Jaguar population model parameters

So I haven't updated this for a while... I've been busy re-doing most of what I've spent all of this year doing. VERY frustrating!

Basically, after finishing my PhD transfer report I showed my work (all the output from my jaguar population model) to my collaborators in Belize - researchers who have been working with jaguars for years, I found that some of the key outputs from the model were not close enough to realistic values for jaguar populations in the wild. Namely, territory sizes and the distances that individuals moved over time. Those things that seemed pretty critical to the emergence of a stable population size. In fact, upon initial attempts to increase territory sizes, my stable population became stable no longer. Hence, I've spent the last 3 months re-doing all the tedious trial and error work I did during the previous 3 months in trying to get a stable population size over time that exhibited more realistic individual behavioural characteristics.

I've just about finished doing all the work and getting all the output. Ive harnessed the power of 2 computers at the university to do the bulk of the simulation work which I have managed to get remote access to. This has made the whole thing a lot easier as I don't have daily access to the computers in person. This has also freed up my own computer to do some other work - the work I should have been doing over the past 3 months instead of re-doing the population model.

So, perhaps I am jumping the gun a bit here as I have yet to fully analyse the output or run it past my field collaborators, but these are the current model parameter settings. First is the least-cost model, and food availability:

 Next comes the agent parameters, dictating the agent behaviours and life history traits:

Then comes the interaction parameters:

In short, parameters I've changed are:

• the *number of time steps per day* - from 4 to 10; 
• the *number of cells males can move when trying to find a female to mate with* - from a maximum of 10 to a max of 25;
• the *pheromone degrade rate* -  to 0.08;
• the *cost of male pheromone to a female* - from p to 0.3*p;
• the *cost of a male pheromone to another male, if the males are on a trail* - from p to -0.001*p;
• *food availability* outside of Cockscomb protected reserve - reduced to 85% of the availability inside CBWS;
• addition of a *post-model setup* period - the initial 10 years (including the 3-year startup period) describe a reduced mortality for all adults, allowing greater time for the population to find suitable territories.

Initial analyses give male territories from around 40 to 70km2 and females around 10-20km2. These seem much closer to realistic sizes. Population sizes also seem to settle around 70-120 in number which also seem pretty good for the location.

These settings also seem to generate larger numbers of individuals being captured by the static model camera traps. Original stats gave an average of around 5 per sampling period versus the 191 collected in the field which is pretty bad. The new settings don't give anything near 191 either, but closer to an average of around 20ish.

Some other points:

• Females undergo typical reproductive rates, being available to mate only for the central third of their oestrus cycle;
• sub-adults leave the mother aged 2 and undergo a single year of 'dispersal' during which time they can move freely within their mothers range, are reproductively inactive and experience a higher mortality rate;
• dispersal is therefore an emergent feature of the model and not hard-coded.

We'll see what the final analysis looks like soon and take it from there.

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'!

Conference season

Conference season is upon us again and I have 3/4 lined up already.

I'll be presenting the model as the southampton uni biology postgrad conference in 2 weeks, and the student conference on complexity science in august, as well as INTECOL2013 (where i originally proposed a poster and I got requested to present a talk instead!). I'm volunteering at this conference as well (which means free registration) so it should be an awesome event and hopefully a good networking opportunity. With only 11 months left on my PhD I have my eyes open and looking for jobs!

I've also submitted an abstract to ISEM2013 the Ecological Modelling conference being held in October in Toulouse and I should here back from them this month. I've opted to submit the paper for a special edition print of that journal so I'll also see if thats been selected. Fingers crossed!