Locally Adaptive Tree-based Thresholding Using the treethresh Package in R

This paper introduces the treethresh package offering accurate estimation, via thresholding, of potentially sparse heterogeneous signals and the denoising of images using wavelets. It gives considerably improved performance over other estimation methods if the underlying signal or image is not homogeneous throughout but instead has distinct regions with differing sparsity or strength characteristics. It aims to identify these different regions and perform separate estimation in each accordingly. The base algorithm offers code which can be applied directly to any one-dimensional potentially sparse sequence observed subject to noise. Also included are functions which allow two-dimensional images to be denoised following transformation to the wavelet domain. In addition to reconstructing the underlying signal or image, the package provides information on the believed partitioning of the signal or image into its differing regions

Non-parametric calibration of multiple related radiocarbon determinations and their calendar age summarisation

Due to fluctuations in past radiocarbon ($^{14}$C) levels, calibration is required to convert $^{14}$C determinations $X_i$ into calendar ages $\theta_i$. In many studies, we wish to calibrate a set of related samples taken from the same site or context, which have calendar ages drawn from the same shared, but unknown, density $f(\theta)$. Calibration of $X_1, \ldots, X_n$ can be improved significantly by incorporating the knowledge that the samples are related. Furthermore, summary estimates of the underlying shared $f(\theta)$ can provide valuable information on changes in population size/activity over time. Most current approaches require a parametric specification for $f(\theta)$ which is often not appropriate. We develop a rigorous non-parametric Bayesian approach using a Dirichlet process mixture model, with slice sampling to address the multimodality typical within $^{14}$C calibration. Our approach simultaneously calibrates the set of $^{14}$C determinations and provides a predictive estimate for the underlying calendar age of a future sample. We show, in a simulation study, the improvement in calendar age estimation when jointly calibrating related samples using our approach, compared with calibration of each $^{14}$C determination independently. We also illustrate the use of the predictive calendar age estimate to provide insight on activity levels over time using three real-life case studies

Attitudes towards the sharing of genetic information with at-risk relatives: results of a quantitative survey

© 2015, The Author(s). To investigate public attitudes towards receiving genetic information arising from a test on a relative, 955 University of Sheffield students and staff were surveyed using disease vignettes. Strength of attitude was measured on whether, in the event of relevant information being discovered, they, as an at-risk relative, would want to be informed, whether the at-risk relative’s interest should override proband confidentiality, and, if they had been the proband, willingness to give up confidentiality to inform such relatives. Results indicated considerably more complexity to the decision-making than simple statistical risk. Desire for information only slightly increased with risk of disease manifestation [log odds 0.05 (0.04, 0.06) per percentage point increase in manifestation risk]. Condition preventability was the primary factor increasing desire [modifiable baseline, non-preventable log odds −1.74 (−2.04, −1.44); preventable 0.64 (0.34, 0.95)]. Disease seriousness also increased desire [serious baseline, non-serious log odds −0.89 (−1.19, −0.59); fatal 0.55 (0.25, 0.86)]. Individuals with lower education levels exhibited much greater desire to be informed [GCSE log odds 1.67 (0.64, 2.66)]. Age did not affect desire. Our findings suggest that attitudes were influenced more by disease characteristics than statistical risk. Respondents generally expressed strong attitudes demonstrating that this was not an issue which people felt ambivalent about. We provide estimates of the British population in favour/against disclosure for various disease scenarios

Reduced visual exploration when viewing photographic scenes in individuals with Autism Spectrum Disorder

Individuals with Autism Spectrum Disorder (ASD) often display enhanced attention to detail and exhibit restricted behaviour. However, due to a lack of comprehensive eye-movement modelling techniques, it is currently unknown whether these behavioural effects are also evident during scene viewing (i.e. detailed visual inspection and restricted visual exploration). Free viewing eye-tracking data from observation of everyday photographic scenes were recorded during two experiments involving high functioning adolescents with ASD and matched typically developing (TD) controls (Experiment 1 ASD n=14; TD n=22; Experiment 2 ASD n=16; TD n=23). Data from both experiments were combined and analysed using five novel methods of eye-tracking time-course analysis, enabling detailed characterisation of viewing strategies. Participants’ verbal descriptions of scenes were also assessed. Scenes either contained a centrally positioned person whose face was in full view or contained no centrally positioned face. For both types of scene, ASD participants displayed significantly less exploration of new areas over time compared to their TD peers. Analyses of scanpath length and recursion suggested a greater tendency to explore areas close to the current fixation in the ASD group, termed visual persistence. Differences were not accounted for by fixation rate. Significantly more areas within the scenes were also missing from the verbal descriptions in the ASD group. Differences were observed for both scene types suggesting a domain-general difference rather than a specific impairment related to face processing. The observed characteristic viewing patterns may explain relative superior processing of local level information in individuals with ASD

On the tuning of plateaus in atmospheric and oceanic 14C records to derive calendar chronologies of deep-sea cores and records of 14C marine reservoir age changes

We assess the methodology of the so-called 14C plateau tuning (PT) technique used to date marine sediment records and determine 14C marine reservoir ages (MRAs) as recently reviewed by Sarnthein et al. (2020). The main identified problems are linked to the assumption of constant MRA during 14C age plateaus; the lack of consideration of foraminifera abundance changes coupled to bioturbation that can create spurious plateaus in marine sediments; the assumption that plateaus have the same shapes and durations in atmospheric and oceanic records; the implication that atmospheric 14C / 12C peaked instantaneously from one plateau to the next; that the 14C plateaus represent 82 % of the total time spent between 14 000 and 29 000 cal yr BP, whereas during the remaining 18 % of the time, the radiocarbon clock was running almost 5 times faster than the radioactive decay; that the sparsity, combined with the level of analytical uncertainties and additional noise, in both atmospheric and marine data do not currently allow one to reliably or robustly identify plateaus (should they exist) beyond 15 000 cal yr BP; and that the determination and identification of plateaus in the deep-sea cores is reliant upon significant changes in sedimentation rate within those marine sediments which are, a priori, unknown and are not verified with an independent method. The concerns we raise are supported and strengthened with carbon cycle box model experiments and statistical simulations of pseudo-atmospheric and pseudo-marine records, allowing us to question the ability to identify and tune 14C age plateaus in the context of noisy and sparse data

IntCal20 tree rings: an archaeological Swot analysis

We undertook a strengths, weaknesses, opportunities, and threats (SWOT) analysis of Northern Hemisphere tree-ring datasets included in IntCal20 in order to evaluate their strategic fit with the demands of archaeological users. Case studies on wiggle-matching single tree rings from timbers in historic buildings and Bayesian modeling of series of results on archaeological samples from Neolithic long barrows in central-southern England exemplify the archaeological implications that arise when using IntCal20. The SWOT analysis provides an opportunity to think strategically about future radiocarbon (14C) calibration so as to maximize the utility of 14C dating in archaeology and safeguard its reputation in the discipline

Recent developments in calibration for archaeological and environmental samples

The curves recommended for calibrating radiocarbon (14C) dates into absolute dates have been updated. For calibrating atmospheric samples from the Northern Hemisphere, the new curve is called IntCal20. This is accompanied by associated curves SHCal20 for the Southern Hemisphere, and Marine20 for marine samples. In this “companion article” we discuss advances and developments that have led to improvements in the updated curves and highlight some issues of relevance for the general readership. In particular the dendrochronological based part of the curve has seen a significant increase in data, with single-year resolution for certain time ranges, extending back to 13,910 calBP. Beyond the tree rings, the new curve is based upon an updated combination of marine corals, speleothems, macrofossils, and varved sediments and now reaches back to 55,000 calBP. Alongside these data advances, we have developed a new, bespoke statistical curve construction methodology to allow better incorporation of the diverse constituent records and produce a more robust curve with uncertainties. Combined, these data and methodological advances offer the potential for significant new insight into our past. We discuss some implications for the user, such as the dating of the Santorini eruption and also some consequences of the new curve for Paleolithic archaeology

A short note on marine reservoir age simulations used in IntCal20

Beyond ~13.9 cal kBP, the IntCal20 radiocarbon (14C) calibration curve is based upon combining data across a range of different archives including corals and planktic foraminifera. In order to reliably incorporate such marine data into an atmospheric curve, we need to resolve these records into their constituent atmospheric signal and marine reservoir age. We present results of marine reservoir age simulations enabling this resolution, applying the LSG ocean general circulation model forced with various climatic background conditions and with atmospheric radiocarbon changes according to the Hulu Cave speleothem record. Simulating the spatiotemporal evolution of reservoir ages between 54,000 and 10,700 cal BP, we find reservoir ages between 500 and 1400 yr in the low- and mid-latitudes, but also more than 3000 yr in the polar seas. Our results are broadly in agreement with available marine radiocarbon reconstructions, with the caveat that continental margins, marginal seas, or tropical lagoons are not properly resolved in our coarse-resolution model

The influence of calibration curve construction and composition on the accuracy and precision of radiocarbon wiggle-matching of tree rings, illustrated by Southern Hemisphere atmospheric data sets from ad 1500–1950

This research investigates two factors influencing the ability of tree-ring data to provide accurate 14C calibration information: the fitness and rigor of the statistical model used to combine the data into a curve; and the accuracy, precision and reproducibility of the component 14C data sets. It presents a new Bayesian spline method for calibration curve construction and tests it on extant and new Southern Hemisphere (SH) data sets (also examining their dendrochronology and pretreatment) for the post-Little Ice Age (LIA) interval AD 1500–1950. The new method of construction allows calculation of component data offsets, permitting identification of laboratory and geographic biases. Application of the new method to the 10 suitable SH 14C data sets suggests that individual offset ranges for component data sets appear to be in the region of ± 10 yr. Data sets with individual offsets larger than this need to be carefully assessed before selection for calibration purposes. We identify a potential geographical offset associated with the Southern Ocean (high latitude) Campbell Island data. We test the new methodology for wiggle-matching short tree-ring sequences and use an OxCal simulation to assess the likely precision obtainable by wiggle-matching in the post-LIA interval

Testing and improving the IntCal20 calibration curve with independent records

Connecting calendar ages to radiocarbon (14C) ages, i.e. constructing a calibration curve, requires 14C samples that represent, or are closely connected to, atmospheric 14C values and that can also be independently dated. In addition to these data, there is information that can serve as independent tests of the calibration curve. For example, information from ice core radionuclide data cannot be directly incorporated into the calibration curve construction as it delivers less direct information on the 14C age–calendar age relationship but it can provide tests of the quality of the calibration curve. Furthermore, ice core ages on 14C-dated volcanic eruptions provide key information on the agreement of ice core and radiocarbon time scales. Due to their scarcity such data would have little impact if directly incorporated into the calibration curve. However, these serve as important “anchor points” in time for independently testing the calibration curve and/or ice-core time scales. Here we will show that such information largely supports the new IntCal20 calibration record. Furthermore, we discuss how floating tree-ring sequences on ice-core time scales agree with the new calibration curve. For the period around 40,000 years ago we discuss unresolved differences between ice core 10Be and 14C records that are possibly related to our limited understanding of carbon cycle influences on the atmospheric 14C concentration during the last glacial period. Finally, we review the results on the time scale comparison between the Greenland ice-core time scale (GICC05) and IntCal20 that effectively allow a direct comparison of 14C-dated records with the Greenland ice core data