Theo Pepler

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Research

Most of my scientific research work is applied in nature, using statistical and simulation methods to investigate biological questions.

On the methodological side, I am most interested in multivariate analysis, spectral decomposition in particular, and nonparametric techniques.

FUNDING

PUBLICATIONS

  1. Assessing Transition Cow Management in Dairy Cows for Improved Health, Milk Production, Pregnancy and Culling Outcomes
    J. G. Cook, P. T. Pepler, L. Viora, D. Hill
    Journal of Dairy Science (accepted)
  2. Biomarker and proteome analysis of milk from dairy cows with clinical mastitis: determining the effect of different bacterial pathogens on the response to infection
    E. L. O'Reilly, L. Viora, F. Malcata, P. T. Pepler, R. Zadoks, N. Brady, H. Q. Hanh, M. McLaughlin, A. Horvatic, A. Gelemanovic, J. Kules, V. Mrljak, P. D. Eckersall
    Research in Veterinary Science (2024), 172: 105240
  3. Assessing teat canal morphology in the dry period and during lactation by high-resolution ultrasound
    M. Berteau, P. T. Pepler, A. Broadhurst, G. Hammond, R. N. Zadoks, L. Viora
    Journal of Dairy Research (2024), Early online publication
  4. Comparison of three reproductive management strategies for lactating dairy cows using combination of estrus detection or ovulation synchronization and Fixed-Timed Artificial Insemination
    R. Vazquez, K. Denholm, P. T. Pepler, J. Cook, P. Pinho, F. Randi, L. Viora
    Animal Reproduction Science (2023), 257: 107331
  5. Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland
    A. Akhmetova, J. Guerrero, P. McAdam, L. C. M. Salvador, J. Crispell, J. Lavery, E. Presho, R. R. Kao, R. Biek, F. Menzies, N. Trimble, R. Harwood, P. T. Pepler, K. Oravcova, J. Graham, R. Skuce, L. du Plessis, S. Thompson, L. Wright, A. W. Byrne, A. R. Allen
    Microbial Genomics (2023), 9(5): mgen001023
  6. Evaluation of a novel infrared thermography projection to assess udder health in primigravid dairy heifers
    P. B. A. Simões, L. Viora, P. T. Pepler, T. Geraghty, D. J. McCafferty, R. N. Zadoks
    Animals (2022), 12(23): 3410
  7. Association of days in close up, gestation length and rumination around time of calving with disease and pregnancy outcomes in dairy cows
    J. G. Cook, P. T. Pepler, L. Viora
    Journal of Dairy Science (2021), 104(8): 9093-9105
  8. Laboratory-based evaluation of a simplified point-of-care test intended to support treatment decisions in non-severe bovine clinical mastitis
    F. B. Malcata, L. Viora, P. T. Pepler, R. N. Zadoks
    Journal of Dairy Research (2021), 88(2): 170-175
  9. Multi-species temporal network of livestock movements for disease spread
    A-S. Ruget, G. Rossi, P. T. Pepler, G. Beaunée, C. J. Banks, J. Enright, R. R. Kao
    Applied Network Science (2021), 6(15)
  10. Point-of-care tests for bovine clinical mastitis: What do we have and what do we need?
    F. B. Malcata, P. T. Pepler, E. O'Reilly, N. Brady, P. D. Eckersall, R. N. Zadoks, L. Viora
    Journal of Dairy Research (2020), 87(S1): 60-66
  11. Regularized covariance matrix estimation under the common principal components model
    P. T. Pepler, D. W. Uys, D. G. Nel
    Communications in Statistics - Simulation and Computation (2018), 47(3): 631-643
  12. Harbin: A quantitation PCR analysis tool
    R. Bester, P. T. Pepler, D. J. Aldrich, H. J. Maree
    Biotechnology Letters (2017), 39(1): 171-178
  13. Discriminant analysis under the common principal components model
    P. T. Pepler, D. W. Uys, D. G. Nel
    Communications in Statistics - Simulation and Computation (2017), 46(6): 4812-4827
  14. A comparison of some methods for the selection of a common eigenvector model for the covariance matrices of two groups
    P. T. Pepler, D. W. Uys, D. G. Nel
    Communications in Statistics - Simulation and Computation (2016), 45(8): 2917-2936
  15. Relative quantitation goes viral: An RT-qPCR assay to determine the concentration of a grapevine virus
    R. Bester, P. T. Pepler, J. T. Burger, H. J. Maree
    Journal of Virological Methods (2014), 210: 67-75
  16. An observational audit of pain scores post-orthopaedic surgery at a level two state hospital in Cape Town
    N. D. Hauser, R. A. Dyer, P. T. Pepler, D. A. Rolfe
    South African Journal of Anaesthesia and Analgesia (2014), 20(2): 110-116
  17. Predicting mortality and length-of-stay for neonatal admissions to private hospital neonatal intensive care units: A Southern African retrospective study
    P. T. Pepler, D. W. Uys, D. G. Nel
    African Health Sciences (2012), 12(2): 166-173

CONFERENCE PRESENTATIONS

Codebases, Pipelines, and Data
P. T. Pepler
EPIC IV Conference 2023, Edinburgh, United Kingdom, Oct 2023

Overview of EPIC AI work
T. Pepler, S. Mohr, K. Adam, G. Innocent
EPIC IV Conference 2023, Edinburgh, United Kingdom, Oct 2023

Exploring the Potential of a Novel Biomarker Panel in Selective Dry Cow Therapy
L. Viora, T. Pepler, E. L. O'Reilly, N. Brady, R. N. Zadoks, P. D. Eckersall
European Buiatrics Congress, Berlin, Germany, Aug 2023

Selective dry cow therapy: the potential role of a novel biomarker panel
L. Viora, T. Pepler, E. L. O'Reilly, N. Brady, R. N. Zadoks, P. D. Eckersall
World Buiatrics Congress, Madrid, Spain, Sep 2022

Animal Movement Analysis
P. T. Pepler
EPIC III Conference 2022, Edinburgh, United Kingdom, Mar 2022

Biomarkers for mastitis diagnostics
E. L. O'Reilly, L. Viora, N. Brady, F. Malcata, A. Gelemanovic, T. Pepler, R. N. Zadoks, P. D. Eckersall
Next Generation Dairying Workshop 2021, Edinburgh, United Kingdom, Nov 2021

Comparison of two point-of-care tests to support treatment decisions in non-severe bovine clinical mastitis
F. B. Malcata, L. Viora, P. T. Pepler, R. N. Zadoks
British Mastitis Conference 2019, Worcester, United Kingdom, Nov 2019

Grouping Scottish Agricultural Premises Based on Estimated Risk for Initiating Epidemic Veterinary Disease Outbreaks
P. T. Pepler, R. R. Kao
EPIC III Conference 2019, Edinburgh, United Kingdom, Sep 2019 [Poster]

New Biomarkers for Selective Dry Cow Therapy
L. Viora, E. O'Reilly, N. Brady, T. Pepler, R. Zadoks, D. Eckersall
European Bovine Congress 2019, 's-Hertogenbosch, The Netherlands, Sep 2019

Haptoglobin and α-lactalbumin biomarkers for selective dry cow therapy?
E. L. O'Reilly, L. Viora, N. Brady, T. Pepler, R. N. Zadoks, P. D. Eckersall
IDF Mastitis Conference 2019, Copenhagen, Denmark, May 2019 [Poster]

Combining Cattle Movement Data with Stochastic Epidemiological Models to Identify Key Premises for Disease Spread
P. T. Pepler, R. R. Kao
7th Channel Network conference of the International Biometric Society, Rothamsted Research, United Kingdom, Jul 2019 [Slides]

Land Use and Disease Risk
L. Gilbert, P. Bessell, I. Hutchinson, H. Auty, T. Pepler, L. Boden
Land-Use Conference, Edinburgh, United Kingdom, Nov 2018 [Poster]

A spatial network model of deer populations in Great Britain to inform surveillance and control strategies for Chronic Wasting Disease
P. T. Pepler
The 29th International Biometric Conference, Barcelona, Spain, Jul 2018 [Slides]

Key premises for disease transmission in movement networks
P. T. Pepler, R. R. Kao
EPIC III Conference 2017, Edinburgh, United Kingdom, Sep 2017 [Video]

A common singular spectrum analysis of bovine tuberculosis incidence in Great Britain
P. T. Pepler, R. R. Kao
Royal Statistical Society (RSS) 2016 International Conference, Manchester, United Kingdom, Sep 2016 [Slides]

Development of alert systems: CUSUM control charts to identify unusual bovine TB outbreaks in Scottish cattle herds
P. T. Pepler, R. R. Kao
Annual Meeting of the Society for Veterinary Epidemiology and Preventive Medicine (SVEPM), Elsinore, Denmark, Mar 2016 [Poster]

On the application of the CPC model in discriminant analysis
P. T. Pepler
The 56th annual conference of the South African Statistical Association (SASA), Grahamstown, South Africa, Oct 2014 [Slides]

The regularised CPC covariance matrix estimator and its application in discriminant analysis
P. T. Pepler
The 27th International Biometric Conference, Florence, Italy, Jul 2014 [Poster]

Efficiency of the CPC estimator in modelling the covariance structures of several populations
P. T. Pepler
The 55th annual conference of the South African Statistical Association (SASA), Polokwane, South Africa, Nov 2013 [Slides]

Comparison of some methods for the identification of common eigenvectors
P. T. Pepler
The 54th annual conference of the South African Statistical Association (SASA), Port Elizabeth, South Africa, Nov 2012 [Slides]

On the identification of common principal components
P. T. Pepler
8th World Congress in Probability and Statistics, Istanbul, Turkey, Jul 2012 [Slides]

On the application of common principal components in biplots
P. T. Pepler
The 53rd annual conference of the South African Statistical Association (SASA), Pretoria, South Africa, Nov 2011 [Slides]

SEMINARS AND OTHER TALKS

CWD Modelling in British Deer
Presentation at Scottish Veterinary Zoonoses Group Meeting, Moredun Research Institute, Scotland, Jun 2018

The SSA-cusum method for monitoring surveillance time series
Seminar at Epidemiology Research Unit, Scotland's Rural College (SRUC), Inverness, Scotland, Jun 2017

Making disease modelling results accessible to farmers
Presentation at Beef & Sheep Industry Interface Meeting, Perth, Scotland, Jan 2017

Applications of the Common Principal Component model: How borrowing information about multivariate data structure can be useful
Seminar at Computing Science and Mathematics, University of Stirling, Stirling, Scotland, Sep 2016 [Slides]

Common principal components
Seminar at the Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa, Sep 2014 [Slides]

Common principal components
Seminar at Department of Statistics and Actuarial Science, Stellenbosch University, Stellenbosch, South Africa, Aug 2011 [Slides]

VON Data Analysis: Interpretation of the statistics
Vermont Oxford Network (VON) Symposium, Somerset West, South Africa, Oct 2008 [Slides]

OTHER RESEARCH OUTPUT

Consistency of measures to identify key premises for disease outbreaks in Scottish cattle movement networks
P. T. Pepler, R. R. Kao
Policy brief to Scottish Government, Sep 2021

Links between Scottish cattle and sheep premises affect disease risk
A-S. Ruget, G. Rossi, P. T. Pepler, G. Beaunée, C. J. Banks, J. Enright, R. R. Kao
Research brief to Scottish Government, Sep 2021

Network Representation of Deer in Great Britain to Inform Surveillance and Control of Infectious Disease
P. T. Pepler, R. R. Kao
Policy brief to Scottish Government, Nov 2018

Investigation of spatial structure in British deer populations to inform surveillance and control of chronic wasting disease
P. T. Pepler, J. Matthiopoulos, S. Croft, R. J. Irvine, G. C. Smith, R. R. Kao
Research Report for Scottish Government, Jul 2018

Evaluation of the quantitative evidence-base to support the construction of surveillance models for Chronic Wasting Disease in British Deer
P. T. Pepler, R. R. Kao
DEFRA Evidence Project Final Report SE2024, Jul 2018

The Identification and Application of Common Principal Components
P. T. Pepler
PhD dissertation, Dec 2014 [Download]

Discovery Health Hospital Rating Index Version 3 Presentation: Medi-Clinic Response
P. T. Pepler
Technical report, Sep 2008

Discovery Health Hospital Rating Index Version 2: Medi-Clinic Response
P. T. Pepler
Technical report, Nov 2007

Discovery Health Hospital Rating Index Version 2: Medi-Clinic Report
P. T. Pepler
Technical report, Sep 2007

Detecting Active Effects in Unreplicated 2k Factorial Experiments: A Simulation Study
P. T. Pepler
Masters degree assignment, Dec 2006 [Download]