rpanel: Simple Interactive Controls for R Functions Using the tcltk Package

In a variety of settings it is extremely helpful to be able to apply R functions through buttons, sliders and other types of graphical control. This is particularly true in plotting activities where immediate communication between such controls and a graphical display allows the user to interact with a plot in a very effective manner. The tcltk package provides extensive tools for this and the aim of the rpanel package is to provide simple and well documented functions which make these facilities as accessible as possible. In addition, the operations which form the basis of communication within tcltk are managed in a way which allows users to write functions with a more standard form of parameter passing. This paper describes the basic design of the software and illustrates it on a variety of examples of interactive control of graphics. The tkrplot system is used to allow plots to be integrated with controls into a single panel. An example of the use of a graphical image, and the ability to interact with this, is also discussed.

Big questions, informative data, excellent science

The expression big data is often used in a manner which implies that immediate insight is readily available. Unfortunately, this raises unrealistic expectations. A model which encapsulates the powerful concepts of statistical thinking remains an invaluable component of good analysis

Anatomical curve identification

Methods for capturing images in three dimensions are now widely available, with stereo-photogrammetry and laser scanning being two common approaches. In anatomical studies, a number of landmarks are usually identified manually from each of these images and these form the basis of subsequent statistical analysis. However, landmarks express only a very small proportion of the information available from the images. Anatomically defined curves have the advantage of providing a much richer expression of shape. This is explored in the context of identifying the boundary of breasts from an image of the female torso and the boundary of the lips from a facial image. The curves of interest are characterised by ridges or valleys. Key issues in estimation are the ability to navigate across the anatomical surface in three-dimensions, the ability to recognise the relevant boundary and the need to assess the evidence for the presence of the surface feature of interest. The first issue is addressed by the use of principal curves, as an extension of principal components, the second by suitable assessment of curvature and the third by change-point detection. P-spline smoothing is used as an integral part of the methods but adaptations are made to the specific anatomical features of interest. After estimation of the boundary curves, the intermediate surfaces of the anatomical feature of interest can be characterised by surface interpolation. This allows shape variation to be explored using standard methods such as principal components. These tools are applied to a collection of images of women where one breast has been reconstructed after mastectomy and where interest lies in shape differences between the reconstructed and unreconstructed breasts. They are also applied to a collection of lip images where possible differences in shape between males and females are of interest

Quasi-periodic spatiotemporal models of brain activation in single-trial MEG experiments

Magneto-encephalography (MEG) is an imaging technique which measures neuronal activity in the brain. Even when a subject is in a resting state, MEG data show characteristic spatial and temporal patterns, resulting from electrical current at specific locations in the brain. The key pattern of interest is a ‘dipole’, consisting of two adjacent regions of high and low activation which oscillate over time in an out-of-phase manner. Standard approaches are based on averages over large numbers of trials in order to reduce noise. In contrast, this article addresses the issue of dipole modelling for single trial data, as this is of interest in application areas. There is also clear evidence that the frequency of this oscillation in single trials generally changes over time and so exhibits quasi-periodic rather than periodic behaviour. A framework for the modelling of dipoles is proposed through estimation of a spatiotemporal smooth function constructed as a parametric function of space and a smooth function of time. Quasi-periodic behaviour is expressed in phase functions which are allowed to evolve smoothly over time. The model is fitted in two stages. First, the spatial location of the dipole is identified and the smooth signals characterizing the amplitude functions for each separate pole are estimated. Second, the phase and frequency of the amplitude signals are estimated as smooth functions. The model is applied to data from a real MEG experiment focusing on motor and visual brain processes. In contrast to existing standard approaches, the model allows the variability across trials and subjects to be identified. The nature of this variability is informative about the resting state of the brain

Translational genetic modelling of 3D craniofacial dysmorphology: elaborating the facial phenotype of neurodevelopmental disorders through the prism of schizophrenia

Purpose of Review: In the context of human developmental conditions, we review the conceptualisation of schizophrenia as a neurodevelopmental disorder, the status of craniofacial dysmorphology as a clinically accessible index of brain dysmorphogenesis, the ability of genetically modified mouse models of craniofacial dysmorphology to inform on the underlying dysmorphogenic process and how geometric morphometric techniques in mutant mice can extend quantitative analysis. Recent Findings: Mutant mice with disruption of neuregulin-1, a gene associated meta-analytically with risk for schizophrenia, constitute proof-of-concept studies of murine facial dysmorphology in a manner analogous to clinical studies in schizophrenia. Geometric morphometric techniques informed on the topography of facial dysmorphology and identified asymmetry therein. Summary: Targeted disruption in mice of genes involved in individual components of developmental processes and analysis of resultant facial dysmorphology using geometric morphometrics can inform on mechanisms of dysmorphogenesis at levels of incisiveness not possible in human subjects

rpanel: Simple interactive controls for R functions using the tcltk package

In a variety of settings it is extremely helpful to be able to apply R functions through buttons, sliders and other types of graphical control. This is particularly true in plotting activities where immediate communication between such controls and a graphical display allows the user to interact with a plot in a very effective manner. The tcltk package provides extensive tools for this and the aim of the rpanel package is to provide simple and well documented functions which make these facilities as accessible as possible. In addition, the operations which form the basis of communication within tcltk are managed in a way which allows users to write functions with a more standard form of parameter passing. This paper describes the basic design of the software and illustrates it on a variety of examples of interactive control of graphics. The tkrplot system is used to allow plots to be integrated with controls into a single panel. An example of the use of a graphical image, and the ability to interact with this, is also discussed

A hierarchical curve-based approach to the analysis of manifold data

One of the data structures generated by medical imaging technology is high resolution point clouds representing anatomical surfaces. Stereophotogrammetry and laser scanning are two widely available sources of this kind of data. A standardised surface representation is required to provide a meaningful correspondence across different images as a basis for statistical analysis. Point locations with anatomical definitions, referred to as landmarks, have been the traditional approach. Landmarks can also be taken as the starting point for more general surface representations, often using templates which are warped on to an observed surface by matching landmark positions and subsequent local adjustment of the surface. The aim of the present paper is to provide a new approach which places anatomical curves at the heart of the surface representation and its analysis. Curves provide intermediate structures which capture the principal features of the manifold (surface) of interest through its ridges and valleys. As landmarks are often available these are used as anchoring points, but surface curvature information is the principal guide in estimating the curve locations. The surface patches between these curves are relatively flat and can be represented in a standardised manner by appropriate surface transects to give a complete surface model. This new approach does not require the use of a template, reference sample or any external information to guide the method and, when compared with a surface based approach, the estimation of curves is shown to have improved performance. In addition, examples involving applications to mussel shells and human faces show that the analysis of curve information can deliver more targeted and effective insight than the use of full surface information

Inference for variograms

The empirical variogram is a standard tool in the investigation and modelling of spatial covariance. However, its properties can be difficult to identify and exploit in the context of exploring the characteristics of individual datasets. This is particularly true when seeking to move beyond description towards inferential statements about the structure of the spatial covariance which may be present. A robust form of empirical variogram based on a fourth-root transformation is used. This takes advantage of the normal approximation which gives an excellent description of the variation exhibited on this scale. Calculations of mean, variance and covariance of the binned empirical variogram then allow useful computations such as confidence intervals to be added to the underlying estimator. The comparison of variograms for different datasets provides an illustration of this. The suitability of simplifying assumptions such as isotropy and stationarity can then also be investigated through the construction of appropriate test statistics and the distributional calculations required in the associated p-values can be performed through quadratic form methods. Examples of the use of these methods in assessing the form of spatial covariance present in datasets are shown, both through hypothesis tests and in graphical form. A simulation study explores the properties of the tests while pollution data on mosses in Galicia (North-West Spain) are used to provide a real data illustration

Cognitive archaeology: estimating the effects of blood-lead concentrations on the neuropsychological function of an officer of the 1845 Franklin expedition

Lead poisoning has been implicated in the loss in the Arctic of all 129 officers and men of the British Royal Naval “Franklin expedition” of 1845. In a unique study, D’Ortenzio et al. (2018) estimated blood-lead concentrations of an officer of the expedition over the three months prior to his death which is thought to have occurred before the desertion of the expedition’s ships. The present study applies regression coefficients which quantify the relationship between blood lead and neuropsychological function to the data of D’Ortenzio et al. to estimate whether the officer’s lead exposure would have impaired his cognitive performance in the critical period prior to the desertion. It is shown that the blood-lead concentrations would have been associated with only small deficits in higher-order cognitive processes including attention, visual scanning, memory and decision-making which would not have been of functional significance. Greater deficits were associated with psychomotor functions involving eye-hand co-ordination and fine motor control which, although not defined formally as “impairment”, might have affected accuracy when using firearms or operating instruments relevant to the scientific objectives of the expedition. The study also reviews evidence that the levels of lead in the Franklin crew, while high relative to today, were typical of those of the lead-exposed Victorian population from which they were recruited. The results contribute to evidence that lead exposure did not play a significant role in the loss of the Franklin expedition