Amy Whitehead's Research

the ecological musings of a conservation biologist


Copying files with R

Following on from my recent experience with deleting files using R, I found myself needing to copy a large number of raster files from a folder on my computer to a USB drive so that I could post them to a colleague (yes, snail mail – how old and antiquated!).  While this is not typically a difficult task to do manually, I didn’t want to copy all of the files within the folder and there was no way to sort the folder in a sensible manner that meant I could select out the files that I wanted without individually clicking on all 723 files (out of ~4,300) and copying them over.  Not only would this have been incredibly tedious(!), it’s highly likely that I would have made a mistake and missed something important or copied over files that they didn’t need. So enter my foray into copying files using R. Continue reading

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This is just a super quick post to say bye for now & have a great (antipodean) summer. Yesterday I flew south from New Zealand to Ross Island in Antarctica to begin an eight week fieldtrip to monitor Adelie penguins.  This is the fourth year I’ve been luckly enough to be involved in this research and it’s always a hectic but exciting time of year.

We don’t have internet out at Cape Bird this year (as we shouldn’t at a remote field camp on a remote island at the bottom of the world), which means I can’t keep you posted with what we are up to.  However, it will mean that I have plenty of time to hone my blog posts for when we get back in early February, so expect a flurry of photos and posts then.  In the meantime, you can find out more about the work that we are doing and meet some of the wildlife out at Cape Bird.

Adélie penguin

Adélie penguin



Weddell seal

Weddell seal

Crabeater seal

Crabeater seal

Leopard seal

Leopard seal



I’ll be back in 2014 – have a fabulous christmas & new year!


Researching Adélie penguins

Today is World Penguin Day (not to be confused with Penguin Awareness Day on January 20 – who makes up this stuff?!) and what better way to celebrate than a look at how I spend my summers, researching Adélie penguins.

One of the perks of being an ecologist is that you often get to go to some pretty amazing places and work with amazing animals.  And I’ve definitely had my share of these experiences.  But one of the coolest (quite literally) projects I have been involved with has been researching Adélie penguins (Pygoscelis adeliae) at Cape Bird on Ross Island, Antarctica.

Penguins on ice

It started out as one of those being in the right place at the right time sort of situations.  I had a gap in my workload as a private consultant and a colleague at Landcare Research asked me to volunteer three months of my time to chase penguins in Antarctica.  Needless to say, I immediately said yes and started on a journey that has been a fascinating experience.  I’ve just completed my third field season at Cape Bird and I’m still pinching myself – it seems unreal to be paid (sometimes good things happen if you volunteer) to spend my summers hanging out with 40,000 Adélie penguins.

The research we do is diverse and multi-faceted, with simultaneous studies occurring at three Adélie penguin colonies varying in size by two orders of magnitude.  Most of the work revolves around studying birds of a known age.  Every year we mark up to 1000 chicks with individually numbered metal flipper bands, with the first bands deployed in 1996.  This enables us to identify how old each banded bird is and to work out survival and recruitment rates.  It also means we have a pretty awesome long-term dataset.

26306 was banded as a chick in 2002.

26306 was banded as a chick in 2002.

Male Adélie penguins start to arrive at the colony in late October and establish nest sites.  Nests are built from small stones and are just far enough apart that your stones can’t be stolen by your neighbour.  The females will arrive a few weeks later and pairs will go through a process of courtship display to establish or renew pair bonds.  After mating, the females will lay 1-2 eggs and then head back out to sea, leaving the male to incubate the eggs for a few weeks.  By the time the female returns again, the males have been at the colony for 3-4 (or more) weeks and are getting fairly hungry!  But from now on in, the males and females will switch roles every 2-5 days or so, with one going out to feed while the other takes on incubation duties.  Eggs will start to hatch after ~31 days and the chicks grow pretty rapidly, gaining over 3 kg in just 6 weeks.

These two chicks are from the same nest and would have hatched within a few days of each other. Clearly somebody has been eating all the pies!

These two chicks are from the same nest and would have hatched within a few days of each other. Clearly somebody has been eating all the pies!

We typically arrive in early November and are straight into monitoring the activities of banded birds.  Each day we walk around a subsection of the colony looking for banded birds and checking out what they are up to.  All nests with banded birds are gpsed and marked with a numbered tag.  These marked nests are checked every five days or so to try and determine the fate of the eggs or chicks through until the end of January.  The primary causes of nest failure seem to be incompetent parenting, fighting neighbours knocking eggs or chicks from the nest, bad weather or skua predation.  Because we spend so much time out in the colony, we often observe some pretty interesting behaviours and it’s hard to not anthropomorphise (but they totally do run around and behave like little people!).

Little penguin "people"

One of the more hands-on projects I’ve been involved with has been conducting the field sampling for a physiology and foraging behaviour study that looks at differences between birds of different ages and breeding experience.  We’ve been catching a subset of the known-age birds and attaching a small device on their backs that records information about their diving behaviour; where they travel to, how long and deep they dive, the water temperature and sudden changes in direction that indicate they might be foraging.  This year at the Cape Crozier colony they were even following the tagged birds around with a remotely operated glider to check out what they were feeding on.  All very technologically cool!

Attaching an accelerometer

Attaching an accelerometer to the back of a penguin using strips of tape.

Once the device is attached, we let them go out for one foraging trip which usually last for 1-4 days and then we catch them again.  This is where my vampire-ish tendencies come in handy as we’re taking blood from the jugular vein for the physiology part of the study.  It’s a pretty quick and easy process but it does involve sticking a one inch needle in the neck of wriggling penguin to extract 5 ml of blood.

Blood sampling

Vampires at work.

Not surprisingly, they aren’t very happy about this and try and extract chunks of flesh from person holding them.  Luckily this isn’t me!  After taking blood, we weigh and measure the chicks.  Then everybody is put back on the nest to continue playing happy families.

weighing chick

Weighing an Adelie penguin chick.

There’s a whole lot of other work that goes on throughout the season, including:

  • counting a subset of the active nests and chicks at each colony to work out the annual productivity rate (the mean number of chicks raised per pair).
  • fencing a small subcolony at each site, where the adults have to cross a weighbridge to get to and from their nests.  This tells us how long they go out to sea for and how much food they are bring back to their chicks.
  • watching adults feed their chicks, and dissecting dead chicks, to work out what they are eating.
  • weighing and measuring 50 randomly selected chicks once a week to look at how chick mass and condition vary within and between seasons.
  • taking photos of all of the Adélie penguin colonies in the Ross Sea and counting the penguin dots to look at trends in population size over time.
Penguins crossing the weighbridge after feeding their chicks.

Penguins crossing the weighbridge after feeding their chicks.

It’s always a very busy season and the fact that the sun never sets means it can be hard to switch out of work mode.  But it’s such a spectacular place with some stunning scenery and wildlife that I sometimes wonder how I managed to get a job like this!

You can find out more about our Adélie penguin research at Landcare Research and, listen to some of the researchers talk about life at a penguin colony or check out some recent publications.

Related articles

Dugger, K., Ainley, D., Lyver, P., Barton, K., & Ballard, G. (2010). Survival differences and the effect of environmental instability on breeding dispersal in an Adélie penguin meta-population. Proceedings of the National Academy of Sciences, 107 (27), 12375-12380 DOI: 10.1073/pnas.1000623107

Lyver, P., MacLeod, C., Ballard, G., Karl, B., Barton, K., Adams, J., Ainley, D., & Wilson, P. (2010). Intra-seasonal variation in foraging behavior among Adélie penguins (Pygocelis adeliae) breeding at Cape Hallett, Ross Sea, Antarctica. Polar Biology, 34 (1), 49-67 DOI: 10.1007/s00300-010-0858-0

Lescroël, A., Ballard, G., Toniolo, V., Barton, K., Wilson, P., Lyver, P., & Ainley, D. (2010). Working less to gain more: when breeding quality relates to foraging efficiency. Ecology, 91 (7), 2044-2055 DOI: 10.1890/09-0766.1

Ballard, G., Dugger, K., Nur, N., & Ainley, D. (2010). Foraging strategies of Adélie penguins: adjusting body condition to cope with environmental variability. Marine Ecology Progress Series, 405, 287-302 DOI: 10.3354/meps08514

Dugger, K., Ballard, G., Ainley, D., & Barton, K. (2006). Effects of flipper bands on foraging behavior and survival of Adélie penguins (Pygoscelis adeliae). The Auk, 123 (3) DOI: 10.1642/0004-8038(2006)123[858:EOFBOF]2.0.CO;2

Ainley, D.G. (2002) The Adélie Penguin. Columbia University Press, New York.

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My academic history (in a word-cloud)

Earlier this week, the postdocs in the QAECO lab presented a short talk about their academic life: past research, current research and future aspirations.  Limited to three powerpoint slides and eight minutes, it was an interesting exercise in brevity and finding ways to clearly communicate the major themes of your research.

My research history hasn’t really followed any obvious themes.  In fact, it’s really been driven by a series of happy accidents and crap-portunities*.   I started out as a field ecologist; studying the habitat use of freshwater fish, and working as a ranger for the Department of Conservation managing threatened bird species.  This was followed by more freshwater fish research, this time on rainbow trout in the United States, before I veered off (due to a crap-portunity) into the mysterious world of modelling (of the mathematical kind).  This fortuitous deviation led to an investigation of the sustainability of harvesting shovelnose sturgeon for caviar for my Masters and greatly influenced my research interests.  Returning to NZ, more ranger work for DOC led to a PhD looking at ways to improve the effectiveness of whio conservation: a glorious combination of fieldwork with spatial, demographic and population modelling.

Another happy accident saw me end up at Landcare Research, where I became the person that analysed all the random data living in the bottom of people’s filing cabinets.  I  investigated the effects of removing livestock from high country farmland, modeled disease transmission in Tasmanian devils, and looked for relationships between rabbit breeding and grass growth.  A short break in contracts provided an opportunity to do volunteer work in Antarctica.  This led to three seasons monitoring Adélie penguins and skua; and research looking at the effects of environmental conditions on Adélie penguin chick condition and the relationship between skua populations and penguin density.  I also spent time estimating the number of burrow-nesting petrels across a group of islands by identifying relationships between burrow density and habitat, burrow occupancy and breeding success.  And I briefly branched out into scary maths when I constructed a virtual model of masting trees to assess the impacts of herbivory.

I summarised all this in my talk by producing a word-cloud (in R because that’s how I roll) that showed the relative importance of keywords from each of these projects (and some pretty pictures of my study subjects to keep people interested).

academic wordcloud

So I guess you could say the central themes of my research to date are the management and conservation of populations threatened by invasive pests.  There will almost certainly be modelling involved, probably in (but not limited to) R, and I’d be keen on doing some fieldwork if possible.  I’m good at sorting out your horribly stored dataset (although I’d rather not) and I can put my hand to most forms of analysis (provided it is google-able and preferably done in R).  I’m currently branching out into yet another new field: conservation planning in the face of regional and urban development in the QAECO lab at the University of Melbourne but that’s another story for another time.

* When new opportunities arise out of the shitty things that happen.

Photo credits
I’d like to claim credit for these amazing photographs but, the truth is, I never actually saw some of my study species  (one of the downsides of being a modeller).  So thanks to the following contributors of the photographs I acquired from the internet.
Anticlockwise from bottom left: kokopu – Steve Moore; tussocks; rabbits; devils – Ian Waldie/Getty; drylands; masting; Adélie penguin – Amy Whitehead; whio – Amy Whitehead; oi – Mike Danzenbaker; kaki – Glenda Rees; shovelnose sturgeon – Konrad P. Schmidt; rainbow trout; kakapo – Mark Carwardine/; skua – Amy Whitehead; takahe

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Spatial troubles: Converting gps data between formats

I work a lot with spatial data which is great but it means I spend a lot of time cursing at my computer.  One of the problems with spatial data is the myriad of formats that it comes in and the intricacies of trying to read it into the variety of hardware and software available to use it.  One of the best ways I have found for navigating my way through this minefield has been drawing on the expertise of others, particularly blog posts where people have outlined potential solutions.  So I’m going to try and document some of my own solutions here.  This is partly for my own benefit, so I don’t have to reinvent the wheel every time I do something, but it would also be great to get feedback from those out in the blogosphere.  So I welcome your comments and suggestions.

I’m currently working with Adélie penguins at Cape Bird on Ross Island in Antarctica. Part of this work involves monitoring the nests of banded birds, where each nest is labelled with a numbered tag.  This is a great system except that the band numbers are not the same as the numbers on the tags and you can’t read the tags after a few weeks anyway as they get covered in penguin poo.  So we quite often need to use a gps to find and identify which nest we are looking at.

Banded Adelie penguin on a marked nest

A banded Adelie penguin with a satellite tag that it will wear for one foraging trip of 1-3 days. Note the yellow nest tag in front of the nest already partially covered in poo.

Our nest location data is entered manually from the gps into a FoxPro database (not the most efficient system) and then can be extracted again as a text file.  Our biggest problem is sharing data between multiple researchers in the field who use different gps units.  Which means converting our basic text file into multiple formats, which can be a trying exercise.

My goal was to find an efficient way of creating a file where the waypoints are labelled by nest number and the band number of the associated bird listed in the comments so we could cross-reference and make sure we were reading the poopy nest tag correctly.  And then convert this file to the appropriate file types needed for each of our gps units.

So I was pleased to discover GPSBabel, a free piece of software for converting gps data between multiple formats.  It took me a wee while to navigate my way around and figure out what I needed to do but now that I have figured it out, it is a very simple process using the Universal CSV option.

Converting spatial data from text file to gdb

1.  Open the text file in Excel (or your favourite spreadsheet program), rename the data columns using the appropriate keywords from the GPSBabel documentation (there are many more keywords listed online) and save as a .csv file.
alt =      Altitude
date =   Date (yyyy/mm/dd)
icon =    Symbol (icon) name
lat =      Latitude
lon =      Longitude
name = Waypoint name (“Shortname”)
comment = Notes

So the top few rows of my file look something like this, where name represents the nest tag number and comment is the band number of the associated bird.


2.  Open GPSBabel and set the input file to your newly formatted csv file, setting the format to Universal csv with field structure in the first line.

3.  Select the appropriate output format (I’ve been mostly using Garmin MapSource – gdb), name the output file and hit apply.

One of the nice features of GPSBabel is that it will open your data in Google Maps after the conversion, which provides a nice check that everything has worked how you expected.

From here, I can open the .gdb file in Garmin’s MapSource and upload it to the gps.  And then use the same .csv input file to generate other output files suitable for upload to our other gps units.  A nice simple solution.