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.
Located in
Library
/
RBINS Staff Publications 2020
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.
Located in
Library
/
RBINS Staff Publications
