Bill Venables

• The Commonwealth Scientific and Industrial Research Organisation

South and Southeast Asia host almost half of the world’s undernourished people. Food and agricultural systems in these regions are highly dependent on the production and consumption of staple cereals such as rice, maize and wheat. More diverse farming systems can potentially improve rural people’s nutrition, while reducing the environmental impact...

We review and develop conceptual models for the bio-transfer of ciguatoxins in food chains for Platypus Bay and the Great Barrier Reef on the east coast of Australia. Platypus Bay is unique in repeatedly producing ciguateric fishes in Australia, with ciguatoxins produced by benthic dinoflagellates (Gambierdiscus spp.) growing epiphytically on free-...

The Gladstone Healthy Harbour Partnership (GHHP) was established in May 2012 to assess the health of Gladstone Harbour following public concern about a range of fish health issues that emerged in 2011. The GHHP is responsible for producing an annual report card on the health of the harbour that includes social, cultural, economic and environmental...

The 2018 Gladstone Harbour Report Card reports on the environmental health of 13 reporting zones in and around Gladstone Harbour and the overall environmental, social, cultural and economic health of the harbour. This report card covers monitoring undertaken in the period 1 July 2017 to 30 June 2018.

• In many wetlands the timing and duration of inundation determine ecological characteristics and the provision of ecosystem services; however, wetland conservation decisions often rely on static maps of wetland boundaries that do not capture their dynamic hydrological variability and connectivity. • The Amazon River basin contains some of the worl...

Building on the 2016 report card, the Gladstone Harbour Report Card 2017 has been informed by 99 measures of the four components of harbour health: environmental, social, cultural and economic. This report card is based on data collected during the period from July 2016 to June 2017. As GHHP continues to expand and refine its monitoring programs, a...

The 2016 Gladstone Harbour Report Card reports on the environmental health of 13 reporting zones in and around Gladstone Harbour and the overall environmental, social, cultural and economic health of the harbour. This report card covers monitoring undertaken in the period 1 July 2015 to 30 June 2016. The report can be downloaded using the following...

Decreases in shorebird populations are increasingly evident worldwide, especially in the East Asian–Australasian Flyway (EAAF). To arrest these declines, it is important to understand the scale of both the problem and the solutions. We analysed an expansive Australian citizen-science dataset, spanning the period 1973 to 2014, to explore factors rel...

S-PLUS is a commercial software environment for data analysis and graphics based on the programming language S, designed and initially implemented by John M. Chambers at Bell Laboratories. In addition to a large suite of software for standard tasks, the system aims to provide users with the means to implement new techniques or combine standard meth...

OUTCOMES • An improved understanding of the available datasets, and data deficiencies, relating to recreational fishing in Australia through the successful collaboration of researchers, fishery managers and recreational fishing groups. • Identification and prioritisation of recreationally-important species at the national level. • A quantitative...

https://cran.r-project.org/package=DescTools

This analysis of all carapace length measurements collected between 1989 and 2009, during scientific surveys, describes the variation of tropical rock lobster, Panulirus ornatus, somatic growth in Torres Strait. Multiple models of carapace length frequency distributions were compared by maximum likelihood to determine which hypotheses were most sup...

Punt, A. E., Deng, R. A., Dichmont, C. M., Kompas, T., Venables, W. N., Zhou, S., Pascoe, S., Hutton, T., Kenyon, R., van der Velde, T., and Kienzle, M. 2010. Integrating size-structured assessment and bioeconomic management advice in Australia's northern prawn fishery. - ICES Journal of Marine Science, 67: 1785-1801. Three species in Australia's n...

Venables, W. N., Ellis, N., Punt, A. E., Dichmont, C. M., and Deng, R. A. 2009. A simulation strategy for fleet dynamics in Australia’s northern prawn fishery: effort allocation at two scales. – ICES Journal of Marine Science, 66: 631–645. We describe simple and effective methods for simulating the movement of a fishing fleet, the spatio-temporal a...

A new approach to inference on variance components is propounded. This approach not only gives a new justification for Fisher's fiducial, distribution for the “between classes” component, but also leads to a new distribution for the “within classes” component. This latter distribution is studied, and has some intuitively very reasonable properties....

The performance of management strategies for a prawn fishery in northern Australia is evaluated using the management strategy evaluation (MSE) approach. The operating model on which the analyses are based includes population dynamics models for four prawn species and five stocks of each species, an effort allocation model and a benthic impacts mode...

We consider a family of effective and efficient strategies for generating experimental designs of several types with high efficiency. These strategies employ randomized search directions and at some stages allow the possibility of taking steps in a direction of decreasing efficiency in an effort to avoid local optima. Hence our strategies have some...

Objectives 1. Determine the spatial and temporal extent of overall fishing effort at a fine scale (~1 n mile resolution) using VMS data (up to 2002) for the entire NPF. 2. Measure the rate of depletion of seabed organisms following exposure to known trawling intensities in experimental plots in two regions within the GoC. 3. Measure the rate of rec...

Bishop, J., Venables, W. N., Dichmont, C. M., and Sterling, D. J. 2008. Standardizing catch rates: is logbook information by itself enough? – ICES Journal of Marine Science, 65: 255–266. The goal of the work was to maximize the accuracy of standardized catch per unit effort as an index of relative abundance. Linear regression models were fitted to...

Assessment of mine waste disposal on benthos and pelagic food webs at Lihir Island, Papua New Guinea. Final report to Lihir Gold

Little is known about the impacts of mine waste disposal, including deep-sea tailings, on tropical marine environments and this study presents the first account of this impact on deepwater fish communities. The Lihir gold mine in Papua New Guinea has deposited both excavated overburden and processed tailings slurry into the coastal environment sinc...

In 2001, paired-trawl comparisons were made during prawn trawl operations to assess the effect of turtle excluder devices and bycatch reduction devices on a range of species groups caught in tropical Australia. This study is one of the first to evaluate the commercial use of these devices in a tropical fishery. Nets with a combination of a turtle e...

The deepwater fishes around the Lihir Island group, Papua New Guinea, were assessed for their vulnerability to exploitation from a potential commercial fishery. Three dropline surveys were made between 1999 and 2002 to estimate catch rates and life-history parameters. Growth parameters were obtained using the von Bertalanffy growth function fitted...

Abstract The effect of mistletoes Amyema preissii on the survival of fast growing trees of Acacia victoriae was investigated in arid central Australia. Trees with different levels of experimentally induced mistletoe infection were monitored for 4 years. Analysis of covariance failed to reveal a treatment effect of infection on host survival. Loss o...

An equation is derived relating tissue water potential to relative water content. This equation may be used to lit a single curve to a set of data such as the standard pressure volume measurements made with a pressure chamber. From such a single curve fitting operation, estimates of the parameters involved may be found, and this allows calculation...

S-PLUS is a commercial software environment for data analysis and graphics based on the programming language S, designed and initially implemented by John M. Chambers at Bell Laboratories. In addition to a large suite of software for standard tasks, the system aims to provide users with the means to implement new techniques or combine standard meth...

This paper provides an overview of the modelling process using generalized linear models (GLMs), generalized additive models (GAMs) and generalized linear mixed models (GLMMs), especially as they are applied within fisheries research. We describe the essential aspect of model interpretation and construction so as to achieve its correct application....

Two biologically distinct species, Penaeus semisulcatus and P. esculentus, are caught in the tiger prawn component of Australia's Northern Prawn Fishery. These species are recorded and marketed together as 'tiger prawns'. A generalised linear model is used to separate the logbook catches of 'tiger prawns' into catches by individual species, even th...

13 Statistical methods are often used to analyse commercial catch and effort data to provide standardised fishing effort and/or a relative index of fish abundance for input into stock assessment models. Achieving reliable results has proved difficult in Australia's Northern Prawn Fishery (NPF), due to a combination of such factors as the biological...

In linear regression the mean surface is a plane in sample space; in non-linear regression it may be an arbitrary curved surface but in all other respects the models are the same. Fortunately the mean surface in most non-linear regression models met in practice will be approximately planar in the region of highest likelihood, allowing some good app...

We collect together several ways to handle linear and non-linear models with random effects, possibly as well as fixed effects.

Statistics is fundamentally about understanding data. We start by looking at how data are represented in S, then move on to importing, exporting and manipulating data.

Statisticians1 often under-estimate the usefulness of general optimization methods in maximizing likelihoods and in other model-fitting problems. Not only are the general-purpose methods available in the S environments quick to use, they also often outperform the specialized methods that are available. A lot of the software we have illustrated in e...

Classification is an increasingly important application of modern methods in statistics. In the statistical literature the word is used in two distinct senses. The entry (Hartigan, 1982) in the original Encyclopedia of Statistical Sciences uses the sense of cluster analysis discussed in Section 11.2. Modern usage is leaning to the other meaning (Ri...

Multivariate analysis is concerned with datasets that have more than one response variable for each observational or experimental unit. The datasets can be summarized by data matrices X with n rows and p columns, the rows representing the observations or cases, and the columns the variables. The matrix can be viewed either way, depending on whether...

A guide to using S environments to perform statistical analyses providing both an introduction to the use of S and a course in modern statistical methods. The emphasis is on presenting practical problems and full analyses of real data sets.

Need Under the Commonwealth Fisheries Management Act (1991), the new Environmental Protection and Biodiversity Conservation (EPBC) Act (effective July 2000) and the Wildlife Protection (regulation of Exports and Imports) Acts 1982, fisheries have to demonstrate their ecological sustainability. In addition the Commonwealth government is committed to...

Significant annual variations in population size of most species were evident with greater abundance of most species in wet years. Habitat variables, particularly vegetation structure, were also an important determinant of the abundance of most bird species and tended to mask the impacts of the land use under investigation. Several bird species had...

This chapter provides a reprise of the material introduced in Chapters 2 and 3 of MASS. Chapter 3 introduces more advanced language concepts that are important for programming: there are also class-oriented features which we discuss in Chapters 4 and 5.

In this chapter we consider the details which are not normally important in interactive use of S, and some more formal aspects of the language.

Most S-PLUS programmers find early in their careers that they have written code which exhausts the physical memory (RAM) available to the S-PLUS process, and then proceeds to spend almost all its time in allocating virtual memory. Such code can reduce the fastest workstation to page thrashing, which will reduce severely the size of problem which ca...

A very important and powerful feature of the S environment is that it is not restricted to functions written in the S language but may load and use compiled routines written in C or Fortran, or perhaps other languages.1 Moreover there are ways in which such externally written and compiled routines may communicate with the S session and make use of...

This chapter covers the class-oriented features of the old S engine and of R. Most of these exist for backward compatibility in the new S engine (see Section 5.4), but the features introduced in the next chapter are preferred for new projects in that system.

In this chapter we consider the tools available for the process of software development in the S language. Such tools are often a matter of personal taste so many are available, and our aim is to cover all the possibilities at fairly shallow level.

The new S engine introduced a very different approach to classes, although backwards compatibility is provided for the classes as described in Chapter 4. The current S-PLUS systems rely very heavily on this backwards compatibility; at present new-style classes are used only at a low level and in the time-series manipulation software. The definitive...

S-PLUS 4.x for Windows introduced a new way to program menus and dialogs. In essence the system programs the Axum engine on which the 4.x GUI is based. Even those who much prefer the command-line interface (including the authors) may find they need to develop a graphical user interface to their functions to enable other people to make use of them.

Multivariate analysis is concerned with datasets that have more than one response variable for each observational or experimental unit. The datasets can be summarized by data matrices X with n rows and p columns, the rows representing the observations or cases, and the columns the variables. The matrix can be viewed either way, depending on whether...

S-PLUS has a ‘Modern Regression Module’ which contains functions for a number of regression methods. These are not necessarily non-linear in the sense of Chapter 8, which refers to a non-linear parametrization, but they do allow nonlinear functions of the independent variables to be chosen by the procedures. The methods are all fairly computer-inte...

In this chapter we cover a number of topics from classical univariate statistics plus some modern versions.

S-PLUS provides comprehensive graphics facilities, from simple facilities for producing common diagnostic plots by plot (object) to fine control over publication-quality graphs. In consequence, the number of graphics parameters is huge. In this chapter, we build up the complexity gradually. Most readers will not need the material in Section 3.4, an...

There are now a large number of books on time series. Our philosophy and notation are close to those of the applied book by Diggle (1990) (from which some of our examples are taken). Brockwell & Davis (1991) and Priestley (1981) provide more theoretical treatments, and Bloomfield (1976) and Priestley are particularly thorough on spectral analysis....

Statistics is fundamentally concerned with the understanding of structure in data. One of the effects of the information-technology era has been to make it much easier to collect extensive datasets with minimal human intervention. Fortunately the same technological advances allow the users of statistics access to much more powerful ‘calculators’ to...

In linear regression the mean surface in sample space is a plane; in non-linear regression it may be an arbitrary curved surface but in all other respects the models are same. Fortunately in practice the mean surface in most non-linear regression models will be approximately planar in the region of highest likelihood, allowing some good approximati...

S-Plus is a powerful environment for statistical and graphical analysis of data. It provides the tools to implement many statistical ideas which have been made possible by the widespread availability of workstations having good graphics and computational capabilities. This book is a guide to using S-Plus to perform statistical analyses and provides...

Statistics is fundamentally concerned with the understanding of structures in data. One of the effects of the information-technology era has been to make it much easier to collect extensive datasets with minimal human intervention. Fortunately the same technological advances allow the users of statistics access to much more powerful ‘calculators’ t...

This cross-disciplinary paper develops random effects and variances methods, especially for small samples within effects, and applies them to mitochondrial enzyme kinetics. A new force flux kinetic model is introduced for the alternative oxidase of plant mitochondria, the results of 42 experiments are published and the force flux function is fitted...

The use of tree-based models will be relatively unfamiliar to statisticians, although researchers in other fields have found trees to be an attractive way to express knowledge and aid decision-making. Keys such as Figure 10.1 are common in botany and in medical decision-making, and provide a way to encapsulate and structure the knowledge of experts...

In linear regression the mean surface in sample space is a plane. In non-linear regression the mean surface may be an arbitrary curved surface but in other respects the models are similar. In practice the mean surface in most non-linear regression models will be approximately planar in the region(s) of high likelihood allowing good approximations b...

Outliers are sample values which cause surprise in relation to the majority of the sample. This is not a pejorative term; outliers may be correct, but they should always be checked for transcription errors. They can play havoc with standard statistical methods, and many robust and resistant methods have been developed since 1960 to be less sensitiv...

Multivariate analysis is concerned with datasets which have more than one response variable for each observational or experimental unit. The datasets can be summarized by data matrices X with n rows and p columns, the rows representing the observations or cases, and the columns the variables. The matrix can be viewed either way, depending whether t...

There are now a large number of books on time series. Our philosophy and notation are close to those of the applied book by Diggle (1990) (from which some of our examples are taken). Brockwell and Davis (1991) and Priestley (1981) provide more theoretical treatments, and Bloomfield (1976) and Priestley are particularly thorough on spectral analysis...

In this chapter we cover a number of topics from classical univariate statistics. Many of the functions used are S-PLUS extensions to S.

S is a language for the manipulation of objects. It aims to be both an interactive language (like, for example, a Unix shell language) as well as a complete programming language with some convenient object-oriented features. In this chapter we shall be concerned with the interactive language, and hence certain language constructs used mainly in pro...

Survival analysis is not part of S, but has been added to S-PLUS based on functions written by Terry Therneau (Mayo Foundation) and available as survival2 code from statlib (see Appendix D for further information.) The functions in survival3 were released in mid-1992. They are not part of S-PLUS 3.2, but are scheduled to be included in late 1994. A...

Generalized linear models (GLMs) extend linear models to accommodate both non-normal response distributions and transformations to linearity. (We will assume that Chapter 6 has been read before this chapter.) The essay by Firth (1991) gives a good introduction to GLMs; the comprehensive reference is McCullagh & Neider (1989).

S-PLUS has a ‘Modern Regression Module’ which contains functions for a number of regression methods. These are not necessarily non-linear in the sense of Chapter 9, which refers to a non-linear parametrization, but they do allow nonlinear functions of the independent variables to be chosen by the procedures. The methods are all fairly computer-inte...

The S language is both an interactive language and a language for adding new functions to the S system. It is a complete programming language with control structures, recursion and a useful variety of data types. The S environment provides many functions to handle standard operations, but most users need occasionally to write new functions. This ch...

S-PLUS provides comprehensive graphics facilities, from simple facilities for producing common diagnostic plots by plot (object) to fine control over publication-quality graphs. In consequence, the number of graphics parameters is huge. In this chapter, we build up the complexity gradually. Most readers will not need to go beyond the first 3 sectio...

Linear models form the core of classical statistics, and S provides extensive facilities to fit and manipulate them. These work with a version of the Wilkinson-Rogers syntax (Wilkinson & Rogers, 1973) for specifying models which we discuss in the Section 6.2, and which is also used for generalized linear models, models for survival analysis and tre...

Statistics is fundamentally concerned with the understanding of structures in data. One of the effects of the information-technology era has been to make it much easier to collect extensive datasets with minimal human intervention. Fortunately the same technological advances allow the users of statistics access to much more powerful ‘calculators’ t...

McKey's (1975) hypothesis that avian dispersers with a specialized gut provide higher quality seed dispersal than unspecialized frugivores was tested using grey mistletoe (Amyema quandang) fruits, and captive mistletoebirds (Dicaeum hirundinaceum) and spinycheeked honeyeaters (Acanthagenys refogularis) in arid South Australia. Mistletoebirds have a...

C. R. Rao (1973, problem 5.11) constructed an example where a minimum variance unbiased estimator exists for the parameter function (1 – α) but no uniformly minimum variance unbiased estimator exists for α itself. The example was further discussed by Romano and Siegel (1986, example 9.6) who exhibited the family of unbiased estimators for α; the no...

In choosing a model, there are important considerations beyond the goodness of fit, namely that the subsequent inferences should not rely on questionable assumptions implicit in the model, because otherwise they will be suspect. The two-parameter lognormal distribution provides an example. The symmetry on the log scale leads to the anomaly that rel...

A procedure similar to an analysis of variance is presented for examining the structure in correlation matrices whose variables are cross-classified by two factors, such as multitrait-multimethod matrices. The method tests an equal correlation hypothesis against natural alternative hypotheses suggested by group representations. When there is signif...

A procedure similar to an analysis of variance is presented for examining the structure in correlation matrices whose variables are cross-classified by two factors, such as multitrait-multimethod matrices. The method tests an equal correlation hypothesis against natural alternative hypotheses suggested by group representations. When there is signif...

An extension of the growth curve model of Potthoff & Roy (1964) is presented. The extension arises naturally when parallel profiles are required, or profiles are concurrent at some known time point and may be of use for the analysis of longitudinal data from designed experiments. Linearization of a nonlinear model also results in this model. Under...

We study the large-sample joint distribution of Z, the 2-Janp(p - 1) Fisher z-transforms of the elements in a p variable correlation matrix. Under the null hypothesis of equal population correlations the variance matrix of Z has just three projector matrices in its spectral decomposition. These define three mutually orthogonal invariant subspaces o...

The Australian Government's Marine and Tropical Sciences Research Facility (MTSRF) supports world-class, public good research. The MTSRF is a major initiative of the Australian Government, designed to ensure that Australia's environmental challenges are addressed in an innovative, collaborative and sustainable way. The MTSRF investment is managed b...