Ben Stevenson
Senior Lecturer

Department of Statistics
University of Auckland
Private Bag 92019
Auckland 1142
New Zealand

Office: Room 303.326
E-mail: ben.stevenson@auckland.ac.nz
Phone: +64 9 923 8474



Research interests
  • Ecological statistics
  • Capture-recapture methods
  • Spatial statistics
  • Statistical computing


Biography

I am a Senior Lecturer in the Department of Statistics at the University of Auckland, New Zealand.

I completed BSc (Hons) and MSc degrees at the University of Auckland before moving to the University of St Andrews, United Kingdom, where I graduated with a PhD in 2016. I remained at St Andrews for a twelve-month research fellowship, joining this department in January 2017.

I develop statistical methods and software to estimate ecological parameters of interest, usually animal abundance or density. My recent work has met statistical challenges that arise when instruments like microphones, video-cameras, and drones are deployed to detect animals on wildlife surveys. New technologies have the potential to collect mountains of data at a low cost, but complicate estimation of ecological parameters because less information is encoded within each detection. For example, we can easily identify an individual on a live-trapping survey via a securely fixed ID tag, but perhaps cannot do so from a fleeting glimpse in a video. Most of my current work involves capture-recapture or spatial capture-recapture models.

I have additional research interests in spatial statistics, statistical computing, and applied statistics in general. My work in these areas sometimes overlaps with ecology, but has also led to publications in the fields of medicine and veterinary science. To get more of a feel for my research, see the section on my current projects below.

My CV is available here.



Research grants

  • co-PI, Marsden Standard Grant, NZ$712k, 2024–2027.
    Fast statistical methods for enigmatic sensor data.
    With Rachel Fewster, Jesse Goodman, Martin Hazelton (co-PIs), and Andrew Robinson (AI).

  • PI, Marsden Fast-Start Grant, NZ$300k, 2020–2024.
    Estimating animal population size in an unobservable spatial obstacle course.
    With Rachel Fewster and David Borchers (AIs).

  • AI, Marsden Grant, NZ$680k, 2018–2021.
    Cells and whistles: Supercharging our biodiversity monitoring toolkit using genetic and acoustic records.
    With Rachel Fewster (PI), David Borchers, and Stephen Marsland (AIs).



Peer-reviewed publications

My Google Scholar citations page can be found here.
  • van Dam-Bates, P., Papathomas, M., Stevenson, B. C., Fewster, R. M., Turek, D., Stewart, F. E. C., and Borchers, D. L. (in press) A flexible framework for spatial capture-recapture with unknown identities. Biometrics.

  • Durbach, I., Chopara, R., Borchers, D. L., Phillip, R., Sharma, K., and Stevenson, B. C. (in press) That's not the Mona Lisa! How to interpret spatial capture-recpature density surface estimates. Biometrics.

  • Martin, L. H., Hepinstall-Cymerman, J. H., Chandler, R. B., Cooper, R. J., Parrish, M. C., Hao, L., and Stevenson, B. C. (in press) Estimating owl population density using acoustic spatial capture-recapture. Journal of Raptor Research.

  • McGrath, S., Liu, J., Stevenson, B. C., and Behie, A. M. (in press) Density and population size estimates of the endangered northern yellow-cheeked crested gibbon Nomascus annamensis in selectively logged Veun Sai-Siem Pang National Park in Cambodia using acoustic spatial capture-recapture methods. PLoS ONE.

  • Stevenson, B. C., Fewster, R. M., and Sharma, K. (2022) Spatial correlation structures for detections of individuals in spatial capture-recapture models. Biometrics, 78(3), 963–973. (link)

  • Setyawan, E., Stevenson, B. C., Erdmann, M. V., Hasan, A. W., Sianipar, A. B., Mofu, I., Putra, M. I. H., Izuan, M., Ambafen, O., Fewster, R. M., Aldridge-Sutton, R., Mambrasar, R., and Constantine, R. (2022) Population estimates of photo-identified individuals using a modified POPAN model reveal that Raja Ampat's reef manta rays are thriving. Frontiers in Marine Science, 9(1), 1014791. (link)

  • Borchers, D. L., Nightingale, P., Stevenson, B. C., and Fewster, R. M. (2022) A latent capture history model for digital aerial surveys. Biometrics, 78(1), 274–285. (link)

  • Setyawan, E., Erdmann, M. V., Mambrasar, R., Hasan, A., Sianipar, A., Constantine, R., Stevenson, B. C., and Jaine, F. R. A. (2022) Residency and use of an important nursery habitat, Raja Ampat's Wayag Lagoon, by juvenile reef manta rays (Mobula alfredi). Frontiers in Marine Science, 9(1), 815094. (link)

  • Setyawan, E., Stevenson, B. C., Izuan, M., Constantine, R., and Erdmann, M. V. (2022) How big is that manta ray? A novel and non-invasive method for measuring reef manta rays using small drones. Drones, 6(3), 63. (link)

  • Baron, H. R., Stevenson, B. C., and Phalen, D. N. (2021) Comparison of in-clinic diagnostic testing methods for Macrorhabdus ornithogaster. Journal of Avian Medicine and Surgery, 35(1), 37–44. (link)

  • Stevenson, B. C., van Dam-Bates, P., Young, C. K. Y., and Measey, J. (2021) A spatial capture-recapture model to estimate call rate and population density from passive acoustic surveys. Methods in Ecology and Evolution, 12(3), 432–442. (link)

  • Samaniego, A., Griffiths, R., Gronwald, M., Holmes, N. D., Oppel, S., Stevenson, B. C., and Russell, J. C. (2020) Risks posed by rat reproduction and diet to eradications on tropical islands. Biological Invasions, 22(4), 1365–1378. (link)

  • Baron, H. R., Stevenson, B. C., and Phalen, D. N. (2020) Inconsistent efficacy of water soluble Amphotericin B for the treatment of Macrorhabdus ornithogaster in a budgerigar (Melopsittacus undulatus) aviary. Australian Veterinary Journal, 98(7), 333–337. (link)

  • Stevenson, B. C., Borchers, D. L., and Fewster, R. M. (2019) Cluster capture-recapture to account for identification uncertainty on aerial surveys of animal populations. Biometrics, 75(1), 326–336. (link)

  • Baron, H. R., Leung, K. C. L., Stevenson, B. C., Sabater Gonzalez, M., and Phalen, D. N. (2019) Evidence of Amphotericin B resistance in Macrorhabdus ornithogaster in Australian cage-birds. Medical Mycology, 57(4), 421–428. (link)

  • Jones-Todd, C. M., Caie, P., Illian, J. B., Stevenson, B. C., Savage, A., Harrison, D. J., and Bown, G. L. (2019) Identifying prognostic structural features in tissue sections of colon cancer patients using point pattern analysis. Statistics in Medicine, 38(8), 1421–1441. (link)

  • Measey, G. J., Stevenson, B. C., Scott, T., Altwegg, R., and Borchers, D. L. (2017) Counting chirps: Acoustic monitoring of cryptic frogs. Journal of Applied Ecology, 54(3), 894–902. (link)

  • Kidney, D., Rawson, B. M., Borchers, D. L., Stevenson, B. C., Thomas, L., and Marques, T. A. (2016) An efficient acoustic density estimation method with human detectors applied to gibbons in Cambodia. PLoS ONE, 11(5), e0155066. (link)

  • Fewster, R. M., Stevenson, B. C., and Borchers, D. L. (2016) Trace-contrast models for capture-recapture without capture histories. Statistical Science, 31(2), 245–258. (link)

  • Borchers, D. L., Stevenson, B. C., Kidney, D., Thomas, L., and Marques, T. A. (2015) A unifying model for capture-recapture and distance sampling surveys of wildlife populations. Journal of the American Statistical Association, 110(509), 195–204. (link)

  • Stevenson, B. C., Borchers, D. L., Altwegg, R., Swift, R. J., Gillespie, D. M., and Measey, G. J. (2015) A general framework for animal density estimation from acoustic detections across a fixed microphone array. Methods in Ecology and Evolution, 6(1), 38–48. (link)

  • Stevenson, B. C., and Millar, R. B. (2013) Promising the moon? Evaluation of indigenous and lunar fishing calendars using semiparametric generalized mixed models of recreational catch data. Environmental and Ecological Statistics, 20(4), 591–608. (link)




Current students

PhD:
  • Rishika Chopara
    Goodness-of-fit for spatial capture-recapture models
    Cosupervisor: Rachel Fewster

  • Pei (Zoe) Luo
    Two-phase subsampling designs for DNA sequencing, with an application to the relatedness in endangered species
    Cosupervisor: Thomas Lumley

MSc/MProfStuds:
  • Melissa Bather
    Fitting acoustic spatial capture-recapture models in acre

  • Yaotian Shi
    A comparison between spatial capture-recapture and occupancy models for passive acoustic surveys

BSc (Hons):
  • Zhitian (Rose) Wang
    Comparing methods to estimate call rate and animal density from passive acoustic surveys
    Cosupervisor: David Chan

Click here for a list of available BSc (Hons) and MSc projects. This document may include some projects that are not yet on the list on the department's webpage. Please e-mail me if you are interested.



Current projects

Here are outlines of some current research projects I am working on, listed roughly in order along a continuum from statistics research to ecology research.

Goodness-of-fit, with applications to capture-recapture

Rishika Chopara, a PhD student cosupervised by myself and Rachel Fewster, is working on various aspects of goodness-of-fit. Often a model's deviance is compared to a chi-squared distribution to assess how well it fits the data. However, in many cases the chi-squared distribution is not a close approximation to the distribution of the deviance under the null hypothesis that the model is correct. Rishika is developing better approximations for the distribution of the deviance, which will be particularly useful for assessing fit of capture-recapture models.

Closed-form likelihoods for spatial capture-recapture

Jing Liu is a Research Fellow working with myself and Rachel Fewster on closed-form likelihoods for spatial capture-recapture. These models treat animals' activity centres as latent variables, which are usually dealt with either by sampling them by MCMC (for Bayesian models) or numerically approximating integrals (for maximum-likelihood models). Jing has been working on exact computations for model likelihoods, which entirely avoids having to sample or approximate.

Density surfaces in spatial capture-recapture

Previously, led by Andrew Seaton and with David Borchers, Gaussian fields were used to fit smooth functions to model spatial variation in animal density from spatial capture-recapture data. This work appeared in Andrew's PhD thesis. Currently, with Charlotte Jones-Todd, I am working on methods to fit similar models that are more computationally efficient.

Accounting for uncertain identification in wildlife surveys

In a project led by Paul van Dam-Bates, and with David Borchers, Michail Papathomas, and Rachel Fewster (among others), we are developing new capture-recapture methods to account for uncertain identification of detected animals.

Linear mixed-effects models under two-phase sampling

Zoe Luo is a PhD student I cosupervise with Thomas Lumley. Among other things, she has developed methods to fit linear mixed-effects models under two-phase sampling, with an application to genetic data of the kākāpō, a (very) endangered New Zealand parrot species.

Method development for acoustic spatial capture-recapture

David Chan, whose PhD I supervised, has been developing new spatial capture-recapture methods for acoustic surveys. One such method is tailored to calling surveys of gibbons, and accounts for movement of gibbon groups from one morning to the next.

Software for acoustic spatial capture-recapture

During my PhD I spent a lot of time writing an R package, ascr, which provides functions to fit acoustic spatial capture-recapture models. Along with Lingyu Hao, Melissa Bather, and other former students, I am creating a new package acre, which will be both more user-friendly (especially when modelling spatial effects) and more flexible in terms of the types of model available to fit.

Applications of acoustic spatial capture-recapture

I have recently been collaborating with Lily Martin and her advisors at the University of Georgia, USA. Lily has been conducting passive acoustic surveys of various owl species, and we are using spatial capture-recapture methods to estimate population densities.

In separate projects with Sarah McGrath and Milou Groenenberg, Jing Liu and myself are fitting acoustic spatial capture-recapture models to estimate density and distribution of gibbon populations in national parks situated in Cambodia and Vietnam.

With Cornelia Oedekoven, David Borchers, and Tarin Eccleston, I am creating software and training materials to help make spatial capture-recapture methods more accessible to researchers conducting acoustic surveys of primates.

Raja Ampat's manta rays

Edy Setyawan is a former PhD student who I cosupervised with Rochelle Constantine, Mark Erdmann, and Fabrice Jaine. His research is focused on manta ray populations in Raja Ampat, Indonesia. Edy is currently finishing off some work on spatial connectivity of Raja Ampat's manta rays. We also have an ongoing project on developing statistical methods to account for measurement error in morphometric data collected by drones.

Lunar cycle effects on fishing catch rates in Corsican fisheries

The first paper I ever published was about estimating relationships between the lunar cycle and catch rates of fish in New Zealand. Marina Luccioni has collated data from commercial fishing operations in Corsica and is fitting generalised linear mixed-effects models to investigate similar relationships. Preliminary results suggest Corsican fish might be even more responsive to lunar illumination than New Zealand's snapper!



Links


Software

The R package ascr fits a range of acoustic spatial capture-recapture models. Find its homepage here.

The R package palm fits various point processes via maximisation of the Palm likelihood, and is available on CRAN. Find its homepage here.

Other software projects can be found on my GitHub page; see the link above.