Alejandra's research: landscape ecology & more!


GIS resources for Ecologists (and others!)

Generate sample plots (polygons) from points.

I ‘ ve been recently (GIS) helping Luis Mata and the Interdisciplinary Conservation Science Research Group of RMIT  with the second phase of a very exciting project they are leading. The project is called ‘The little things that run the city’ and seeks to evaluate the diversity of insects that populate the City of Melbourne, the ecological functions and services they provide to society, and to assess the ecological processes that explain where the insects are found. On top of the scientific discoveries, the project seeks to get Melbournians interested in bugs, by showing how wonderful these little creatures are (with the most bizarre shapes and colours) and what important roles they play for us (e.g. pollinating our trees, decomposing organic matter, controlling pests, etc.).

Luís and colleagues have set a wide network of sampling plots (approx. 130 sites) across the green spaces within the city of Melbourne. They have sampled the insects within each of these plots several times over the course of an entire year, stratifying the surveys by habitat type (grassland, lawn, mid-story vegetation and trees). As part of the project we need to generate a shapefile that depicts the sampling plots and that indicate the species found in each sampling plot.

In this post you will learn how to generate a shapefile of sampling plots from point data using ArcGIS. The method I´ll show is not very sophisticated but it works well and it is very intuitive. It will allow you to generate hundreds of sampling points at once (no need to manually draw any polygon ;-o) and in an accurate and easy manner. I am sure this can be quickly done in R (using a very neat and short code, especially for handling the tabular data), as well as in other GIS software. But let´s focus here on how to do it using ArcGIS and a calculus spreadsheet.
Continue reading!


Extract stats from a given area using spatial data. How much did it rain?

In this blog post you will learn how to extract stats from spatial data to respond to questions like: how much did it rain in a given catchment last year? what is the dominant land use/forest type in a given area (e.g. region)? what is the total population of a given area?

 Why is this type of data/information important in Ecology? Most of the time, a phenomenon that is observed at a given spot (e.g. % of organic matter in a given river segment/strech) depends not just on what´s happening in that particular place (e.g. is there livestock using that stretch of the river for drinking? or is there any kind of punctual discharge of organic matter at that place?) but also on what´s happening in its surroundings or other connected parts of the landscape (e.g. how much did it rain in the upper parts of the catchment last week? after a heavy rain lots of nutrients can be washed out from the soils to streams increasing the loads of organic matter). Continue reading!

Is your spatial data in two (or more) different coordinate systems? No problem!

Sometimes you get spatial data from different sources. This usually means the data are in different coordinate systems. If you are not aware of this issue, you will load the data in ARCGIS to find out that the data (e.g. point locations, polygons, etc.) are not placed where they should be (there is a geographical displacement).  In the most frustrating case, you´ll load your data in ARCGIS on top of a reference layer (e.g. aerial image) and your sample locations won´t overlap at all with your reference layer (they are floating somewhere in the Universe…).

In this blog post you will learn how to integrate spatial data in different coordinate systems using ArcGIS (but as I´ve said in other posts, this applies equally to other GIS software and even to data handling & processing in R). This is very important not just for visualization purposes (everything is located where it should be and there is perfect match/overlap between layers) but also for data processing (GIS calculations). To perform calculations all layers involved in the analysis have to specify the same coordinate system. If they don´t you need to reproject them to make sure that the calculations are accurate. Continue reading!

GIS resources

Are you a GIS -Geographic Information System– sufferer?  Have you ever asked yourself any of the following questions?

How the world is viewed in a GIS. Source: Geographic Information System Basics v1.0
How the world is viewed in a GIS. Source: Geographic Information System Basics v1.0
  • I have ArcGIS (or any other GIS software, e.g. QGIS, DIVAGIS) installed in my computer and I´ve opened it once (mainly to check the installation worked) or twice (to check it was still operative: I´ve got overwhelmed by so many tools, and buttons, the unfamiliar terminology and closed the program; I took leave for a couple of days after this).
  • I only need to use/extract GIS data or run spatial analysis for a small – but essential- part of my research/work but I don´t know how to start.
  • What on Earth are coordinate systems and how do I know which one should I use?
  • Where can I source GIS data?
  • Someone is going to collect spatial data for me (e.g. locations of sampling sites, observations of a given species) or passing to me spatial layers. Do I have to give her/him particular instructions about what I´d like to get from the survey?
  • How do I make a pretty figure for publication (a figure that integrates a map, a plot and a picture) ?
  • Can I use R to handle my spatial data?

Welcome to the club! Continue reading!

What on Earth are coordinate systems and which one should I use? Part 1/3. Let´s clarify some concepts.

If you have ever dealt with spatial data you might have heard (at least once) one of these three words: datum, coordinate system and projection. What do they mean?

Datums and projections

Datums and projections are algorithms that help us represent real-world objects sitting on a 3D surface (the Earth surface with its topographic features: mountains, valleys and submarine chasms) into a plane or 2D surface (our beloved map). Continue reading

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