Using information criteria to select the correct variance–covariance structure for longitudinal data in ecology

1. Ecological data sets often use clustered measurements or use repeated sampling in a longitudinal design. Choosing the correct covariance structure is an important step in the analysis of such data, as the covariance describes the degree of similarity among the repeated observations. 2. Three methods for choosing the covariance are: the Akaike information criterion (AIC), the quasi-information criterion (QIC), and the deviance information criterion (DIC). We compared the methods using a simulation study and using a data set that explored effects of forest fragmentation on avian species richness over 15 years. 3. The overall success was 80.6% for the AIC, 29.4% for the QIC and 81.6% for the DIC. For the forest fragmentation study the AIC and DIC selected the unstructured covariance, whereas the QIC selected the simpler autoregressive covariance. Graphical diagnostics suggested that the unstructured covariance was probably correct. 4. We recommend using DIC for selecting the correct covariance structure.

Relationship over time between psychological distress and physical activity in colorectal cancer survivors

Purpose Increased physical activity in colorectal cancer patients is related to improved recurrence free and overall survival. Psychological distress after cancer may place patients at risk of reduced physical activity; but paradoxically also act as a motivator for positive lifestyle change. The relationship between psychological distress and physical activity after cancer over time has not been described. Methods A prospective survey of 1966 (57% response) colorectal cancer survivors assessed the psychological distress variables of anxiety, depression, somatisation, cancer threat appraisal as predictors of physical activity five, 12, 24 and 36 months post-diagnosis 978 respondents had valid data for all time points. Results Higher somatisation was associated with greater physical inactivity (Relative risk ratio (RRR) =1.12; 95% CI=[1.1, 1.2]) and insufficient physical activity (RRR=1.05; [0.90, 1.0]). Respondents with a more positive appraisal of their cancer were significantly (p=0.031) less likely to be inactive (RRR=0.95; [0.90, 1.0]) or insufficiently active (RRR=0.96). Fatigued and obese respondents and current smokers were more inactive. Respondents whose somatisation increased between two time periods were less likely to increase their physical activity over the same period (p<0.001). Respondents with higher anxiety at one time period were less likely to have increased their activity at the next assessment (p=0.004). There was no association between depression and physical activity. Conclusions Cancer survivors who experience somatisation and anxiety are at greater risk of physical inactivity. The lack of a clear relationship between higher psychological distress and increasing physical activity argues against distress as a motivator to exercise in these patients.

Safeguarding Rural Australia : Introduction, Framework and Background to Secondary Data Analysis

This report provides an introduction to our analyses of secondary data with respect to violent acts and incidents relating to males living in rural settings in Australia. It clarifies important aspects of our overall approach primarily by concentrating on three elements that required early scoping and resolution. Firstly, a wide and inclusive view of violence which encompasses measures of violent acts and incidents and also data identifying risk taking behaviour and the consequences of violence is outlined and justified. Secondly, the classification used to make comparisons between the city and the bush together with associated caveats is outlined. The third element discussed is in relation to national injury data. Additional commentary resulting from exploration, examination and analyses of secondary data is published online in five subsequent reports in this series.

Data Report No. 1 : Self-harm Including Suicide

This report focuses on our examination of extant data which have been sourced with respect to self-harm and suicide in Australia. Moreover, specific areas of concern regarding elevated rates of suicide for rural males and data anomalies which emerged during our examination of these data are discussed. Additional commentary resulting from exploration, examination and analyses of secondary data is published online in complementary reports in this series.

Safeguarding Rural Australia : Data Report No. 2 - Intentional Violence

This report focuses on our examination of extant data which have been sourced with respect to intentional violence perpetrated or experienced by males in regional and remote Australia. The nature of intentional violent acts can be physical, sexual or psychological or involve deprivation or neglect. We have presented under the headings of: self-harm including suicide; homicide; assault, sexual assault and the threat of assault; child abuse; other family and intimate partner violence; harassment, stalking and bullying; alcohol related social violence; and animal abuse. State variations in interpersonal violence are also presented. Additional commentary resulting from exploration, examination and analyses of secondary data is published online in complementary reports in this series.

Safeguarding Rural Australia: Data Report No. 3 - Unintentional Violence

This report focuses on our examination of extant data which have been sourced with respect to unintentional serious and violent injuries to males living in regional and remote Australia. Such injuries typically might be caused by, for example, transport accidents, occupational exposures and hazards, burns and so on. Thus unintentional violent incidents cause physical trauma the consequences of which can sometimes lead to chronic conditions including psychological harm or substance abuse. Additional commentary resulting from exploration, examination and analyses of secondary data is published online in complementary reports in this series.

Safeguarding rural Australia : addressing masculinity and violence in rural settings. Data report No. 4 - Risky behaviour - misuse of alcohol, illicit drugs, firearms use and abuse, other risky behaviour

This report focuses on our examination of extant data which have been sourced with respect to personally and socially risky behaviour associated with males living in regional and remote Australia . The AIHW (2008: PHE 97:89) defines personally risky behaviour, on the one hand, as working, swimming, boating, driving or operating hazardous machinery while intoxicated with alcohol or an illicit drug. Socially risky behaviour, on the other hand, is defined as creating a public disturbance, damaging property, stealing or verbally or physically abusing someone while intoxicated with alcohol or an illicit drug. Additional commentary resulting from exploration, examination and analyses of secondary data is published online in complementary reports in this series.

Safeguarding rural Australia : addressing masculinity and violence in rural settings. Data report no. 5. Consequences of violence - juvenile offenders, long-term health consequences, anxiety and repression, other chronic disabilities

This report considers extant data which have been sourced with respect to some of the consequences of violent acts and incidents and risky behaviour for males living in regional and remote Australia . This has been collated and presented under the headings: juvenile offenders; long-term health consequences; anxiety and repression; and other chronic disabilities. Additional commentary resulting from exploration, examination and analyses of secondary data is published online in complementary reports in this series.

CTCombine : rotating and combining CT data with an accurate detector model, to simulate radiotherapy portal imaging at non-zero beam angles

Established Monte Carlo user codes BEAMnrc and DOSXYZnrc permit the accurate and straightforward simulation of radiotherapy experiments and treatments delivered from multiple beam angles. However, when an electronic portal imaging detector (EPID) is included in these simulations, treatment delivery from non-zero beam angles becomes problematic. This study introduces CTCombine, a purpose-built code for rotating selected CT data volumes, converting CT numbers to mass densities, combining the results with model EPIDs and writing output in a form which can easily be read and used by the dose calculation code DOSXYZnrc. The geometric and dosimetric accuracy of CTCombine’s output has been assessed by simulating simple and complex treatments applied to a rotated planar phantom and a rotated humanoid phantom and comparing the resulting virtual EPID images with the images acquired using experimental measurements and independent simulations of equivalent phantoms. It is expected that CTCombine will be useful for Monte Carlo studies of EPID dosimetry as well as other EPID imaging applications.

Is the new age phenomenon connected to delusion-like experiences? Analysis of survey data from Australia

Recent studies have shown that delusion-like experiences (DLEs) are common among general populations. This study investigates whether the prevalence of these experiences are linked to the embracing of New Age thought. Logistic regression analyses were performed using data derived from a large community sample of young adults (N = 3777). Belief in a spiritual or higher power other than God was found to be significantly associated with endorsement of 16 of 19 items from Peters et al. (1999b) Delusional Inventory following adjustment for a range of potential confounders, while belief in God was associated with endorsement of four items. A New Age conception of the divine appears to be strongly associated with a wide range of DLEs. Further research is needed to determine a causal link between New Age philosophy and DLEs (e.g. thought disturbance, suspiciousness, and delusions of grandeur).

Eco-structure data forms : classification of data analysis using perceived design affordances for musical outcomes

This paper explores a method of comparative analysis and classification of data through perceived design affordances. Included is discussion about the musical potential of data forms that are derived through eco-structural analysis of musical features inherent in audio recordings of natural sounds. A system of classification of these forms is proposed based on their structural contours. The classifications include four primitive types; steady, iterative, unstable and impulse. The classification extends previous taxonomies used to describe the gestural morphology of sound. The methods presented are used to provide compositional support for eco-structuralism.

Bayesian latent trait modeling of migraine symptom data

Definition of disease phenotype is a necessary preliminary to research into genetic causes of a complex disease. Clinical diagnosis of migraine is currently based on diagnostic criteria developed by the International Headache Society. Previously, we examined the natural clustering of these diagnostic symptoms using latent class analysis (LCA) and found that a four-class model was preferred. However, the classes can be ordered such that all symptoms progressively intensify, suggesting that a single continuous variable representing disease severity may provide a better model. Here, we compare two models: item response theory and LCA, each constructed within a Bayesian context. A deviance information criterion is used to assess model fit. We phenotyped our population sample using these models, estimated heritability and conducted genome-wide linkage analysis using Merlin-qtl. LCA with four classes was again preferred. After transformation, phenotypic trait values derived from both models are highly correlated (correlation = 0.99) and consequently results from subsequent genetic analyses were similar. Heritability was estimated at 0.37, while multipoint linkage analysis produced genome-wide significant linkage to chromosome 7q31-q33 and suggestive linkage to chromosomes 1 and 2. We argue that such continuous measures are a powerful tool for identifying genes contributing to migraine susceptibility.

Linkage and heritability analysis of migraine symptom groupings: A comparison of three different clustering methods on twin data

Migraine is a painful disorder for which the etiology remains obscure. Diagnosis is largely based on International Headache Society criteria. However, no feature occurs in all patients who meet these criteria, and no single symptom is required for diagnosis. Consequently, this definition may not accurately reflect the phenotypic heterogeneity or genetic basis of the disorder. Such phenotypic uncertainty is typical for complex genetic disorders and has encouraged interest in multivariate statistical methods for classifying disease phenotypes. We applied three popular statistical phenotyping methods—latent class analysis, grade of membership and grade of membership “fuzzy” clustering (Fanny)—to migraine symptom data, and compared heritability and genome-wide linkage results obtained using each approach. Our results demonstrate that different methodologies produce different clustering structures and non-negligible differences in subsequent analyses. We therefore urge caution in the use of any single approach and suggest that multiple phenotyping methods be used.

Copyright and Data

ANDS Guides http://ands.org.au/guides/index.html These guides provide information about ANDS services and some fundamental issues in data-intensive research and research data management. These are not rules, prescriptions or proscriptions. They are guidelines and checklists to inform and broaden the range of possibilities for researchers, data managers, and research organisations.