Bird’s-eye-view reveals priority habitat for threatened shorebirds

16/05/2017 by

U.S. Fish and Wildlife Service Northeast Region

As the national lead biologist for the recovery of the threatened red knot, and the Service’s state lead (N.J.) for threatened piping plover, Wendy Walsh thinks a lot about managing the impact people can have on the habitat these species depend upon: sandy beaches and tidal inlets.

Wendy-Walsh-FWS.JPG A new inventory of modifications to beach and tidal inlet habitat from Maine to Virginia has given Wendy Walsh — the Service’s lead biologist for the recovery of the threatened red knot — new perspective on habitat availability for shorebirds. Credit: FWS

During Hurricane Sandy, barrier beaches overwashed around Little Egg Inlet, an opening into Great Bay in the wilderness portion of  Edwin B. Forsythe National Wildlife Refuge. And that turned out to be a good thing for plover. “It created great habitat,” Walsh said. “Plover numbers really increased.”

Did they ever.

Today, Walsh said, “Beaches around Little Egg Inlet provide habitat for…

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How to visualize bird migration data with QGIS TimeManager

14/05/2017 by

Free and Open Source GIS Ramblings

A common use case of the QGIS TimeManager plugin is visualizing tracking data such as animal migration data. This post illustrates the steps necessary to create an animation from bird migration data. I’m using a dataset published on Movebank:

Fraser KC, Shave A, Savage A, Ritchie A, Bell K, Siegrist J, Ray JD, Applegate K, Pearman M (2016) Data from: Determining fine-scale migratory connectivity and habitat selection for a migratory songbird by using new GPS technology. Movebank Data Repository. doi:10.5441/001/1.5q5gn84d.

It’s a CSV file which can be loaded into QGIS using the Add delimited text layer tool. Once loaded, we can get started:

1. Identify time and ID columns

Especially if you are new to the dataset, have a look at the attribute table and identify the attributes containing timestamps and ID of the moving object. In our sample dataset, time is stored in the aptly named timestamp attribute and uses ISO standard…

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Getting multipolygon vertexes using PostGIS

14/05/2017 by


Source: Getting multipolygon vertexes using PostGIS

Getting multipolygon vertexes using PostGIS

14/05/2017 by

GIS Unchained


Today I needed to create a view in PostGIS that returned the vertexes of a multi-polygon layer. Besides, I needed that they were numerically ordered starting in 1, and with the respective XY coordinates.

Screenshot from 2015-11-05 23:58:19

It seemed to be a trivial task – all I would need was to use the ST_DumpPoints() function to get all vertexes – if it wasn’t for the fact that PostGIS polygons have a duplicate vertex (the last vertex must be equal to the first one) that I have no interess in showing.

After some try-and-fail, I came up with the following query:

The interesting part occurs in the WHERE clause, basically, from the list of all vertexes, only the ones not included in the list of vertexes with the maximum index by polygon part are showed, that is, the last vertex of each polygon part.

Here’s the result:

Screenshot from 2015-11-05 23:58:40

The advantage of this…

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I’ve finally gone and done it: announcing a new MA in Data Journalism

14/05/2017 by

Online Journalism Blog

Data journalism UK conference The Data Journalism UK conference, shown above, is part of the course

Well I had to do it at some point, didn’t I? From today I am accepting applications for a new MA in Data Journalism.

The MA, which starts in September and runs alongside the new MA Multiplatform and Mobile Journalism that I posted about previously, addresses many of the changes that the field has undergone in the last few years. In particular I’ll be focusing on:

  • Telling data-driven stories across different platforms (not just text or visualisation)
  • Automation, augmented journalism and the issues that those raise
  • Coding and computational thinking being applied journalistically (I cover using JavaScript, R, and Python, command line, SQL and regex to pursue stories)
  • Security and ethics (integrated into media law)
  • Investigative techniques such as network analysis, text mining, and advanced techniques for finding human sources (OSINT).
  • Partnerships with media…

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Harmful Algal Blooms – Part 5: Trouble in Data Land

11/05/2017 by

NEXT >Tobler, Steno and Geologic Maps

Source: Harmful Algal Blooms – Part 5: Trouble in Data Land

Harmful Algal Blooms – Part 5: Trouble in Data Land

11/05/2017 by

This Map Rocks

If you’ve read Harmful Algal Blooms, Part 4, you know that I had developed a plan to obtain the spectral signature of the Alexandrium monilatum, a toxic dinoflagellate that causes harmful algal blooms in the Chesapeake Bay watershed, from the hyperspectral data that was collected August 17, 2013. I wanted to use spectral signatures to map the extent of harmful algal blooms in the James and York Rivers. However, lots of data doesn’t always mean good data.

The hyperspectral data was collected using a sensor that was mounted on a NASA airplane. The angular cone of visibility detected by a sensor at a given time is called the Instantaneous Field of View (IFOV). The size of the IFOV determines the resolution or minimum size of a pixel.

In this image from Natural Resources Canada, area A is the IFOV and area B is the area on Earth’s surface that that can be seen at a given…

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Taking Slices from LiDAR data: Part IX

10/05/2017 by

Smathermather's Weblog

Part 9 of N… , see e.g. my previous post on the topic.

We’ve been working to reduce the effect of overlapping samples on statistics we run on LiDAR data, and to do so, we’ve been using PDAL’s filters.sample approach. One catch: this handles the horizontal sampling problem well, but we might want to intentionally retain samples from high locations — after all, I want to see the trees for the forest and vice versa. So, it might behoove us to sample within each of our desired height classes to retain as much vertical information as possible.

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Why Open Research?

05/05/2017 by

Source: Why Open Research?

Why Open Research?

05/05/2017 by

Erin C. McKiernan

In May of this year, I was awarded a flash grant by the Shuttleworth Foundation to make an ‘open’ project of my choosing a reality. On November 14th, at OpenCon 2015 in Brussels, I announced the launch of Why Open Research?, an educational resource for researchers to learn about the benefits of sharing their work. This is the story of how the project was born and what I hope it will accomplish.

For the last 20 months, I’ve traveled to conferences and universities, speaking to scholarly communications professionals and researchers about open access, open data, and open science. Many of these events were excellent and have been crucial in shaping my thinking about open scholarship. But after awhile I became frustrated that I was often ‘preaching to the choir’. The scholarly communications people in the room needed no convincing that ‘open’ is the way to go, and…

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