog. The first of these is a post about Landsat 8 Live and how you can use this to get up-to-date satellite imagery. This will be particularly useful for those who are wanting to use remote sensing to monitor what is going on in a particular part of the world. The second useful post from this blog is short, but useful, and it about how to convert shapefiles into ArcGIS layer files when using ESRI’s Moodelbuilder option to create custom GIS tools. This is a neat little trick, and one that is always work remembering if you run into problems when using Modelbuilder.

Thirdly, there are a couple of useful tutorials on how to do various useful things in QGIS, the learing open source, and so free, GIS software (and one I’d heartily recommend). The first looks at creating Hillshade maps, while the second is about georectifying maps (that is, taking a scanned or digital map and manipulating it so that it plots in the right place in your GIS project), and both are well worth checking out if you wish to develop your GIS skills.

For ArcGIS users, it maybe worth checking out the Maybe It’s A Map blog as it has a number of useful little tips on it, including advice on how to fix a broken shapefile (something that is always useful to know how to do).

Finally, for this week, there’s an interesting post which uses GIS to map the ‘Arc of Affluence’ in London, by drawing together data from a wide variety of sources. It’s not really biologically relevant, but it does show the type of thing that can be done when you draw data together from a wide variety of difference sources. It’s also quite interesting it its own right.

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.

========================
Dr Colin D. MacLeod,
Founder, GIS In Ecology
========================

What’s New In GIS And Biological Research: 30 March 2015

30 Mar

In  this week’s picks of software releases, blog posts and articles from the last seven days (or so), you’ll find a number of interesting things for those who use GIS for biological research.

Firstly, if you’re interested in doing GIS on a computer running a Unix operating system, then you should check out Haojie Zhu’s GIS On Unix blog. It’s not been up and running for long, but it already has some good tips for those who wish to do GIS in this way.

Secondly, there’s a new release of the Time Manager plug in for QGIS. This allows you to add time controls to the functionality of QGIS, and is likely to be of particular interest to those who work with tracking data or animal movements. If this sounds like something you’d find useful, you can find out more about it on Anita Graser’s Free and Open Source GIS Ramblings blog .

In terms of actually doing GIS, there’s a rather useful post on the ProximityOne blog about how to create and use shapefiles of address locations. This is something which can be particularly useful to be able to do if you are dealing with data collected by members of the public as part of Citizen  Science projects. Unfortunately, this article only covers US addresses, but there are likely to be similar resources for other countries.

Another useful ‘how to’ post from the last week comes from James’ GIS Blog, and provides advice on how to merge more than 3 layers in ArcGIS, without needing a costly Advanced licence. The approach suggested, based around using Modelbuilder to run repeated tasks, will also work in other circumstances, and is a trick which it is always worth remembering if you get stuck in ArcGIS because of licence issues.

For those interested in using GIS to create a land suitability model (LSM), there’s a nice ‘how to’ post by Michele Goe on their blog. As biologists, you might at first struggle to work out how this might be relevant to you research, but LSMs are just another way of saying habitat suitability analysis, or even species distribution modelling.

Another post which might, at first, seem to be rather irrelevant to ecologists is Shredding with Satellites: Creating A DEM from GPS Collection Points. However, it’s a nice informal introduction into how you can collect elevation data and use it to create a land elevation raster data layer. This is just the type of thing you might need to do if you wanted to conduct a habitat suitability analysis (or even a land suitability model!).

On a more ecological note, there’s an interesting article on rewilding and the re-introduction of the Eurasian lynx into the UK. This has been a topic which seems to be becoming more and more talked about recently. However, much of the groundwork behind exploring whether such a re-introduction would even be feasible was done by using GIS to identify suitable habitat patches for Lynx (another biological version of the geographer’s land suitability analysis) and then look at the connectivity between these patches to see if they could support viable populations (which they can in Scotland). If you want to find out more about how this was done, you can download PDF of a paper which I co-authored on this subject a few years ago here.

Finally for this week, check out this post about movements of Africa White-backed vultures. The accompanying image of the tracks of tagged vultures is a nice example of how Google Earth can be used to share spatial data and the results of GIS-based analyses to non-spatial specialists, members of the public and other potential stakeholders. This is something I have long been passionate about, and it is something I feel we should all do more often.

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

========================
Dr Colin D. MacLeod,
Founder, GIS In Ecology
========================