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:


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......)


Displaying movement map in R as raster

So I've been busy trying to output suitable information from my model to demonstrate the area sin which agents are moving. I want to get some idea of how well used the map is, and if agents are able to successfully negotiate the central section of the landscape where heterogeneity is highest.

I've outputted a text file that has the number of steps taken in each grid cell and converted this to an ASCII file, replacing all commas with spaces and adding the relevant information at the start of the file as below:

ncols         608
nrows         506
xllcorner     299006.96538007
yllcorner     1898128.1510276
cellsize      100
NODATA_value  0

I can now read this into R with the following:
(which requires several packages - raster, rgdal and scales)

Map1 <- raster ("/Users/aw4g09/Dropbox/ThesisChapters/CorridorLandscapePaper/simulationData/RawData/long_corridorModelOutput/GISMovementMap_1.txt")

and display with several options:

map.spdf <- as(Map1, "SpatialPixelsDataFrame")
map.df <- as.data.frame(map.spdf)
gMap <- ggplot(map.df, aes(x=x, y=y)) + geom_tile(aes(fill=layer)) + coord_equal()
gMap <- gMap + theme(panel.background = element_rect(fill='white'))
gMap <- gMap + scale_fill_gradient2(limits = c(0, 30000), low=muted("green"), mid="red", high="white", midpoint=15000)
This latter option allows me to manipulate the legend extent, choose gradient colours etc.

I also found a VERY cool way to generate a 3D plot of the raster which can be manipulated. This requires some extra packages including rasterVis, rgl and sp, at which point you can simply enter plot3D(Map1). Another application opens to display the 3d plot.

although I am still struggling to figure out how to save an image of the output!

now I'm starting to try and figure out how to compare movement across simulations, i.e. compare the distribution and density of movements between different rasters... I found a very useful website that is helping with this


so I'm hoping I should have something more solid to present in my last thesis chapter than a subjective description of movement... fingers crossed.