This page contains links to freely available software I have (co-)authored. If you have trouble downloading or using any of it, please email me.

  • Distance sampling
  • WinBUGS code...
    • ... for simulating and fitting spatial capture-recapture data [zip file]
      See Marques et al. (In press - Ecology comment, in refs). (Zip file contains all of the paper's supplementary material.)
    • ...for fitting simple state-space models of population dynamics to count data, plus other WinBUGS code by coauthors for fitting various models to capture-recapture data. [zip file (in Eprints archive)]
      See Giminez et al. (2008) [abstract and manuscript (in Eprints archive)].
  • Particle filtering (aka Sequential Importance Sampling, SIS) code for seal models
    • sealpf28
      C code with R helper files and data to implement the particle filtering algorithms used to fit Bayesian population dynamics models of British grey seals to pup production data. This is the version used to produce the results in Thomas et al. (2019).
      [zip file]
      See Thomas (2019) in refs.
    • sealpf28 (older version)
      Same C code, but different R helper files used to produce the results in Thomas (2016).
      [zip file]
      See Thomas (2016) Special Committee on Seals (SCOS) briefing paper in refs.
    • sealpf18
      C code with R helper files to implement an earlier version of the same model, published in Newman et al. (2009).
      [zip file]
      See Newman et al. (2009) Biometrics in refs
    • sis.seal
      SPlus code to implement an even earlier version of the same model. [3 ASCII files (in Eprints archive)]
      See Thomas et al. (2005) Australian and New Zealand Journal of Statistics [abstract and reprint (in Eprints archive)].
    • S3sisAPF - by Phil Harrison
      R code to implement a similar model. [zip file]
      See Harrison et al. (2006) Journal of Animal Ecology (in refs).
  • Deepwater Horizon cetacean population simulations
    R code and associated data files to reproduce the population simulations in Schwacke et al. 2022, Thomas et al. 2022 and Marques et al. 2023.
    [R markdown files (in Github repository curated by Tiago Marques)]
  • dose-response
    R code to reproduce the numerical example and figures in Tyack and Thomas (2019).
    [R file]
  • population-impact
    R code to simulate the population impact of cumulative anthropogenic stressors on wildlife populations (operating via prey reduction).
    [R code and data files (in Github archive)]
    See Williams et al. (2016) Marine Policy (in refs).
  • RTrend
    R code to estimate power to detect linear and log-linear trends. [zip file]
    Used to generate Figure 5.6 of Thomas, Burnham and Buckland (2004) Advanced Distance Sampling (in refs).
    SAS Macros that estimate power and confidence intervals for simple linear regression. [ASCII file (in Eprints archive)]
    See Thomas (1997) Conservation Biology [abstract and reprint (in Eprints archive)].
    SAS programs for power analysis of the Wilcoxon signed rank test on binary data using Monte-Carlo simulations. [zip file]
    See Thomas and Juanes (1996) Animal Behaviour (in refs).