Back in harness with some book reviews

It has been a while since I last put pen (so to speak) to paper and produced a blog post. I got caught up in writing up my MSc by research thesis and then took some time away from university to gather my thoughts and prepare myself for the forthcoming PhD (now started in earnest). While I’ve been away I have kept myself busy (either earning money or overland travelling with my family in our classic Land Rover) but it is amazing how quickly one gets out of practice when it comes to studying, and how tiring it is when you return to reading!

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The revised version

My current project is largely computational and I have had to re acquaint myself with R, it is shocking just how much gets pushed to the back of the mind over the course of a year and it was an eye opening experience to sit in front of a PC and think “I am sure that I know how to do multiple regression in R, if only I could remember where to start!” I am pleased to say that a few hours with a trusted text has brought all of this back to me and I am now pushing ahead and learning new techniques.

The testats1xt that I have found most helpful in getting back to using R has been Mark Gardeners “Statistics for Ecologists Using R and Excel” . This excellent little book leads the reader nicely through the basics. Starting with how to down load R and getting data into the programme through exploratory statistics and into basic analysis with a section on reporting results which includes visualising data. It also makes it easy for the reader to synthesise R and Excel and there is extra help and sample data available on the free companion webpage if needed.  I recommended this text to the university library as well as to colleagues at my student workshops on R. Although I  initially bought this book when I wanted to discover R I actually also learned new techniques for data manipulation and management in Excel. I am given to understand that this book is being revised by Gardener  and look forward to seeing the new version.
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My new project will include some community ecology and a good deal of spatial analysis. I was looking around for a decent GIS text when a colleague pointed me in the direction of Brunsdon and Comber’s “An introduction to R for spatial analysis and mapping” . As a GIS novice I have found this book really useful although the data in the examples may be less overtly biological. I really like the way that the authors do not assume that the re reader is an expert in R but show where basic tuition is freely available rather than filling the book with very basic techniques. The book tells the GIS student at which level in R they need to be to start and this allows it to lead more or less  straight into the spatial content, it then combines this with more advanced R use such as writing functions and programming. Again data is provided via the companion website and the book is packed full of illustrations and code snippets, many of which have been added to my personal library for future use!

The final text that I have been using recently is another offering from Mark Gardener in the form of “Community Ecology, analytical methods using R and Excel”. In the interest of openness I should tell you that the publisher sent me a copy of this book and asked me to review it. This is a fairly substantial work from Gardener at well over 500 pages and the publishers say that it is aimed at advanced undergrads and post grads/ researchers beginning in community ecology. Without a doubt there is a challenge here since Gardener seekComm-Ecol-Covers to enlighten the reader about both community ecology as a topic (although he admits in the foreword that this is not exhaustive) and the analytical techniques needed to successfully study it. This is a feat which I felt that he managed reasonably well. I find his style easy going and he does well at not assuming the reader has expert knowledge. The book follows a logical path and is packed with reassuring screen shots and coding advice. The fact that it is written by an ecologist makes the data relevant to biologists and it all seems easy to follow, specimen data are again provided on the website. Gardener offers alternative analyses for each type of data, explains clearly when he thinks a particular analysis is most useful and then encourages the reader to ‘have a go’. I do have a couple of small criticisms though, firstly the book starts with a very basic introduction and I felt that it would better to point the reader to another source for this and secondly I have personally found that since using R for analysis my use of Excel has been limited to storing, manipulating and basic visualisation of data. With this in mind I found that the explanations of how to use Excel and then R, for the same analysis, were superfluous and that I skipped past the Excel parts to find how to do it with R. That being said, I guess that it is better to have too much information than not enough! Overall I found Community Ecology to be well written, useful and informative, and, as with the other volumes here I would recommend seeking it out.

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Thinking about output and health and safety.

As an early career ecologist I seem to spend a bit of time generally ruminating and mulling over ideas whilst making decisions and choices. Recently I have been thinking about the output that my current project might generate and . having recently developed an interest in citizen science I think that if we are to use data collected by the masses then we should at least make the output that is generated accessible to any interested party who had a hand in generating the data. This means writing in a manner that is intelligible and interesting (see Sand-Jensen’s  How to write consistently boring scientific literature)  but also publishing somewhere that people can access the stuff! So one of the things I have recently been pondering is whether to try and persuade more senior co-authors that we should publish work in open access journals such as f1000 research which is publishing ecology papers free of charge until the end of this year. The whole open access debate has been focused to some degree by the recent ‘who is afraid of peer review article in Science Magazine. Responses to this article seem to range from quiet approval from those happy with the print journal system to this blog post by Jeroen Bosman with Bob O’Hara writing what seems to be a moderate and well thought out response in the Guardian. You don’t need to be Einstein to look at the author pays model to work out that it is readily open to abuse and that  junior scientists who are keen to get work published and are perhaps more naive are susceptible to being targeted.

I wrote in a recent blog post about Hoffmann discovering the effects of LSD by taking some and then going on a bicycle ride. Thinking of this while considering COSHH, risk assessments and ethics forms for my current project my attention was drawn to Micheal Mosley’s current BBC 4 series Pain Pus and Poison. With no mention of health and safety, Mosley details how, in 1815 Friedrich Serturner had isolated some crystals which he and his  lab group tried in different doses to see what effect they might have. It is staggering enough when you realise that the crystals  that they were gaily knocking back were morphine but Mosley goes on to detail how  Serturner and his colleagues were dissolving these opiates in alcohol to aid ingestion! Now there is a risk assessment I would like to read!

As conference season draws to a close I had the good fortune to attend my first BES special interest group meeting. This was organised jointly between the computational ecology group and the International Biometric Society and it looked at species distribution modelling, my thanks go to all who were involved in organising this informative event.

Rock pooling with Yorks branch Society of Biology

My trip to London followed hot on the heels of a weekend visit to the N. Yorks coast for, among other things, a  day of rock pooling at Boggle Hole with the Yorks branch of the Society of Biology. Thanks go to Clive Tiney and others for organising this and to all of those who attended with more knowledge than Henry and I and who helped to make this an enjoyable day by selflessly sharing their time and knowledge. Henry (aged 8) has decided that he wants to be a marine ecologist because “crabs are really cool”

I’d like to finish by mentioning a funded studentship at Lincoln with Anna Wilkinson on social cognition and reminding the students out there that you can get a years free membership of the BES here this applies to undergrad / masters level and again for PHD.