reading_list.md

title	author	layout
Reading list	David L Miller	index

Reading list

Here is a list of extra reading that may be interesting and provide further insight into particular topics. This is by no means a complete bibliography and we welcome any additions!

Key links:

• Distance sampling bibliography maintained by Tiago Marques, Eric Rexstad and David L Miller.
• Distance software examples examples of R packages developed at CREEM.
• DenMod wiki for frequently asked questions and more

Overall

Canonical books and papers:

• Distance sampling:
  • Buckland, S. T., Anderson, D. R., Burnham, K. P., Borchers, D. L., & Thomas, L. (2001). Introduction to Distance Sampling. Oxford University Press, Oxford, UK.
  • Buckland, S. T., Rexstad, E. A., Marques, T. A., & Oedekoven, C. S. (2015). Distance Sampling: Methods and Applications. Springer International Publishing.
    • Available for around £20 if your library has "Springer Link" access, look for "MyCopy".
• Density surface models
  • Hedley, S. L., & Buckland, S. T. (2004). Spatial models for line transect sampling. Journal of Agricultural, Biological, and Environmental Statistics, 9(2), 181–199.
  • Miller, D. L., Burt, M. L., Rexstad, E. A., & Thomas, L. (2013). Spatial models for distance sampling data: recent developments and future directions. Methods in Ecology and Evolution, 4(11), 1001–1010.
• Generalized additive models
  • Wood, S. (2006, 1st edition; 2017, 2nd edition). Generalized Additive Models. CRC Press.

The sperm whale data

Estimation of sperm whale abundance in the North Atlantic by NOAA:

• Analysis of 2004 surveys, plus a 1998 survey.
• Results from 2011 survey (currently used for management purposes to set things like PBR, the number of sperm whales that can be killed) and details of that methodology.
• Data were a subset of those used in:
• Roberts, J. J., Best, B. D., Mannocci, L., Fujioka, E., Halpin, P. N., Palka, D. L., Garrison, L. P., Mullin, K. D., Cole, T. V. N., Khan, C. B., McLellan, W. A., Pabst, D. A., & Lockhart, G. G. (2016). Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico. Scientific Reports, 6(1). https://doi.org/10.1038/srep22615
• Online appendix with all analyses

Introduction to distance sampling

Field methods, survey design etc

• Buckland et al (2015) chapters 2 & 4
• Strindberg, S., & Buckland, S. T. (2004). Zigzag survey designs in line transect sampling. Journal of Agricultural, Biological, and Environmental Statistics, 9(4), 443–461. http://doi.org/10.1198/108571104X15601
• Thomas, L., & Williams, R. (2007). Designing line transect surveys for complex survey regions. Journal of Cetacean Research and Management 9(1):1–13.
• Camphuysen, C.J., Fox, A.D., Leopold, M., Petersen, I.K., 2004. Towards standardized seabirds at sea census techniques in connection with environmental impact assessments for offshore wind farms. In: UK COWRIE 1 Report. Royal Netherlands Institute for Sea Research, Texel, Netherlands.

• Small boat work for cetaceans -Animal Counting Toolkit : a practical guide to small-boat surveys for estimating abundance of coastal marine mammals
  • Design and field methods for sighting surveys of cetaceans in coastal and riverine habitats
  • A Suite of Field Manuals for Marine Sampling to Monitor Australian Waters

Other stuff

• Covariates in the detection function
  • Marques, T. A., Thomas, L., Fancy, S. G., & Buckland, S. T. (2007). Improving estimates of bird density using multiple-covariate distance sampling. The Auk, 124(4).
• Movement in distance sampling:
  • Glennie, R., Buckland, S. T., & Thomas, L. (2015). The Effect of Animal Movement on Line Transect Estimates of Abundance. PLoS ONE, 10(3), e0121333–15.
• Overlapping transects
  • Buckland, ST (2006), Point transect surveys for songbirds: robust methodologies The Auk, vol. 123, no. 2, pp. 345-357.
• Distance measurement error:
  • Marques, T. A. (2004). Predicting and correcting bias caused by measurement error in line transect sampling using multiplicative error models. Biometrics, 60(3), 757–763.
• Camera traps
  • Howe, E. J., Buckland, S. T., Després‐Einspenner, M. and Kühl, H. S. (2017), Distance sampling with camera traps. Methods in Ecology and Evolution, 8: 1558-1565.
• Availability by simple correction
  • Winiarski, K. J., Burt, M. L., Rexstad, E., Miller, D. L., Trocki, C. L., Paton, P. W. C., & McWilliams, S. R. (2014). Integrating aerial and ship surveys of marine birds into a combined density surface model: A case study of wintering Common Loons. The Condor, 116(2), 149–161.

Response distributions

• Papers about using the Tweedie distribution
  • Shono, H. (2008). Application of the Tweedie distribution to zero-catch data in CPUE analysis. Fisheries Research, 93(1-2), 154–162. http://doi.org/10.1016/j.fishres.2008.03.006
  • Foster, S. D., & Bravington, M. V. (2012). A Poisson–Gamma model for analysis of ecological non-negative continuous data. Environmental and Ecological Statistics, 20(4), 533–552. http://doi.org/10.1007/s10651-012-0233-0

• Comparison of negative binomial and quasi-Poisson
  • Ver Hoef, J. M., & Boveng, P. L. (2007). Quasi-Poisson vs. negative binomial regression: how should we model overdispersed count data? Ecology, 88(11), 2766–2772. http://doi.org/10.2307/25590942

Smooths

• Within mgcv the ?smooth.terms manual page lists all spline bases available in mgcv (and therefore dsm)
• Paper on ts/shrinkage smoothers
  • Marra, G., & Wood, S. N. (2011). Practical variable selection for generalized additive models. Computational Statistics & Data Analysis, 55(7), 2372–2387. https://doi.org/10.1016/j.csda.2011.02.004
• Tensor product space-time model of Hawaiian songbirds
  • Camp, RJ, DL Miller, L Thomas, ST Buckland and SJ Kendall (2020). Using density surface models to estimate spatio-temporal changes in population densities and trend. Ecography http://dx.doi.org/10.1111/ecog.04859
• Soap film smoothing
  • Wood, S. N., Bravington, M. V., & Hedley, S. L. (2008). Soap film smoothing. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 70(5), 931–955. https://doi.org/10.1111/j.1467-9868.2008.00665.x
  • Scripts to help in setting-up a soap film

Selecting basis size

• Pya, N., & Wood, S. N. (2016). A note on basis dimension selection in generalized additive modelling. ArXiv Preprint ArXiv:1602.06696.
• Practical advice in mgcv ?choose.k manual page

Checking and validation

• Randomised quantile residuals
  • Dunn, P. K., & Smyth, G. K. (1996). Randomized quantile residuals. Journal of Computational and Graphical Statistics, 5(3), 236–244.
• Spatial model checking plots using deviance residuals (preprint)
  • Marra, G., Miller, D. L., & Zanin, L. (2011). Modelling the spatiotemporal distribution of the incidence of resident foreign population. Statistica Neerlandica, 66(2), 133–160.
• Validating spatial models
  • Assessing transferability of ecological models: an underappreciated aspect of statistical validation

Covariates

• Using in situ vs. remotely sensed covariates
  • Becker, E. A., Forney, K. A., Ferguson, M. C., Foley, D. G., Smith, R. C., Barlow, J., & Redfern, J. V. (2010). Comparing California Current cetacean–habitat models developed using in situ and remotely sensed sea surface temperature data. Marine Ecology Progress Series, 413, 163–183.
• Can we trust covariates from GIS?
  • Stoklosa, J., Daly, C., Foster, S. D., Ashcroft, M. B., & Warton, D. I. (2015). A climate of uncertainty: Accounting for error in climate variables for species distribution models. Methods in Ecology and Evolution, 6(4), 412–423.

Multiple smooths and model selection

• Paper about shrinkage selection in GAMs
  • Marra, G., & Wood, S. N. (2011). Practical variable selection for generalized additive models. Computational Statistics and Data Analysis, 55(7), 2372–2387.
• Approximate $p$-values:
  • Marra, G., & Wood, S. N. (2012). Coverage properties of confidence intervals for generalized additive model components. Scandinavian Journal of Statistics, 39(1), 53–74.

• Example sensitivity analysis for DSMs, appendix of this paper (preprint available on DLM's website
  • Winiarski, K. J., Burt, M. L., Rexstad, E., Miller, D. L., Trocki, C. L., Paton, P. W. C., & McWilliams, S. R. (2014). Integrating aerial and ship surveys of marine birds into a combined density surface model: A case study of wintering Common Loons. The Condor, 116(2), 149–161.

Variance

• Propagating variance from the detection function
  • Williams, R., Hedley, S. L., Branch, T. A., Bravington, M. V., Zerbini, A. N., & Findlay, K. P. (2011). Chilean blue whales as a case study to illustrate methods to estimate abundance and evaluate conservation status of rare species Conservation Biology, 25(3), 526–535.
  • Appendix B of Miller et al (2013) available on DLM's website (more technical)
  • Bravington, M. V., Miller, D. L. and Hedley, S. L. Reliable variance propagation for spatial density surface models available on arXiv

Extrapolation

• dsmextra package
  • Package website
  • Bouchet, PJ, Miller, DL, Roberts, JJ, Mannocci, L, Harris, CM, Thomas, L. dsmextra: Extrapolation assessment tools for density surface models. Methods Ecol Evol. 2020; 00: 1– 6. https://doi.org/10.1111/2041-210X.13469
  • Bouchet, PJ, Miller, DL, Roberts, J, Mannocci, L, Harris, CM & Thomas, L (2019) From here and now to there and then: practical recommendations for extrapolating cetacean density surface models to novel conditions. CREEM Technical Report, no. 2019-1, University of St Andrews, 59 p.
• Transferability
  • Yates, K. L., Bouchet, P. J., Caley, M. J., Mengersen, K., Randin, C. F., Parnell, S., Fielding, A. H., Bamford, A. J., Ban, S., Barbosa, A. M., Dormann, C. F., Elith, J., Embling, C. B., Ervin, G. N., Fisher, R., Gould, S., Graf, R. F., Gregr, E. J., Halpin, P. N., … Sequeira, A. M. M. (2018). Outstanding Challenges in the Transferability of Ecological Models. Trends in Ecology & Evolution, 33(10), 790–802.
  • Sequeira, A. M. M., Bouchet, P. J., Yates, K. L., Mengersen, K., & Caley, M. J. (2018). Transferring biodiversity models for conservation: Opportunities and challenges. Methods in Ecology and Evolution, 9(5), 1250–1264.

Practical advice

• Paper looking at segment size and covariate resolution (also paper with a separate group size model)
  • Redfern, J. V., Barlow, J., Ballance, L. T., Gerrodette, T., & Becker, E. A. (2008). Absence of scale dependence in dolphin–habitat models for the eastern tropical Pacific Ocean. Marine Ecology Progress Series, 363, 1–14.