William J. Browne

University of Bristol | UB · Graduate School of Education

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting is vital to this process; it allows readers to assess the reliability of the findings and repeat or build upon the work of other researchers. The ARRIVE guidelines (Animal Research: Reporting In Vivo Experiments) were developed in 2010 to h...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

A first step when fitting multilevel models to continuous responses is to explore the degree of clustering in the data. Researchers fit variance-component models and then report the proportion of variation in the response that is due to systematic differences between clusters. Equally they report the response correlation between units within a clus...

Aggression in group-housed laboratory mice is a serious animal welfare concern. Further understanding of the causes of mouse aggression could have a significant impact on a large number of laboratory animals. The NC3Rs led a crowdsourcing project to collect data on the prevalence and potential triggers of aggression in laboratory mice. The crowdsou...

Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting are vital to this process; it allows readers to assess the reliability of the findings, and repeat or build upon the work of other researchers. The NC3Rs developed the ARRIVE guidelines in 2010 to help authors and journals identify the mini...

Reproducible science requires transparent reporting. The ARRIVE guidelines were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and rep...

The rapid global spread of artificial light at night is causing unprecedented disruption to ecosystems. In otherwise dark environments, street lights restrict the use of major flight routes by some bats, including the threatened lesser horseshoe bat Rhinolophus hipposideros, and may disrupt foraging. Using radio tracking, we examined the response o...

In 2010, the NC3Rs published the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines to improve the reporting of animal research. Despite considerable levels of support from the scientific community, the impact on the quality of reporting in animal research publications has been limited. This position paper highlights the strategy...

In this paper we consider the impact of both missing data and measurement errors on a longitudinal analysis of participation in higher education in Australia. We develop a general method for handling both discrete and continuous measurement errors that also allows for the incorporation of missing values and random effects in both binary and continu...

Aim To present a flexible model for repeated measures longitudinal growth data within individuals that allows trends over time to incorporate individual-specific random effects. These may reflect the timing of growth events and characterise within-individual variability which can be modelled as a function of age. Subjects and methods A Bayesian mo...

Obesity is considered the second most common health problem in pet cats in developed countries. This study used prospective data from a longitudinal study of pet cats (‘C.L.A.W.S.’, www.bristol.ac.uk/vetscience/claws) to identify early-life risk factors for feline overweight/obesity occurring at around two years of age. Data were collected via five...

R2MLwiN is a new package designed to run the multilevel modeling software program MLwiN from within the R environment. It allows for a large range of models to be specified which take account of a multilevel structure, including continuous, binary, proportion, count, ordinal and nominal responses for data structures which are nested, cross-classifi...

Highly trained observers can show near-optimal visual search strategies, similar to those of a Bayesian ideal observer. Based on two participants, Najemnik & Geisler (2005, 2008) demonstrate that optimal search can be identified with a stereotypical pattern of eye movements when searching for a target (short horizontal saccades and occasional jumps...

Importance of the dry period with respect to mastitis control is now well established although the precise interventions that reduce the risk of acquiring intramammary infections during this time are not clearly understood. There are very few intervention studies that have measured the clinical efficacy of specific mastitis interventions within a c...

The aim of the current study was to investigate the social relationships between individual sheep, and factors that influence this, through the novel application of the statistical multiple membership multiple classification (MMMC) model. In study one 49 ewes (ranging between 1 and 8 years old) were fitted with data loggers, which recorded when pai...

Multilevel models, also often known as random effects or mixed models, are now a well-established statistical technique with applications in many disciplinary areas, most notably the social and medical sciences. In this article, we provide a basic introduction to these models and discuss extensions that deal with data structures of increasing compl...

The use of statistical modelling by researchers in all disciplines is growing in prominence. There is an increase in the availability and complexity of data sources, and an increase in the sophistication of statistical methods that can be used. For the novice practitioner of statistical modelling it can seem like you are stuck at the bottom of a mo...

We develop a random effects discrete choice model for the analysis of households' choice of neighbourhood over time. The model is parameterised in a way that exploits longitudinal data to separate the in uence of neighbourhood characteristics on the decision to move out of the current area ("push" effects) and on the choice of one destination over...

Multilevel models, also often known as random effects or mixed models, are now a well-established statistical technique with applications in many disciplinary areas, most notably the social and medical sciences. In this article, we provide a basic introduction to these models and discuss extensions that deal with data structures of increasing compl...

We present a technique to capture retrospective provenance across a number of tools in a statistical software suite. Our goal is to facilitate portability of processes between the tools to enhance usability and to support reproducibility. We describe an intermediate notation to aid runtime capture of provenance and demonstrate conversion to an exec...

[This corrects the article DOI: 10.1371/journal.pone.0146782.].

Bats frequently roost in historic churches, and these colonies are of considerable conservation value. Inside churches, bat droppings and urine can cause damage to the historic fabric of the building and to items of cultural significance. In extreme cases, large quantities of droppings can restrict the use of a church for worship and/or other commu...

The main aim of this study was to replicate methodology used to estimate the size of the UK pet cat and dog populations in 2006 and the proportion of households owning cats/dogs in 2007, to produce updated data to compare trends in ownership and population sizes. A cross-sectional study design was used to collect telephone interview data from 3155...

Conflict can arise when bats roost in human dwellings and householders are affected adversely by their presence. In the United Kingdom, the exclusion of bats from roosts can be licensed under exceptional circumstances to alleviate conflict, but the fate of excluded bats and the impact on their survival and reproduction is not well understood. Using...

Obesity is considered the second most common health problem in pet cats in developed countries. Previous studies investigating risk factors for feline obesity have been cross-sectional, where reverse causality cannot be ruled out. This study is the first to use prospective data from a large scale longitudinal study of pet cats ('Bristol Cats') to i...

Neuronal brain activity in response to repeated stimuli can be perceived using functional magnetic resonance imaging (fMRI). In this paper, we develop a statistical model for fMRI data that estimates both the associated haemodynamic response function and the within and between trial variability through maximum likelihood estimation. We discuss our...

Applications of multilevel models to continuous outcomes nearly always assume constant residual variance and constant random effects variances and covariances. However, modeling heterogeneity of variance can prove a useful indicator of model misspecification and in some educational and behavioral studies, it may even be of direct substantive intere...

Lameness in dairy cows is an important welfare issue. As part of a welfare assessment, herd level lameness prevalence can be estimated from scoring a sample of animals, where higher levels of accuracy are associated with larger sample sizes. As the financial cost is related to the number of cows sampled, smaller samples are preferred. Sequential sa...

The 3Rs-replacement, reduction, and refinement-can be applied to any animal experiment by researchers and other bodies seeking to conduct those studies in as humane a manner as possible. Key to the success of this endeavor is an appreciation of the principles of good experimental design and analysis; these need to be considered in concert before an...

This paper reports radial colour and longitudinal mitral annulus pulsed-wave tissue Doppler findings in a large cohort of healthy, adult pet rabbits. Thirty-nine rabbits (22 Dwarf Lops, 14 French Lops and 3 Alaskan) underwent conscious echocardiography. The median age of the rabbits was 22 months and the median weight was 2.8 kg (Dwarf Lop 2.4kg/Fr...

The reliability of scientific research is under scrutiny. A recently convened working group proposes cultural adjustments to incentivize better research practices.

Farm animal welfare assessment is used to provide an overall picture of the welfare status of the animals on a farm. It is rarely practical or feasible to assess every animal on the farm, therefore some form of sampling scheme is used where a trade-off is made between time taken and accuracy of the results. Here, how representative the sample resul...

The theoretical concept of ‘iceberg indicators’ suggests that by measuring only a subset of animal-based measures it may be possible to predict the overall welfare state of an animal. To test the concept of iceberg indicators, a Welfare Quality assessment was carried out on 92 UK dairy farms which were found to have an overall Welfare Quality class...

The Welfare Quality ® protocols provide a multidimensional assessment of welfare, which is lengthy, and hence limited in terms of practicality. The aim of this study was to investigate potential ‘iceberg indicators’ which could reliably predict the overall classification as a means of reducing the length of time for an assessment and so increase th...

The theoretical concept of ‘iceberg indicators’ suggests that by measuring only a subset of animal-based measures it may be possible to predict the overall welfare state of an animal. To test the concept of iceberg indicators, a Welfare Quality assessment was carried out on 92 UK dairy farms which were found to have an overall Welfare Quality class...

Objectives The aim of the study was to report normal two-dimensional, M-mode, and Doppler echocardiographic findings from a large cohort of healthy, manually restrained, adult pet rabbits. Animals and Methods Forty healthy pet rabbits [22 Dwarf Lops (DL), 14 French Lops (FL) and 4 Alaskan (AL)] underwent a full physical examination and conscious t...

Elastography is a simple, expedient and noninvasive technique that may be used to assess the elasticity or stiffness of a tissue, in conjunction with traditional B-mode ultrasonography. Quantitative assessment of tissue stiffness can be made which involves measurement of the shear wave velocity within the tissue of interest. The goal of this study...

This paper presents an account of a Welfare Quality® assessment of 92 dairy farms carried out by seven experienced assessors. The aim was to evaluate the potential of the Welfare Quality® assessment protocol with respect to its uptake by UK farm assurance schemes. Data collection, and measure aggregation were performed according to the Welfare Qual...

In the last decade the number of bioscience journals has increased enormously, with many filling specialised niches reflecting new disciplines and technologies. The emergence of open-access journals has revolutionised the publication process, maximising the availability of research data. Nevertheless, a wealth of evidence shows that across many are...

The paper extends existing models for multilevel multivariate data with mixed response types to handle quite general types and patterns of missing data values in a wide range of multilevel generalized linear models. It proposes an efficient Bayesian modelling approach that allows missing values in covariates, including models where there are intera...

We analysed two consecutive inspection reports for each of 136 British zoos made by government-appointed inspectors between 2005 and 2011 to assess how well British zoos were complying with minimum animal welfare standards; median interval between inspections was 1,107 days. There was no conclusive evidence for overall improvements in the levels of...

The social network literature on network dependences has largely ignored other sources of dependence, such as the school that a student attends, or the area in which an individual lives. The multilevel modelling literature on school and area dependences has, in turn, largely ignored social networks. To bridge this divide, a multiple-membership mult...

The paper extends existing models for multilevel multivariate data with mixed response types to handle quite general types and patterns of missing data values in a wide range of multilevel generalized linear models. It proposes an efficient Bayesian modelling approach that allows missing values in covariates, including models where there are intera...

Laying hens with keel fractures (n = 35) and control hens with no fractures (n = 12) were trained to associate the colour and position of an environment with the effects of either a subcutaneous injection of an opioid analgesic drug (butorphanol) or a subcutaneous injection of saline in a conditioned place preference experiment. Each hen experience...

Bayesian mixture models can be used to discriminate between the distributions of continuous test responses for different infection stages. These models are particularly useful in case of chronic infections with a long latent period, like Mycobacterium avium subsp. paratuberculosis (MAP) infection, where a perfect reference test does not exist. Howe...

Experiments to investigate bone's physiological adaptation to mechanical loading frequently employ models that apply dynamic loads to bones in vivo and assess the changes in mass and architecture that result. It is axiomatic that bones will only show an adaptive response if the applied artificial loading environment differs in a significant way fro...

A very general class of multilevel factor analysis and structural equation models is proposed which are derived from considering the concatenation of a series of building blocks that use sets of factor structures defined within the levels of a multilevel model. An MCMC estimation algorithm is proposed for this structure to produce parameter chains...

The incidence of herd breakdown (HBD) with bovine tuberculosis (bTB) has continued to increase year on year since the 1980s in Great Britain. The management of bTB constitutes a major challenge for government and the cattle industry. Whilst various factors have been implicated with the risk of HBD with bTB, factors involved in recovery are less wel...

In a cross-sectional study, data from records of cattle slaughtered over a 1-year period at a large abattoir in South West England were analysed using an ordered category response model to investigate the inter-relationships between age, sex and breed on development of the permanent anterior (PA) teeth. Using the model, transition points at which t...

Stat-JR is a software environment for promoting interactive complex statistical modelling.This is an introduction to Stat-JR's menu-driven TREE (Template Reading and Execution Environment) interface, and includes a quick-start guide. The software can be dowloaded from http://www.bristol.ac.uk/cmm/software/statjr/

Stat-JR is a software environment for promoting interactive complex statistical modelling. This manual looks 'under the bonnet' of the Stat-JR system, and provides guidance for those wishing to write their own templates.Software can be dowloaded from here: http://www.bristol.ac.uk/cmm/software/statjr/

SUMMARY Disease cases are often clustered within herds or generally groups that share common characteristics. Sample size formulae must adjust for the within-cluster correlation of the primary sampling units. Traditionally, the intra-cluster correlation coefficient (ICC), which is an average measure of the data heterogeneity, has been used to modif...

Imperfect diagnostic testing reduces the power to detect significant predictors in classical cross-sectional studies. Assuming that the misclassification in diagnosis is random this can be dealt with by increasing the sample size of a study. However, the effects of imperfect tests in longitudinal data analyses are not as straightforward to anticipa...

MCMC algorithm. Expression of the likelihood for discrete time survival model with multiple patterns. (DOCX)

Full correlation tables for the predictor variables appearing in table 5 of the main text. Only Spearman or Pearson correlation coefficients over 0.20 are shown. In bold, are indicated Spearman correlations over 0.5. (DOCX)

There is a widely held view that the relationship between mechanical loading history and adult bone mass/strength includes an adapted state or "lazy zone" where the bone mass/strength remains constant over a wide range of strain magnitudes. Evidence to support this theory is circumstantial. We investigated the possibility that the "lazy zone" is an...