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StratigrapheR: making and using lithologs in R
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StratigrapheR is an open-source integrated stratigraphy package. It is available in the free software environment R (https://CRAN.R-project.org/package=StratigrapheR) and is designed to generate lithologs in a semi-automated way, to process stratigraphical information, and to visualize any plot along the lithologs in the R environment. The basic graphical principle behind StratigrapheR is the incremental addition of elements to a drawing: a plot is opened, and graphical elements are successively added. This allows compartmentalisation of the drawing process, as well as the superposition of different plots for comparison. For instance a litholog of a single section can be written as a single function including all the drawing sub-functions, and be integrated in a larger plot, for instance to be correlated to other sections or to show proxy data. The StratigrapheR package is designed for efficient work, and minimum coding, while still allowing versatility. The lithological information of beds (upper and lower boundary, hardness, lithology, etc.) is converted into polygons. All polygons are drawn together using a single function, and each polygon can have its personalised symbology allowing to distinguish lithologies. A similar workflow can be used for plotting proxies while distinguishing each sample by their lithology. Vector graphics can be imported as SVG files, and precisely drawn with the lithologs to serve as symbols or complex elements. Every type of symbol is plotted by calling one single function which repeats the drawing for each occurrence of the represented feature. This illustrates that the amount of work invested to make lithologs using StratigrapheR is related to their complexity rather than their length: a long but monotonous litholog (e.g. of marl-limestone alternations) only takes a few lines of code to generate. The StratigrapheR package also provides a set of functions to deal with selected stratigraphic intervals (for instance in the [0,1[ form): they allow simplification, merging, inversion and visualisation of intervals, as well as identifying the samples included in the given intervals, and characterising the relation of the intervals with each other (overlap, neighbouring, etc.). StratigrapheR includes PDF and SVG generation of plots, of any dimension. The generated PDF can even store multiple plots in a single file (each plot on a different page) to document data processing comprehensively.
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RBINS Staff Publications 2020
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Stratigraphic context and dating of the Middle and Late Eocene vertebrate localities of the Fayum.
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The Fayum Oasis and surrounding areas in Egypt include a number of exceptionally rich and important fossil vertebrate sites. These include the Wadi Al-Hitan World Heritage Site, made famous by the abundance of archaeocete whale remains, and the site BQ-2 with its diverse terrestrial mammals, including primates. Despite the importance of this area, the stratigrapby is poorly understood and there has be little agreement in the dating of the fossiliferous units. This is in large part due to the extreme diachroneity of some of the rock units and paucity of biostratigraphically useful fossils within the shallow water facies. Platform carbonates are overlain by condensed open marine mudstones of the Gebannam Formation. These span the Bartonian-Priabonian boundary, with a diverse offhore marine fauna being present throughout, including marine mammals. Four units of shoreface sandstone of the Birkel Qarun Formation overlie and partly pass into the Gehannam Formation. The lowest of these sandstone units is dated to nannofossil zone NP19/20, and hence 'mid' Priabonian, and contains the oldest archaeocetes described from the region. Diverse fossils, including abundant whales, are present throughout the Birket Qarun Formation, but these are especially concentrated at the top of the lowest sandstone (lowstand systems tract) and in the transgressive lower part of the third sandstone and its lateral equivalent within the Gehannam Formation (transgressive systems tract). The overlying Qasr el Sagha Formation is a very rapidly deposited deltaic/lagoonal complex. Tidal channels from two to over 40 metres deep are present throughout. The lower part of this formation is still in nannofossil zone NP19/20. INterchannel deposits contain a fully marine, but probably shallow water, assemblage. Larger channels also include deeper water elements near the base, with transported terrestrial and quasimarine elements being present within the uppermost part of a small channel fill at quarry BQ-2. The transition to the non-marine units above is sharp but conformable and coincides with the base of the Oligocene. The clastic succession indicates the initiation of Nile-type drainage and coincides with the uplift of East Africa, preventing drainage to the east. It is likely that clastic successions in the Qattara Depression and Libya can be related to the same sedimentological episodes. This is largely based on, and dedicated to, the work of Chris King, who passed away earlier this year.
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RBINS Staff Publications
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Stratigraphical context of the Pliocene right whales (Balaenidae) from the North Sea
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RBINS Staff Publications 2021
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Stratigraphy and Commissions. Do we need stratigraphic commissions ?
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RBINS Staff Publications 2016
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Stratochip, a dual balloon high-altitude platform: controlled altitude flight experiments and potential applications in geosciences.
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A high-altitude dual balloons system, the 'Stratochip', was designed at the Geological Survey of Belgium to serve as a development platform to carry measurement and earth observation equipments, in altitudes comprised between 1000 and 25000m. These working altitudes far exceed the range of current motor powered unmanned aerial vehicules, with a higher weight carrying capacity (up to 10-15kg). This platform is built around a two helium balloons configuration, than can be released one by one at a target altitude or location, allowing a partially controlled drift of the platform. Using a 'nowcasting' meteorological model, updated by flight telemetry, the predicted path can be refined live to follow and retrieve the equipment in a predicted landing area. All subsystems (balloon cut-off devices, flight controller, telemetry system) have been developed in-house. Three independent communication channels, designed to work at extremely low temperature (up to -60° C) ensure a continuous tracking until landing. A calibrated parachute is used to control the safe descent of the equipment. Several flight tests have been performed in Belgium to control the meteorological model accuracy for wind predictions (model based on National Oceanic and Atmospheric Administration data). Those tests demonstrated the capability of the platform to maintain its altitude in a predicted path, allowing using the platform for new types of atmospheric studies and affordable high-altitude remote-sensing applications (i.e. sub-meter resolution stereo imagery).
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Structural framework as the new fundament for international geoscientific cooperation and policy support
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The transition towards a clean and low carbon energy system in Europe will increasingly rely on the use of the subsurface. Communicating the potential and limitations of subsurface resources and applications remains challenging. This is partly because the subsurface is not part of the world people experience, leaving them without reference frame to understand impacts or consequences. A second element is that the geological context of a specific area is very abstract, three dimensional, and hence difficult to correctly and intuitively disclose using traditional geological maps or models. The GeoConnect³d project is finalising the development and testing of a new type of information system that can be used for various geo-applications, decision-making, and subsurface spatial planning. This is being accomplished through the innovative structural framework model, which reorganises, contextualises, and adds value to geological data. The model is primarily focused on geological limits, or broadly planar structures that separate a given geological unit from its neighbouring units. It also includes geomanifestations, highlighting any distinct local expression of ongoing or past geological processes. These manifestations, or anomalies, often point to specific geologic conditions and therefore can be important sources of information to improve geological understanding of an area and its subsurface (see Van Daele et al., this volume, Rombaut et al., this volume ). Geological information in this model is composed of spatial data at different scales, with a one-to-one link between geometries and their specific attributes (including uncertainties), and of semantic data, categorised conceptually and/or linked using generic SKOS hierarchical schemes. Concepts and geometries are linked by a one-to-many relationship. The combination of these elements subsequently results in a multi-scale, harmonised and robust model. In spite of its sound technical basis, consultation is highly intuitive. The underlying vocabulary is of high scientific standard and linked to INSPIRE and GeoSciML schemes, but can also automatically, both visually and semantically, be simplified to be understood by non-experts. The structural framework-geomanifestations methodology has now been applied to different areas in Europe. The focus on geological limits brings various advantages, such as displaying geological information in an explicit, and therefore more understandable way, and simplifying harmonisation efforts in large-scale geological structures crossing national borders originating from models of different scale and resolution. The link between spatial and semantic data is key in adding conceptual definitions and interpretations to geometries, and provides a very thorough consistency test for present-day regional understanding of geology. As a framework, other geological maps and models can be mapped to it by identifying common limits, such as faults, unconformities, etc, allowing to bring together non-harmonised maps in a meaningful way. The model demonstrates it is possible to gather existing geological data into a harmonised and robust knowledge system. We consider this as the way forward towards pan-European integration and harmonisation of geological information. Moreover, we identify the great potential of the structural framework model as a toolbox to communicate geosciences beyond our specialised community. Making geological information available to all stakeholders involved is an important step to support subsurface spatial planning to move forward towards a clean energy transition. . This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 731166.
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RBINS Staff Publications 2021
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Structural framework: a new way to organise and communicate geological information
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A structural framework is a well-defined concept, being used primarily to add structural understanding to a geological model. Within GeoConnect³d, a new approach is used, i.e. the structural framework concept is modified to become the leading model, in which geological maps and models can be inserted and related to. This structural framework is being developed and implemented for two areas of interest - Roer-to-Rhine in northwest Europe and Pannonian Basin in eastern Europe - and will soon be implemented in two pilot areas, Ireland and Bavaria. The organisation of information is strongly linked to different scales of visualisation, starting from the pan-European view (1:15,000,000) with the possibility to zoom in to the scale of local geological models and maps in these four areas. The GeoConnect³d structural framework reorganises geological information in terms of geological limits and geological units. Limits are defined as broadly planar structures that separate a given geological unit from its neighbouring units, e.g. faults (limits) that define a graben (unit), or an unconformity (limit) that defines a basin (unit). Therefore, the key relationship between these two structural framework elements is that units are defined by limits i.e. all units must be bounded by limits. It is important to note that this relationship is not necessarily mutual: not all limits have to be unit-defining. A first test of the structural framework methodology was carried out in the Netherlands and Belgium for the Roer Valley graben, as the faults in this area were already modelled in a cross-boundary project (H3O-Roer Valley Graben). Displaying different elements according to scale of visualisation coupled with vocabulary information (definition, grouping and semantic relations between elements, etc.) following the SKOS-system proved a powerful tool to display geological information in an understandable way and improve insights in large-scale geological structures crossing national borders. Additionally, links with other GeoERA projects such as HIKE and its fault database are being successfully established. We consider the outcomes of this test promising to fulfil one of the main goals of GeoConnect³d, i.e. preparing and disclosing geological information in an understandable way for stakeholders. We also consider this as the way forward towards pan-European integration and harmonisation of geological information, where the ultimate challenge is to correlate or otherwise link information from different geological domains and of different scales. This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 731166.
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RBINS Staff Publications 2020
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Structure of an ant assemblage in the canopy of a tropical rainforest in Papua New Guinea.
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RBINS Staff Publications
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Study of fossil feathers using infrared spectroscopy and imagery.
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RBINS Staff Publications
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Study of fossil feathers using infrared spectroscopy and imagery.
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RBINS Staff Publications
