Provides researchers with a reproducible research workflow for using R/RStudio to make the entire researchprocess reproducible; from data gathering, to analysis, to presentation Includes instructions not only for creating reproducible research in R, but also extensively discusses how to take advantage of recent developments in RStudio. Emphasizes the presentation of reproducible research with non-print formats such as HTML5 slideshows, blogs, and other web-based content. Covers a range of techniques to organize and remotely store files at all stages of the research process. These techniques both streamline the research process, especially by making revisions easier, and enhance The book itself will be reproducible, as all of the data, analysis, and markup files will be made available online.

Addressing the preservation of an increasingly important group of materials, this book outlines techniques for processing minerals and rocks in the field and laboratory, as well as the effects of treatments on specimens. The effects of light, temperature and relative humidity are covered and particularly sensitive minerals such as sulphides, including pyrite, meteorites and lunar rocks, are dealt with in detail.

Molybdenum (Mo) is a widely used trace metal for investigating redox conditions. However, unanswered questions remain that concentration and bulk isotopic analysis cannot specially answer. Improvements can be made by combining new geochemical techniques to traditional methods of Mo analysis. In this Element, we propose a refinement of Mo geochemistry within aquatic systems, ancient rocks, and modern sediments through molecular geochemistry (systematically combining concentration, isotope ratio, elemental mapping, and speciation analyses). Specifically, to intermediate sulfide concentrations governing Mo behavior below the 'switch-point' and dominant sequestration pathways in low oxygen conditions. The aim of this work is to 1) aid and improve the breadth of Mo paleoproxy interpretations by considering Mo speciation and 2) address outstanding research gaps concerning Mo systematics (cycling, partitioning, sequestration, etc.). The Mo paleoproxy has potential to solve ever complex research questions. By using molecular geochemical recommendations, improved Mo paleoproxy interpretations and reconstruction can be achieved.

Lithium isotopes are a relatively novel tracer of present and past silicate weathering processes. Given that silicate weathering is the primary long-term method by which CO2 is removed from the atmosphere, Li isotope research is going through an exciting phase. We show the weathering processes that fractionate dissolved and sedimentary Li isotope ratios, focusing on weathering intensity and clay formation. We then discuss the carbonate and silicate archive potential of past seawater 7Li. These archives have been used to examine Li isotope changes across both short and long timescales. The former can demonstrate the rates at which the climate is stabilised from perturbations via weathering, a fundamental piece of the puzzle of the long-term carbon cycle.

Natural radiation arises from many sources, from the unstable atoms within our own bodies and in the materials around us, from the Sun, and even from beyond the Solar System. Additional sources include the legacy of testing nuclear weapons, nuclear waste, and nuclear accidents. All these sources have provided means of dating environmental materials and tracing the movements of substances through land, sea, and air. But ionising radiation also interacts with DNA, which has led to a remarkable range of studies to examine how and how quickly these unstable atoms are accumulated by both humans and biota, and their various effects on both. Providing an overview of the sources, uses and impacts of ionising radiation in the environment, and the frameworks developed to manage exposures to them, this is a valuable reference for graduate students and researchers interested in radioecology, environmental science and radiological protection.

Develop analytical and visualization skills for investigating the behavior of agricultural and natural resources data. Become competent in importing, analyzing, and visualizing complex data sets in the R environment. Recode, combine, and restructure data sets for statistical analysis and visualization. Appreciate probability concepts as they apply to environmental problems. Understand common distributions used in statistical applications and inference. Summarize data effectively and efficiently for reporting purposes. Learn the tasks required to perform a variety of statistical hypothesis tests and interpret their results. Understand which modeling frameworks are appropriate for your data and how to interpret predictions. Includes over 130 exercises in R, with solutions available on the book's website.

In the modern marine environment, barium isotope ( 138Ba) variations are primarily driven by barite cycling-barite incorporates 'light' Ba isotopes from solution, rendering the residual Ba reservoir enriched in 'heavy' Ba isotopes by a complementary amount. Since the processes of barite precipitation and dissolution are vertically segregated and spatially heterogeneous, barite cycling drives systematic variations in the barium isotope composition of seawater and sediments. This Element examines these variations; evaluates their global, regional, local, and geological controls; and, explores how 138Ba can be exploited to constrain the origin of enigmatic sedimentary sulfates and to study marine biogeochemistry over Earth's history.

Diverse and abundant lipid biomarker assemblages have been reported from a variety of Proterozoic marine environments from the careful analysis of well-preserved rocks and oils. These molecular biosignatures have provided unique insights into the communities and the environmental conditions which characterized the Proterozoic marine biosphere. We summarize some of the major temporal patterns evident in Proterozoic lipid biomarkers found to date, whilst emphasizing the scale of local heterogeneity found within Neoproterozoic oceans from region to region, and their relationship with the evolving ecological, climatic and ocean/atmospheric redox conditions. Short commentaries on a selection of papers published from the last 15 years of biomarker literature are given. The focus here is on key studies, highlighted for further reading, which have helped to better constrain the timing of the ecological expansion of eukaryotes in Proterozoic oceans or which have impacted on our knowledge of the biological sources of Proterozoic biomarkers.

Paleosols formed in direct contact with the Earth's atmosphere, so they can record the composition of the atmosphere through weathering processes and products. Herein we critically review a variety of different approaches for reconstructing atmospheric O2 and CO2 over the past three billion years. Paleosols indicate relatively low CO2 over that time, requiring additional greenhouse forcing to overcome the 'faint young Sun' paradox in the Archean and Mesoproterozoic, as well as low O2 levels until the Neoproterozoic. Emerging techniques will revise the history of Earth's atmosphere further and may provide a window into atmospheric evolution on other planets.

In one form or another, iron speciation has had a long history as a paleoredox proxy. The technique has been refined considerably over the years, and the most recent scheme is unique in its potential to distinguish three major oceanic redox states - oxygenated, ferruginous and euxinic. This Element covers the theory behind the proxy, methods involved in applying the technique, and potential complications in interpreting Fe speciation data. A series of case studies are also provided, which highlight how more advanced consideration of the data, often in concert with other techniques, can provide unprecedented insight into the redox state of ancient oceans.

The stable chromium (Cr) isotope system has emerged over the past decade as a new tool to track changes in the amount of oxygen in earth's ocean-atmosphere system. Much of the initial foundation for using Cr isotopes ( 53Cr) as a paleoredox proxy has required recent revision. However, the basic idea behind using Cr isotopes as redox tracers is straightforward-the largest isotope fractionations are redox-dependent and occur during partial reduction of Cr(VI). As such, Cr isotopic signatures can provide novel insights into Cr redox cycling in both marine and terrestrial settings. Critically, the Cr isotope system-unlike many other trace metal proxies-can respond to short-term redox perturbations (e.g., on timescales characteristic of Pleistocene glacial-interglacial cycles). The Cr isotope system can also be used to probe the earth's long-term atmospheric oxygenation, pointing towards low but likely dynamic oxygen levels for the majority of Earth's history.

Ce anomalies track changes in oxygen availability due to the anomalous redox-sensitivity of Ce compared with the other rare earth elements. The proxy systematics have been calibrated experimentally as well as in modern anoxic water bodies. Ce anomalies are unique because they track intermediate manganous conditions, rather than fully anoxic conditions. In addition, they are sensitive to local-regional redox conditions, and can be analysed in chemical sediments such as carbonate rocks. This makes them especially useful as a tool to track local oxygen distribution in shallow shelf environments, where biodiversity is highest. This review focusses on the systematics of the Ce anomaly proxy, the preservation and extraction of the signal in sedimentary rocks, and the potential applications of the proxy.

Chemical Oceanography: Element Fluxes in the Sea focuses on the use of chemical distributions to understand mechanisms of physical, chemical, biological, and geological processes in the ocean. After an introduction describing observed chemical concentrations, chapters focus on using chemical tracers to determine fluxes on a variety of time scales. Long-term chemical cycles are dominated by exchanges between seawater and land, sediments, and underwater volcanoes. Biological and ocean mixing processes dominate internal chemical cycles that respond to changes on hundred- to thousand-year time scales. Stable and radioactive isotopes trace the fluxes of nutrients and carbon to quantify the rates and mechanisms of chemical cycles. Anthropogenic influences - which have grown to be of the same magnitude as some natural cycles - are a specific focus throughout the book. Discussion boxes and quantitative problems help instructors to deepen student learning. Appendices enhance the book's utility as a reference text for students and researchers.

This second edition is fully updated to include new developments in the study of metamorphism as well as enhanced features to facilitate course teaching. It integrates a systematic account of the mineralogical changes accompanying metamorphism of the major rock types with discussion of the conditions and settings in which they formed. The use of textures to understand metamorphic history and links to rock deformation are also explored. Specific chapters are devoted to rates and timescales of metamorphism and to the tectonic settings in which metamorphic belts develop. These provide a strong connection to other parts of the geology curriculum. Key thermodynamic and chemical concepts are introduced through examples which demonstrate their application and relevance. Richly illustrated in colour and featuring end-of-chapter and online exercises, this textbook is a comprehensive introduction to metamorphic rocks and processes for undergraduate students of petrology, and provides a solid basis for advanced study and research.

Vanadium isotope ratios (51V/50V) have potential to provide information about changes in past ocean oxygen contents. In particular, V isotopes may find utility in tracing variations at non-zero oxygen concentrations because the redox couple that controls V elemental and isotopic abundances in seawater (vanadate-vanadyl) appears to operate around 10M O2. This characteristic sets V isotopes apart from many other metal isotope redox proxies that require more reducing conditions to register significant changes in their isotope budgets. The oxygen abundance sensitivity range of V isotopes suggests that this paleoproxy could be particularly useful in tracing marine oxygenation changes throughout the Phanerozoic and potentially beyond.

The use of the trace element content of sedimentary pyrite as a proxy for the trace element composition of past oceans has recently emerged. The pyrite proxy has several potential advantages over bulk sample analysis: preservation through metamorphism; little dilution during analysis (samples are ablated not dissolved, allowing for the less abundant elements commonly held in the sulfide fraction to be investigated as proxies); accurate measurement of several elements simultaneously; the ability to screen sediments for hydrothermal overprint; and the technique can give information regarding trace element availably at multiple stages of diagenesis. Because of these multiple strengths, the pyrite trace element proxy is a valuable potential addition to the paleo-ocean chemistry tool kit.

The TEX86 paleothermometer is based upon the distribution of archaeal membrane lipids ('GDGTs') in marine sediments. GDGTs are ubiquitous, abundant and relatively resistant to degradation; as such, the TEX86 paleothermometer has been used to reconstruct sea surface temperature (SST) during the Cenozoic and early Mesozoic. We review the principles of the TEX86 proxy and developments made over the last two decades. We also discuss its application as a paleotemperature proxy and explore existing challenges and limitations.

The attraction of selenium isotopes as a paleoenvironmental tracer lies in the high redox potential of selenium oxyanions (SeIV and SeVI), the dominant species in the modern ocean. The largest isotopic fractionations occur during oxyanion reduction, which makes selenium isotopes a sensitive proxy for the redox evolution of our planet. As a case study we review existing data from the Neoarchean and Paleoproterozoic, which show that significant isotopic fractionations are absent until 2.5 Ga, and prolonged isotopic deviations only appear around 2.3 Ga. Selenium isotopes have thus begun to reveal complex spatiotemporal redox patterns not reflected in other proxies.

This book provides a wealth of geomathematical case history studies performed by the author during his career at the Ministry of Natural Resources Canada, Geological Survey of Canada (NRCan-GSC). Several of the techniques newly developed by the author and colleagues that are described in this book have become widely adopted, not only for further research by geomathematical colleagues, but by government organizations and industry worldwide. These include Weights-of-Evidence modelling, mineral resource estimation technology, trend surface analysis, automatic stratigraphic correlation and nonlinear geochemical exploration methods. The author has developed maximum likelihood methodology and spline-fitting techniques for the construction of the international numerical geologic timescale. He has introduced the application of new theory of fractals and multi fractals in the geostatistical evaluation of regional mineral resources and ore reserves and to study the spatial distribution of metals in rocks. The book also contains sections deemed important by the author but that have not been widely adopted because they require further research. These include the geometry of preferred orientations of contours and edge effects on maps, time series analysis of Quaternary retreating ice sheet related sedimentary data, estimation of first and last appearances of fossil taxa from frequency distributions of their observed first and last occurrences, tectonic reactivation along pre-existing schistosity planes in fold belts, use of the grouped jackknife method for bias reduction in geometrical extrapolations and new applications of the theory of permanent, volume-independent frequency distributions.

Tracking initial ocean (de)oxygenation is critical to better constrain the coevolution of life and environment. Development of thallium isotopes has provided evidence to track the global manganese oxide burial which responds to early (de)oxygenation for short-term climate events. Modern oxic seawater thallium isotope values are recorded in organic-rich sediments deposited below an anoxic water column. An expansion of reducing conditions decrease manganese oxide burial and shifts the seawater thallium isotope composition more positive. Recent work documents that thallium isotopes are perturbed prior to carbon isotope excursions, suggesting ocean deoxygenation is a precursor for increased organic carbon burial. This Element provides an introduction to the application of thallium isotopes, case studies, and future directions.

The 'detective' power of stable isotopes for processes that occurred in the past, and for elucidating mechanisms at the molecular level, has impressed researchers over the past 100 years, since the time when isotopes of elements were first discovered. While most are interested in the normalized abundance ratios of two isotopes of an element, further power was unleashed when researchers investigated the relationship of three or more isotopes of the same element, e.g. 16O, 17O, and 18O for oxygen. This Element focuses on the history of discovery of triple isotope effects, the conceptual framework behind these effects, and major lines of development in the past few years of triple oxygen isotope research.

Uranium isotopes (238U/235U) have emerged as a proxy to reconstruct the redox conditions of the Earth's oceans and atmosphere based upon the large isotopic fractionation between reduced U(IV) and oxidized U(VI). Variations in 238U/235U, particularly when recorded in carbonate sediments, can track global trends in marine oxygenation and de-oxygenation. It is unique from other proxies because reduction primarily occurs at the sediment-water interface, and this sensitivity makes U isotopes especially relevant for the habitability of benthic animals. This Element covers the background, methods, and case studies of this promising tool for understanding Earth's environmental transitions, as rapid development continues to refine the accuracy of interpretations of 238U/235U records.

Geochemistry at the surface of the earth is dominated by two somewhat antagonistic forces: chemical reactions which attempt to attain a steady state (equilibrium) and geological movement of materials in time and space which changes the parameters that control chemical equilibrium. Another aspect that is extremely important to earth surface geochemistry is the effect of plants on the chemical and physical stability of materials (soils). Plant systems in fact work against the normal chemical changes (loss of silica, potassium, etc.) and the normal physical changes (stabilizing fine grained materials (clays) in the surface zones to avoid erosion). Biological effects are clearly seen in redox effects in the various parts of the earth surface movement cycle; soil formation, stream transport, sedimentation. This book attempts to outline these different parameters and their interactions as they affect earth surface geochemsitry in order to give a better understanding of movement and accumulation of elements at the surface of the earth.

Extreme weather and climate change aggravate the frequency and magnitude of disasters. Facing atypical and more severe events, existing early warning and response systems become inadequate both in scale and scope. Earth Observation (EO) provides today information at global, regional and even basin scales related to agrometeorological hazards. This book focuses on drought, flood, frost, landslides, and storms/cyclones and covers different applications of EO data used from prediction to mapping damages as well as recovery for each category. It explains the added value of EO technology in comparison with conventional techniques applied today through many case studies.