SDAR: a package for plotting and analyzing stratigraphy data in R

Stratigraphic Columns (SC) are the most useful and common ways to represent the eld descriptions (e.g., grain size, thickness of rock packages, and fossil and lithological components) of rock sequences and well logs. In these representations the width of SC vary according to the grain size (i.e., the wider the strata, the coarser the rocks (Miall 1990; Tucker 2011)), and the thickness of each layer is represented at the vertical axis of the diagram. Typically these representations are drawn 'manually' using vector graphic editors (e.g., Adobe Illustrator®, CorelDRAW®, Inskape). Nowadays there are various software which automatically plot SCs, but there are not versatile open-source tools and it is very di cult to both store and analyse stratigraphic information. This document presents Stratigraphic Data Analysis in R (SDAR), an analytical package1 designed for both plotting and facilitate the analysis of Stratigraphic Data in R (R Core Team 2014). SDAR, uses simple stratigraphic data and takes advantage of the exible plotting tools available in R to produce detailed SCs. The main bene ts of SDAR are: (i) used to generate accurate and complete SC plot including multiple features (e.g., sedimentary structures, samples, fossil content, color, structural data, contacts between beds), (ii) developed in a free software environment for statistical computing and graphics, (iii) run on a wide variety of platforms (i.e., UNIX, Windows, and MacOS), (iv) both plotting and analysing functions can be executed directly on R's command-line interface (CLI), consequently this feature enables users to integrate SDAR's functions with several others add-on packages available for R from The Comprehensive R Archive Network (CRAN).

Microcharcoal concentration and elongation, and age model of sediment core MD96-2098

Although grassland and savanna occupy only a quarter of the world's vegetation, burning in these ecosystems accounts for roughly half the global carbon emissions from fire. However, the processes that govern changes in grassland burning are poorly understood, particularly on time scales beyond satellite records. We analyzed microcharcoal, sediments, and geochemistry in a high-resolution marine sediment core off Namibia to identify the processes that have controlled biomass burning in southern African grassland ecosystems under large, multimillennial-scale climate changes. Six fire cycles occurred during the past 170,000 y in southern Africa that correspond both in timing and magnitude to the precessional forcing of north-south shifts in the Intertropical Convergence Zone. Contrary to the conventional expectation that fire increases with higher temperatures and increased drought, we found that wetter and cooler climates cause increased burning in the study region, owing to a shift in rainfall amount and seasonality (and thus vegetation flammability). We also show that charcoal morphology (i.e., the particle's length-to-width ratio) can be used to reconstruct changes in fire activity as well as biome shifts over time. Our results provide essential context for understanding current and future grassland-fire dynamics and their associated carbon emissions.

Stratigraphic interpretation of Well-Log data of the Athabasca Oil Sands of Alberta Canada through Pattern recognition and Artificial Intelligence

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Three-dimensional sequence stratigraphy and subtle stratigraphic traps associated with systems tracts: West Cameron region, offshore Louisiana, Gulf of Mexico

Three-dimensional sequence stratigraphy is a potent exploration and development tool for the discovery of subtle stratigraphic traps. Reservoir morphology, heterogeneity and subtle stratigraphic trapping mechanisms can be better understood through systematic horizontal identification of sedimentary facies of systems tracts provided by three-dimensional attribute maps used as an important complement to the sequential analysis on the two-dimensional seismic lines and the well log data. On new prospects as well as on already-producing fields, the additional input of sequential analysis on three-dimensional data enables the identification, location and precise delimitation of new potentially productive zones. The first part of this paper presents four typical horizontal seismic facies assigned to the successive systems tracts of a third- or fourth-order sequence deposited in inner to outer neritic conditions on a elastic shelf. The construction of this synthetic representative sequence is based on the observed reproducibility of the horizontal seismic facies response to cyclic eustatic events on more than 35 sequences registered in the Gulf coast Plio-Pleistocene and Late Miocene, offshore Louisiana in the West Cameron region of the Gulf of Mexico. The second part shows how three-dimensional sequence stratigraphy can contribute in localizing and understanding sedimentary facies associated with productive zones. A case study in the early Middle Miocene Cibicides opima sands shows multiple stacked gas accumulations in the top slope fan, prograding wedge and basal transgressive systems tract of the third-order sequence between SB15.5 and SB 13.8 Ma.

Stratigraphic correlation of ODP Site 199-1218 and 199-1219

During Ocean Drilling Program Leg 199 a high-resolution (~1-2 cm/k.y.) biogenic sediment record from the late Paleocene to the early Miocene was recovered, containing an uninterrupted set of geomagnetic chrons as well as a detailed record of calcareous and siliceous biostratigraphic datum events. Shipboard lithologic proxy measurements and shore-based determinations of CaCO3 revealed regular cycles that can be attributed to climatic forcing. Discovering drill sites with well defined magneto- and biostratigraphic records that also show clear lithologic cycles is rare and valuable and creates the opportunity to develop a detailed stratigraphic intersite correlation, providing the basis to study paleoceanographic processes and mass accumulation rates at high resolution. Here we present extensive postcruise work that extends the shipboard composite depth stratigraphy by providing a high-resolution revised meters composite depth (rmcd) scale to compensate for depth distortion within individual cores. The depth-aligned data were then used to generate stacked records of lithologic proxy measurements. Making use of the increased signal-to-noise ratio in the stacked records, we then proceeded to generate a detailed site-to-site correlation between Sites 1218 and 1219 in order to decrease the depth uncertainty for magneto- and biostratigraphic datums. Stacked lithologic proxy records in combination with discrete measurements of CaCO3 were then exploited to calculate high-resolution carbonate concentration curves by regression of the multisensor track data with discrete measurements. By matching correlative features between the cores and wireline logging data, we also rescaled our core rmcd back to in situ depths. Our study identifies lithology-dependent core expansion due to unloading as the mechanism of varying stratigraphic thicknesses between cores.

Tie points and log-adjusted depth scales for ODP Leg 207 Sites

Multiple copies of Cretaceous black shales extending from the early Cenomanian to the end of the Santonian were recovered at five sites on Demerara Rise during Leg 207 of the Ocean Drilling Program. These sediments are primarily composed of laminated organic-rich claystones interbedded with coarser, lightly laminated foraminferal-bearing packstones and wackestones. The black shales represent the local expression of widespread organic-rich sedimentation in the Atlantic during the mid-Cretaceous. However, incomplete recovery prevented construction of continuous composite sections, resulting in uncertainties concerning the correct stratigraphic placement of individual cores. By combining high-resolution measurements of bulk density collected shipboard on the multisensor track with continuous downhole measurements of formation resistivity using the Formation MicroScanner, an equivalent logging depth scale was constructed for black shales recovered from Sites 1258, 1260, and 1261. The integrated depths approach centimeter-scale resolution and are supported by comparisons of coarser resolution natural gamma ray emissions collected on cores and through downhole logging operations. The new depths highlight the extent of both intra- and intercore gaps and provide an opportunity to further constrain temporal and spatial paleoceanographic changes captured in proxy records from these sediments.

Residuals for log-Burr XII regression models in survival analysis

In this paper, we compare three residuals to assess departures from the error assumptions as well as to detect outlying observations in log-Burr XII regression models with censored observations. These residuals can also be used for the log-logistic regression model, which is a special case of the log-Burr XII regression model. For different parameter settings, sample sizes and censoring percentages, various simulation studies are performed and the empirical distribution of each residual is displayed and compared with the standard normal distribution. These studies suggest that the residual analysis usually performed in normal linear regression models can be straightforwardly extended to the modified martingale-type residual in log-Burr XII regression models with censored data.

A log-extended Weibull regression model

A bathtub-shaped failure rate function is very useful in survival analysis and reliability studies. The well-known lifetime distributions do not have this property. For the first time, we propose a location-scale regression model based on the logarithm of an extended Weibull distribution which has the ability to deal with bathtub-shaped failure rate functions. We use the method of maximum likelihood to estimate the model parameters and some inferential procedures are presented. We reanalyze a real data set under the new model and the log-modified Weibull regression model. We perform a model check based on martingale-type residuals and generated envelopes and the statistics AIC and BIC to select appropriate models. (C) 2009 Elsevier B.V. All rights reserved.

The generalized log-gamma mixture model with covariates: local influence and residual analysis

In a sample of censored survival times, the presence of an immune proportion of individuals who are not subject to death, failure or relapse, may be indicated by a relatively high number of individuals with large censored survival times. In this paper the generalized log-gamma model is modified for the possibility that long-term survivors may be present in the data. The model attempts to separately estimate the effects of covariates on the surviving fraction, that is, the proportion of the population for which the event never occurs. The logistic function is used for the regression model of the surviving fraction. Inference for the model parameters is considered via maximum likelihood. Some influence methods, such as the local influence and total local influence of an individual are derived, analyzed and discussed. Finally, a data set from the medical area is analyzed under the log-gamma generalized mixture model. A residual analysis is performed in order to select an appropriate model.

Log-modified Weibull regression models with censored data: Sensitivity and residual analysis

This paper proposes a regression model considering the modified Weibull distribution. This distribution can be used to model bathtub-shaped failure rate functions. Assuming censored data, we consider maximum likelihood and Jackknife estimators for the parameters of the model. We derive the appropriate matrices for assessing local influence on the parameter estimates under different perturbation schemes and we also present some ways to perform global influence. Besides, for different parameter settings, sample sizes and censoring percentages, various simulations are performed and the empirical distribution of the modified deviance residual is displayed and compared with the standard normal distribution. These studies suggest that the residual analysis usually performed in normal linear regression models can be straightforwardly extended for a martingale-type residual in log-modified Weibull regression models with censored data. Finally, we analyze a real data set under log-modified Weibull regression models. A diagnostic analysis and a model checking based on the modified deviance residual are performed to select appropriate models. (c) 2008 Elsevier B.V. All rights reserved.

A Log-Linear Regression Model for the Beta-Weibull Distribution

We introduce the log-beta Weibull regression model based on the beta Weibull distribution (Famoye et al., 2005; Lee et al., 2007). We derive expansions for the moment generating function which do not depend on complicated functions. The new regression model represents a parametric family of models that includes as sub-models several widely known regression models that can be applied to censored survival data. We employ a frequentist analysis, a jackknife estimator, and a parametric bootstrap for the parameters of the proposed model. We derive the appropriate matrices for assessing local influences on the parameter estimates under different perturbation schemes and present some ways to assess global influences. Further, for different parameter settings, sample sizes, and censoring percentages, several simulations are performed. In addition, the empirical distribution of some modified residuals are displayed and compared with the standard normal distribution. These studies suggest that the residual analysis usually performed in normal linear regression models can be extended to a modified deviance residual in the proposed regression model applied to censored data. We define martingale and deviance residuals to evaluate the model assumptions. The extended regression model is very useful for the analysis of real data and could give more realistic fits than other special regression models.

Sudden onset of log-periodicity and superdiffusion in non-Markovian random walks with amnestically induced persistence: exact results

Random walks can undergo transitions from normal diffusion to anomalous diffusion as some relevant parameter varies, for instance the L,vy index in L,vy flights. Here we derive the Fokker-Planck equation for a two-parameter family of non-Markovian random walks with amnestically induced persistence. We investigate two distinct transitions: one order parameter quantifies log-periodicity and discrete scale invariance in the first moment of the propagator, whereas the second order parameter, known as the Hurst exponent, describes the growth of the second moment. We report numerical and analytical results for six critical exponents, which together completely characterize the properties of the transitions. We find that the critical exponents related to the diffusion-superdiffusion transition are identical in the positive feedback and negative feedback branches of the critical line, even though the former leads to classical superdiffusion whereas the latter gives rise to log-periodic superdiffusion.

Development of a short-term model using petrophysical logging at Century Mine, North Queensland

Pasminco Century Mine has developed a geophysical logging system to provide new data for ore mining/grade control and the generation of Short Term Models for mine planning. Previous work indicated the applicability of petrophysical logging for lithology prediction, however, the automation of the method was not considered reliable enough for the development of a mining model. A test survey was undertaken using two diamond drilled control holes and eight percussion holes. All holes were logged with natural gamma, magnetic susceptibility and density. Calibration of the LogTrans auto-interpretation software using only natural gamma and magnetic susceptibility indicated that both lithology and stratigraphy could be predicted. Development of a capability to enforce stratigraphic order within LogTrans increased the reliability and accuracy of interpretations. After the completion of a feasibility program, Century Mine has invested in a dedicated logging vehicle to log blast holes as well as for use in in-fill drilling programs. Future refinement of the system may lead to the development of GPS controlled excavators for mining ore.