Conferences/Meetings/Workshops

NCSE Summer 2017 meeting at the University of Kent

The Statistical Ecology @ Kent (SE@K) group will host the next NCSE summer meeting, which is returning to the University of Kent after 10 years and will take place in the w/c 26th of June 2017.

Click for  Programme and  Abstracts.

The meeting will include an invited talk by Professor Robert P Freckleton, University of Sheffield, and a one-day workshop by Professor David Borchers, University of St Andrews, and Professor Finn Lindgren, University of Edinburgh, on “Spatial Point Process Modelling with INLAbru”.

Meeting Location:

Registration will take place in the foyer of the Grimond building on the University of Kent campus, at 2pm on Monday, 26th June. The talks and workshop will take place in Grimond Lecture Theatre 2 (GLT2). The location indicated can be found on the University map at  https://www.kent.ac.uk/maps/canterbury/canterbury-campus/building/grimond-building/glt2

Drinks Reception:

There will be a drinks reception on Monday at 5.20pm in Grimond Foyer.

Meeting dinner:

The meeting dinner will take place on Tuesday at 7pm.  It will be free for NCSE members, excluding drinks and take place in a private room in Café du Soleil in Canterbury; see www.cafedusoleil.co.uk

Workshop:

On Thursday there will be a workshop  on Spatial Point Process Modelling with INLAbru by David Borchers and Finn Lindgren. Participants in the workshop will need to bring their own laptop and install the packages listed in: workshop preparation

Travel to Canterbury:

A campus map and travel instructions can be found at https://www.kent.ac.uk/maps/canterbury

Accommodation:

There are various possibilities, including Air B&B. The University campus is on a hill outside Canterbury. There are buses regularly connecting the campus to the city, and the walk takes less than 30 minutes each way. General information is to be found at: www.canterbury.co.uk

– We should be able to make a block booking in student accommodation on campus; this is probably going to be an economic option. In order to do this we will need to know how many people would be interested. If you are interested then let us know by the 7 April deadline.

– A B&B at the entrance to the campus is the City of Canterbury: www.thecityofcanterbury.co.uk/

Outing:

Tuesday afternoon will be free for an outing.

The first railway in the world to issue season tickets ran from Canterbury to Whitstable, opening in 1830. We propose a walk along the line of this historic railway (the Crab and Winkle line) for those who may be interested. From the campus the 6-mile walk to Whitstable passes through  woods and  countryside. At Whitstable it would be possible to take refreshment at local pubs around the harbour, and possibly sample Whitstable oysters. If walking back is unattractive then there are regular buses.

The walk will leave Grimond Foyer at 12.30 and go via the campus shop to buy yourself a packed lunch.

There is no shortage of alternative activities for individuals. Canterbury contains a UNESCO World Heritage site, comprising the Cathedral, St Augustine’s Abbey and St. Martin’s church.  See http://www.canterbury.co.uk/things-to-see-and-do. In addition there are possibilities of visiting Faversham, home to Shepherd Neame brewery, Britain’s oldest brewer, and Dover and Leeds castles.

Bird watching is possible at various local sites, including at Stodmarsh Natural Nature Reserve, which we visited when the last NCSE summer meeting was held in Canterbury. This is home to Bearded reedlings, Marsh harriers, Cetti’s warblers, Bitten and many more. The reserve is 20 minutes drive from the campus. Blean woods is walking distance from the campus, and is one of just a few sites in the UK where there is a chance of seeing the rare Heath Fritillary butterfly, weather permitting.

 

 

Standard
Conferences/Meetings/Workshops

NERC-funded advanced short course run by SE@K

The course took place 9-13 January 2017 at the University of Kent and was run by SE@K’s Diana, Eleni, and Rachel and DICE’s Richard Griffiths with the help of SE@K PhD students  Alex, Anita, Marina and Ming.

30 participants travelled from all around the UK for the course which involved lectures, R practicals, talks by Humphrey Crick from Natural England and Rufus Howard from IEMA, round table discussions on ecological challenges and the role of statistical modelling in dealing with some of these challenges and 1-1 sessions with the course organisers for all participants who wanted to discuss their studies and data.

On Tuesday Richard kicked off the day by discussing the types of population data that we need in conservation practice. Humphrey  then went on to discuss problems in modern conservation and the role of statistical modelling. Finally Rufus Howard talked about Big Data (Gaps) in EIA. A round table discussion then  focused on obstacles to incorporating statistical models and priorities of ecologists.

The rest of the week focused on statistical methods used in statistical ecology including abundance estimation, capture-recapture, occupancy modeling, distance sampling, citizen science data, modelling movement, species interaction models, spatial models and integrated modelling.

The course was successful at introducing complex statistical ideas, exposing participants to a wide range of statistical techniques and discussing state-of-the-art statistical methods. Below is a list of comments received about the course:

“Attending the course has enabled me to see how my data can be utilised in a better way..”

 

“Great materials and trainers”

 

“There were difficult concepts but it was very well presented and very accessible”

 

“Training was fantastic throughout”

 

“Good course and definitely beneficial”

 

“Great comprehensive course addressing many scenarios and how to deal with different datasets”

 

“I really appreciated the level of explanation given by all of the speakers”

 

“Incredibly well presented”

 

“Really great overview of the topics and great practical session”

 

“1-1 meetings were a great idea”

 

“I thought all lecturers were really very good and explained things very clearly and simply with good repetition”.

 

Standard
Books, Papers, Publications

50th anniversary of the Cormack-Jolly-Seber model

 

Just over 50 years ago, three papers appeared which independently described the fundamental approach for analyzing capture-recapture data. It is now called the Cormack-Jolly-Seber model. This anniversary is celebrated in the second issue of Statistical Science, 2016, guest edited by Steve Buckland and Byron Morgan. It features transcribed interviews with George Seber and Richard Cormack. In addition there are eight research papers that demonstrate how the capture- recapture area is still developing, with applications to genetics, social and medical areas, as well as ecology.

steve    rachel     byron

Shown in the photographs are Steve presenting a copy of the issue to Richard, in St Andrews University, Rachel Fewster, a co-author of two of the papers in the issue, presenting a copy to George, in the University of Auckland, and Byron presenting two copies to George Jolly’s two daughters Heather Hannah and Fiona Davies. A third copy goes to their brother David Jolly, who lives in Saudi Arabia.

Standard
Publications

Rachel and Byron have had a paper published in Journal of the Royal Statistical Society – series C (Applied Statistics).

A new strategy for diagnostic model assessment in capture–recapture

Common to both diagnostic tests used in capture–recapture and score tests is the idea that starting from a simple base model it is possible to interrogate data to determine whether more complex parameter structures will be supported. Current recommendations advise that diagnostic tests are performed as a precursor to a model selection step. We show that certain well-known diagnostic tests for examining the fit of capture–recapture models to data are in fact score tests. Because of this direct relationship we investigate a new strategy for model assessment which combines the diagnosis of departure from basic model assumptions with a step-up model selection, all based on score tests. We investigate the power of such an approach to detect common reasons for lack of model fit and compare the performance of this new strategy with the existing recommendations by using simulation. We present motivating examples with real data for which the extra flexibility of score tests results in an improved performance compared with diagnostic tests.

The full pdf of the paper can be accessed at: http://onlinelibrary.wiley.com/doi/10.1111/rssc.12197/pdf

 

Standard
Conferences/Meetings/Workshops

Diana gave talk as part of Statistical Ecology seminar double bill

On Thursday 6th October Diana gave a talk as part of Statistical Ecology seminar double bill. The other speaker was Ruth King from the University of Edinburgh. The Seminar was jointly hosted by the Royal Statistical Society (RSS) Glasgow Local Groups, the RSS Environmental Statistics Section and the Boyd Orr Centre for Population and Ecosystem Health.

The talk was entitled Parameter Redundancy and Identifiability in Ecological Models and talk slides are available here: Talk Slides

Standard
News

New SE@K PhD student – Alex Diana

SE@K has welcomed new PhD student, Alex Diana, who is supervised by Dr Eleni Matechou and Professor Jim Griffin as well as Dr Alison Johnston from the BTO.

He is working on “Bayesian nonparametric models for the study of migration patterns of UK bird populations.”

Standard
Uncategorized

Paper: Temporally varying natural mortality: Sensitivity of a virtual population analysis and an exploration of alternatives

The paper

Temporally varying natural mortality: Sensitivity of a virtual population analysis and an exploration of alternatives

by

Shanae Allen, William Satterthwaite, David Hankin, Diana Cole and Michael Mohr

will appear in Fisheries Science, and is available online early at http://www.sciencedirect.com/science/article/pii/S0165783616302958

Abstract:

Cohort reconstructions (CR) currently applied in Pacific salmon management estimate temporally variantexploitation, maturation, and juvenile natural mortality rates but require an assumed (typically invariant)adult natural mortality rate (dA), resulting in unknown biases in the remaining vital rates. We exploredthe sensitivity of CR results to misspecification of the mean and/or variability of dA, as well as the potentialto estimate dAdirectly using models that assumed separable year and age/cohort effects on vital rates(separable cohort reconstruction, SCR). For CR, given the commonly assumed dA= 0.2, the error (RMSE) inestimated vital rates is generally small (≤ 0.05) when annual values of dAare low to moderate (≤ 0.4). Thegreatest absolute errors are in maturation rates, with large relative error in the juvenile survival rate. Theability of CR estimates to track temporal trends in the juvenile natural mortality rate is adequate (Pearson’scorrelation coefficient > 0.75) except for high dA(≥ 0.6) and high variability (CV > 0.35). The alternativeSCR models allowing estimation of time-varying dAby assuming additive effects in natural mortality,fishing mortality, and/or maturation rates did not outperform CR across all simulated scenarios, and areless accurate when additivity assumptions are violated. Nevertheless an SCR model assuming additiveeffects on fishing and natural (juvenile and adult) mortality rates led to nearly unbiased estimates of allquantities estimated using CR, along with borderline acceptable estimates of the mean dAunder multiplesets of conditions conducive to CR. Adding an assumption of additive effects on the maturation ratesallowed nearly unbiased estimates of the mean dAas well. The SCR models performed slightly betterthan CR when the vital rates covaried as assumed. These separable models could serve as a partial checkon the validity of CR assumptions about the adult natural mortality rate, or even a preferred alternativeif there is strong reason to believe the vital rates, including juvenile and adult natural mortality rates,covary strongly across years or age classes as assumed.

Standard
Publications

New paper by Eleni, Rachel, Byron and colleagues

The Annals of Applied Statistics
2016, Vol. 10, No. 3, 1572–1589
DOI: 10.1214/16-AOAS949
© Institute of Mathematical Statistics, 2016

OPEN MODELS FOR REMOVAL DATA

BY ELENI MATECHOU, RACHEL S. MCCREA1, BYRON J. T. MORGAN,
DARRYN J. NASH AND RICHARD A. GRIFFITHS

University of Kent

Individuals of protected species, such as amphibians and reptiles, often
need to be removed from sites before development commences. Usually, the
population is considered to be closed. All individuals are assumed to (i) be
present and available for detection at the start of the study period and (ii) remain
at the site until the end of the study, unless they are detected. However,
the assumption of population closure is not always valid. We present
new removal models which allow for population renewal through birth and/or
immigration, and population depletion through sampling as well as through
death/emigration. When appropriate, productivity may be estimated and a
Bayesian approach allows the estimation of the probability of total population
depletion. We demonstrate the performance of the models using data on
common lizards, Zootoca vivipara, and great crested newts, Triturus cristatus.

Read the full paper here https://kar.kent.ac.uk/55734/

Standard