Paper Published

I've finally had my main thesis chapter published! A lot of hard work and two rounds of edits following reviewer comments and it has finally been released online. See it here for non-paywall freely available copy:

A spatially explicit agent-based model of the interactions between jaguar populations and their habitats:

https://drive.google.com/file/d/0B2itFn5PP0TCenl5cWpKazFBUmM/view?usp=sharing

This should be freely available now. Let me know if there are any problems.

Wrapping up

The last 2 months have been intensive. I finally handed in my thesis, and only about 1 1/2 weeks late. Which personally I think is quite impressive! Although, I honestly have never found anything so stressful.

Following a bit of a break down and a cry, the pressure just seemed so great and I just needed it all to be over. The last four weeks of work nearly broke me. Looking back on it now, I wonder why I put so much pressure on myself, but the end was getting nearer and nearer and yet I couldn't see any light at the end of the tunnel. It just seemed like the final weeks would just stretch on and on and on and on. Nothing would change and I would be stuck in the groundhog day of writing and writing, and stressing, and writing, and getting so entwined in everything that I almost couldn't breathe.

You would think that I would have had this magical moment upon my final hand in. However, I found the whole experience a complete anti-climax. I handed in a complete first draft, and waited a week for comments from my supervisors, before doing another weeks work and finally handing it in. Although at this point, I had found out that my viva couldn't be when I wanted and that I would have to wait 2 months before finally being able to close the door on the last 4 1/2 years. In fact, it will be 5 years almost to the day since I started this whole journey before I will finally hand in the hard copy of the final final final thesis. Dr. Watkins here I come, I hope.

Not only did I have to hand in my thesis, but I have also been furiously hunting for jobs. With a husband and a 2-year old to support I can't sit around and enjoy a nice long break, I need to get right back on the bandwagon and bring in some wages. Luckily, I was able to apply for 2 very good jobs during the last 2 months of my thesis, and scored 2 interviews that coincided nicely (or not) with the same week that I handed in my thesis. Considering I needed to prepare a 5 minute talk for each interview this only added to the stress of the whole experience.

I heard from the first interview within the week. Disappointment was only overshadowed with knowledge of the inevitable. I knew I wasn't going to get the job, after an interview that did not go well and I have to admit I was underprepared and did not show myself off in the best light. The second interview went much better (for the same organisation as the first) and I was pretty convinced that they would have to give me the job. 3 weeks later and I finally found out that I was again unlucky, only getting 1st reserve. This did not offer me the consolation I was looking for. I then spent the next 2 weeks getting more and more worried that I would be in the unemployed limbo forever, as no 2 more job applications didn't even land me an interview.

Still, 2 weeks to the day of getting the rejection from the second interview, I got an email saying that the job had become available and was mine if I wanted it! Thank goodness. Here was the relief and climatic finish I was looking for. I am still waiting to start (over a month after getting that email) but am hoping to hear this week about a start date.

So the last 5 years have not been for nothing. They have been some of the best years of my life and I have found lifelong friends. My research project has been an enjoyable experience, from which I have learned a lot and hopefully opened up the possibility of new applications of modelling for conservation benefits. Now I just need to work on editing a manuscript for publication before I can leave this period of life and move on to the next.

The joys of finally securing a job have now meant that I can enjoy my time off with my little girl and spend some quality summer time together before the reality of working life hits me with a vengeance. It could only be for another week, so I'm off to enjoy my summer.

I'll post back with updates on my viva and any possible publications. But for now, this is me signing off.

Good luck to those still working for your phd. There is an end!

Less haste, more speed.

Todays lesson is a harsh one. Less haste = more speed.

Time and the again I find myself with a significant set back in running simulations due to some stupid, pathetic, rage-inducing idiotic mistake that if I had just taken an extra second to think about things and run through the logical steps of the programme, I could have very easily avoided it!

You would think, after 4 years of doing this that I would have learnt my lesson. But no. Here I am, with less than a month to go and I have just found another completely moronic mistake in model settings that means my lovely model output is now all wrong and has to be re-done. Whats worse is that to was actually *TWO* mistakes, leading to more food in the landscape and more individuals being introduced into the model so that I had a lovely stable long-term population.

I fixed the errors and my population now dies by year 30. This itself is fine, as it actually what I would have expected in the region I'm modelling, but what it does mean is that I now have to re-do the focus of my last chapter, re-think the order of experimental steps, re-think the implications for real-world conservation and what this means for interpretation and future recommendations for conservation management. *aarrgghh*

Some days I wonder how I've managed to survive into my thirties. I think I might just walk around with a giant DUNCE written on my head and be done with it.

Not a good day when I have 4 weeks and counting to hand in the final thesis!

Breathe. Think. Take a second. Fix the error. Check. Check. Double check. Look at the fix. Check it again. Breathe. Look at Facebook. Look at Twitter. Check. Check. .... Run....

(fingers crossed......)

Completion of example model data chapter

So its been a while since my last blog post. On a personal note I have been busy with Christmas and my young daughter and we have also just moved house again - all of which have distracted me from doing the finishing touches to my PhD. I have also just applied for a NERC grant with cardiff University. That was a terrific amount of work in a short space of time, for which I am not going to know the outcome until June!

With all that going on, I'm surprised to have got so far with things.

To make a general update:

I have now completed my third data chapter - the big beast of a chapter that describes my entire model in detail and publishes the model outcomes, sensitivity analysis and validation with empirical data. What a feat! At every turn I felt like mistakes were arising and the model seemed to crash every time I tried to improve things and make output more ecologically realistic. But time waits for no-one and some sage advice form my supervisor has allowed me to close the door on the continually effort for improvement and concentrate on getting it done and moving on to the landscape analysis.

Some bits and pieces from this chapter:

1. territories and population size. females in red, males in blue.

population remains fairly stable, increasing slightly to fill the useable space and has some good stats for individuals inside and outside of the protected areas. agents are younger in the matrix than inside the protected area, have lower energy reserves and less fecundity.

2. Population stats, protected vs non-protected areas

I still have some issues with validation via the empirical data with the number and distribution of agents being captured by model camera traps not matching the empirical data. The fine and local scale movement of agents does not seem to be adequately captured by the model, but considering the landscape scale nature of the simulation and the scale of movements and number of individuals, then its not surprising to get some scaling issues. A higher resolution landscape and were individuals would allow for a bit more work to be done in this area, but this was not the focus of the piece of work so I'm not too worried. As long as the population level events are being captured, and match the empirical population data then I believe we can be happy with the outcome of the model so far.

Its not my intention to get a model that fully encapsulate the complexity of real individual jaguar movements, as this is going to be pretty much impossible. The need to reduce model complexity, but increase model realism is always going to be a battle. We just have to hope that we reduce model complexity in the right places that model outcomes are not adversely affected. 

The next, and last(!) chapter of my thesis will take a look at this by using the model to investigate connectivity and landscape utilisation in a population of jaguars in a far more fragmented area of Belize.  This should give me a better idea of the issues with the model and how these need to be addressed (if any exist).

For now, I'm pleased to have got this chapter done and happy to be moving onto the last phase of my PhD. The end is in sight!

Wife, mother and PhD student - the balance is possible

Up until now, I have remained quiet with news of my personal life having set up this blog to track and store useful information regarding the research subject of my PhD at the University of Southampton. However, there has been much debate on twitter (find me @ecologyWatkins) and in the news on the state of the integration of women in the top level of academic and science careers, and as I near the end of my PhD life, balancing a career with a family has never been more in the forefront of my mind.

I recently tweeted "Why postdoc life with young family is not an easy option MT:@AstroMeg: in 6 years I have worked from 10 desks & moved internationally 4 times". 

I think this encapsulates the issues with pursuing an academic career if you already have settled, have a family and have ties to any particular location. Without the freedom to pursue national and international positions, finding funding and career opportunity as an early career academic seems flawed and particularly challenging. So how do you juggle, as a woman, a family life and a career? 

Unfortunately I do not yet have the answer, but no matter how relaxed I become of the situation and think that sexist traits can surely no longer exist in 2013 I get a nasty reminder. One academic, who shall remain nameless, recently admitted that he would not have appointed a female PhD student if he had known before hand that she had a young family, but would not have thought twice about appointing a male in the same position. How can this possibly be the case?

So today, I describe how life has changed for me since giving birth to my daughter almost one year ago and how it is possible to juggle a successful PhD with raising a family. 

Having been married for 3 years, my husband and I decided we wanted to start a family. My daughter arrived during my second year of PhD after I had already taken a 3-month suspension to pursue a policy placement secondment at the National Assembly of Wales. I took 5 months maternity leave (generously funded at full stipend rate by the University) and resumed my studies at the beginning of January of this year, 2013. Currently myself and my husband undertake full childcare duties between us whilst both undertaking full-time employment. Luckily my husband does shift work and has managed to squash his full-time hours into around 3 days a week and alternate weekends. I work from home mainly and manage to go into Southampton (which is a hour and a half trip each way from home) one day a week. I fit the rest f my work around my daughters naps and in the evening/weekend.

In real terms, with the knowledge that I don't have the liberty of time to waste I have found that I have never been more productive! My life is busy and full and I have forgotten what it is to be bored(!) but otherwise I have found the balance of childcare and work quite feasible. My daughter is now almost 1 year old and it is only now that we are considering some alternative childcare arrangements to allow me some extra time to make the final push in my last year and get my PhD done. In fact I am on track to hand-in my thesis early and have my viva and corrections submitted by the time my funding runs out at the end of May 2014.

I know of two other female students who have successfully managed to juggle motherhood and PhD life and in my experience, we tend to be the most organised, productive and committed students (although I know I can't say that definitively for all PhD students who are mothers). We no longer fall into the trap of being too absorbed by student life and social activities and in fact all three of us are probably in the top tier in terms of getting the thesis handed-in either in or before the deadline. In fact, of the 20 students in my PhD cohort (we are started a 4-year integrated PhD in the Doctoral Training Centre within the Institute for Complex Systems Simulation at Southampton in 2009), myself and the other 'mother' in the group also still manage to attend more group events and compulsory workshop sessions than many others who do not have such family and time commitments.

In short, I am as committed to my PhD as I was before I became a mother. I am still on track to submit my thesis early. I continue to attend conferences and have recently won runner-up oral presentation prize in a postgraduate conference and have had a recent paper acknowledged as a good example paper.

My answer therefore to those who baulk at the idea of employing a young mother in an academic career: judge us on our outputs, not on our inputs. Judge us on how we perform academically, judge us on our competence in our chosen field and judge us on our ability to conduct effective, robust and novel research. To judge us on anything else is to fail the women in our society. To judge us on anything else is just plain wrong.

Runner-up prize at University of Southampton Biology PostGrad Symposium 2013

Yesterday I presented my current work as part of the 2013 University of Southampton Biology Post-Grad Symposium. This event involved all third year PhD students presenting their work to other biology postgrad students and 2nd years presenting their work as posters. Participation was around 100 people.

Entitled "A spatially-explicit agent-based model of jaguar population dynamics", my presentation focused on the model I have just finished working on and submitted to the university as the latest chapter in the transfer report.

Aside form some technical problems which meant that I couldn't include a movie clip of my simulation in action, or some footage from a camera-trap of a jaguar at a kill, I think my talk went down quite well. Some examples slides can be seen below and the whole talk is on figshare:

As part of a small group of conservationists/ecologists within Southamptons Biology department, mine was the only talk that focused on a whole organism/ landscape-scale events. As such, I really struggled to keep up with most of the presentations and this was not made easier by the quality of talks. Most lost me with information that was too detailed and assumed too much background knowledge. Others, to be a bit harsh, had lazy structuring and I struggled to follow the progression of the talk.

Having said that, I was quite impressed by the level of work being done by PhDs at Southampton and some of the work had real potential application for disease control and treatment.

To cap it all off, I won runner-up for oral presentation!

Not bad considering I am really out of the biology 'loop'. Being based partly in Biology and partly in computer science I have never really felt at home in the mainstream biology department, but I really felt like the audience were receptive to my work and open to the idea of modelling as a useful tool for exploring population persistence issues.

All in all, I'm glad I took part and put a bit of effort into the talk and it gives me hope that my future similar talks at INTECOL2013 and ISEM2013 (hopefully) may be also well received. Talking to a room full of people has never been my strength and in the past I have really struggled with nerves so I am promoting the old adage of 'the more you practice, the better it gets'!

Policy placement with the National Assembly for Wales

So i've been quiet for a while now due to me doing a PhD placement for 3 months with the Research Service of the National Assembly for Wales. I'd definitely recommend doing something similar if given the opportunity and you are thinking about a career outside of academia. This particular placement was quite politics heavy which isn't necessarily what I want to get involved with, but it did give me a tremendous insight into how policy is formed and amended and what goes into devising and publishing national strategy documents.

I was based in the Environment and Sustainability research team meaning I got to be involved with a lot for work currently being undertaken within the Assembly - namely a review of all things Energy in Wales, the publication of the 'Sustaining a Living Wales' Green Paper and the review of merging the three statutory environmental bodies (Countryside Council for Wales, Environment Agency Wales and Forestry Commission Wales) in Wales into a Single Environment Body. Some really interesting topics which meant I got to develop, prepare and publish useful documents on these subjects to the Assembly Members and the general public.

A list of my contributions during the placement:

1. An introduction to natural environment policy in Wales and a comparison with natural environment policies for other parts of the UK (Research paper)
2. Ecosystems and the Ecosystem Approach (Quick Guide)
3. Nature Conservation Designations (Quick Guide)
4. Briefing on Legal Enforcement of European Statutory Legislation (internal briefing to the Environment and Sustainability Committee)
5. Briefing on Tidal Flooding and Coastal Erosion (internal briefing to the Environment and Sustainability Committee)
6. Briefing on Technical Report to Environment Agency Wales on an Investigation into Cockle Mortalities at Burry Inlet (internal briefing to Petitions Committee).

About me

A bit more background about me so far.

I started my academic life at Royal Holloway, University of London where I completed a BSc in Zoology. I gained a first class honours degree and spent my second year at the University of Western Ontario, Canada, as part of the study abroad scheme: probably the best decision I have ever made. I made a lot of good friends and had a really amazing experience.

Following this I headed back to my home town of Cardiff and after a stint working in a bar, doing some volunteer work with the National Trust, and heading to South Africa to participate in a volunteer research programme at Edeni Game Reserve (via GVI), I started working for Defra at my local Animal Health Office.

Two years later I had had enough of working in an admin role, even if it was vaguely related to farming and hence conservation, so I applied to the University of Leeds for the master programme in Biodiversity and Conservation. Choosing the Master of Research (MRes) programme instead of the usual Master of Science (MSc) I did fewer taught courses with two full-length theses, instead of the usual one.

After a failed attempted for a PhD that, looking back on it, I probably only half wanted to do, I got a job with Natural England as a Senior Land Management and Conservation Adviser. Now this was more like it. Not only was I getting paid to learn about conservation and land/habitat management but I also got to spend half my working life walking around farms talking to farmers and looking for opportunities to enhance the wildlife on the farm. A pretty good job that also included some 'training' opportunities that took me on two week long trips learning about upland farming and grassland ecology, as well as other workshops looking at wet grasslands and farmland birds.

I learnt a hell of a lot at this job. Not only about wildlife, habitat management and farming but also about what I wanted to get out of my career and what I was willing to do to get it.

So, after nearly two years in a well paid and really great job, I quit!

Signal, the next step in my varied work life: the Institute for Complex Systems Simulation.

I applied for, and got offered a place on the four-year PhD programme at the University of Southampton. It was the first year they had run the programme and I, along with 20 others, became the Southampton Complexity Science guinea pigs. As part of a Doctoral Training Centre, it is a four-year PhD programme with a taught year equivalent to a masters followed by a three-year research programme.

There are only three universities in the UK with research specifically related to complex systems; Southampton, Bristol and Warwick. Of course, the course at Southampton is the best :)

Pages devoted to the research that goes on as part of this programme, encompassing a wide range of departments and academics can be found here, on the Computational Modelling Group website.

So, after doing some pointless and dreary jobs, and having a sporadic education, I am finally on the way to getting that all important PhD!

Next post: my PhD research so far.

Hello and Welcome

This is my first post on this new blogging site, so hello!

To introduce myself, my name is Angela Watkins. I am currently in the second year of a four-year PhD programme with the University of Southampton within the Institute of Complex Systems Simulation. I sit jointly within the School of Biological Sciences and the School of Electronics and Computer Science.

My research aims to look at the effect of habitat fragmentation and corridor design on the permeability of habitat for jaguars within the Central Belize Corridor. This research links into ongoing work assessing the functionality of the corridor area for a range of local wildlife, see Belize Wildlife Research, as part of the Jaguar Corridor Initiative.

I have done some preliminary work on designing and building agent-based simulations of jaguar movements in some simple and abstract landscapes, with some promising results. My next step is to integrate these simulations with some real GIS (Geographic Information System) data in order to validate and tune jaguar movements to existing data obtained from camera-trap studies.

This blog will aim to chart my progress and hopefully provide some useful information to others working in the same field.

Feel free to contact me with any questions or suggestions.