burnr: Fire history analysis and graphics in R

We developed a new software package, burnr, for fire history analysis and plotting in the R statistical programming environment. It was developed for tree-ring fire-scar analysis, but is broadly applicable to other event analyses (e.g., avalanches, frost rings, or culturally modified trees). Our new package can read, write, and manipulate standard tree-ring fire history FHX files, produce fire—demography charts, calculate fire frequency and seasonality statistics, and run superposed epoch analysis (SEA). A key benefit of burnr is that it enables automation of analyses and plotting, especially for large data sets. The package also facilitates creative plotting, mapping, and analyses when combined with the thousands of packages available in R. In this paper, we describe the basic functionality of burnr and introduce users to fire history analyses in R.     

Cyclic environmental changes during the Early Toarcian at the Mochras Farm Borehole (Wales): a variable response of the foraminiferal community

Cyclostratigraphical analysis of the foraminiferal assemblages from the Early Toarcian at the Mochras Farm Borehole (Wales) was conducted in order to evaluate the incidence of cyclic palaeoenvironmental changes on the foraminiferal community. Different variables such as type of morphogroup, evolutionary strategy, habitat, particular taxa, diversity and abundance were studied using the Lomb–Scargle periodogram implemented in the computer program SLOMBS. A well‐developed cyclostratigraphical pattern is recognized, with the presence of several cycles (in metres) at 3.4–4/7.2–7.5/10.1–10.6/32.1–33.3/104.2–111.2/128.2/166.7, belonging to the high‐, middle‐, middle‐/low‐, and low‐frequency bands. The incidence and relevance of the cycles is found to be related to particular variables marking the global and local character of the involved processes. Cyclic changes in the organic matter input are found to be the most relevant palaeoenvironmental factor, oxygenation being secondary. A correspondence with specific Milankovitch cycles is, at present, difficult to determine.     

Brachiopod shell thickness links environment and evolution

While it is well established that the shapes and sizes of shells are strongly phylogenetically controlled, little is known about the phylogenetic constraints on shell thickness. Yet, shell thickness is likely to be sensitive to environmental fluctuations and has the potential to illuminate environmental perturbations through deep time. Here we systematically quantify the thickness of the anterior brachiopod shell which protects the filtration chamber and is thus considered functionally homologous across higher taxa of brachiopods. Our data come from 66 genera and 10 different orders and shows well-defined upper and lower boundaries of anterior shell thickness. For Ordovician and Silurian brachiopods we find significant order-level differences and a trend of increasing shell thickness with water depth. Modern (Cenozoic) brachiopods, by comparison, fall into the lower half of observed shell thicknesses. Among Ordovician–Silurian brachiopods, older stocks commonly have thicker shells, and thick-shelled taxa contributed more prominently to the Great Ordovician Biodiversification but suffered more severely during the Late Ordovician Mass Extinction. Our data highlight a significant reduction in maximum and minimum shell thickness following the Late Ordovician mass extinction. This points towards stronger selection pressure for energy-efficient shell secretion during times of crisis.     

First record of the Late Cretaceous starfish Metopaster parkinsoni (Forbes, 1848) in Iran

A body fossil of the starfish Metopaster parkinsoni was collected from chalky rocks of the Coniacian – Santonian transition in the Abderaz Formation at the Padeha section, east of Mashhad (Kopet-Dagh, Iran). The species is common in the English Chalk and is well known from the Cenomanian to the Maastrichtian of Europe. The new Iranian occurrence of M. parkinsoni extends its geographical range of 700 km to the South and 2500 km to the East. The species proliferated in upper offshore environments of the North Tethyan continental shelves. The outstanding occurrence of many well-preserved specimens during the Coniacian – Santonian transition in Europe and Iran may be related to favorable taphonomic conditions driven by the Ocean Anoxic Event (OAE III).     

多通道局部场电位时变频谱的同步模式及其对行为事件的编码

用时变相干（time-varying coherence）频谱方法分析多通道局部场电位（local field potentials, LFPs）随时间变化的同步模式及其对行为事件的编码。实验数据为行为事件前后3秒的28通道LFPs。分别计算每个通道LFP的功率谱密度（power spectral density, PSD）及多通道LFPs各个特征频段的PSD,选取PSD分布集中的?兹频段为LFPs的特征频段;应用离散二进小波变换获取LFPs的?兹频段分量;从28通道LFPs中选取PSD最大的通道作为参考通道。选取计算窗口为50 ms,从初始点开始计算每个窗口中每个通道LFP及其?兹分量对参考通道的频谱相干分析。移动窗口步长为25 ms,获取多通道LFPs及其?兹分量的时变频谱相干动态分布。研究结果显示,?兹频段分量的PSD占LFPs总功率的71.95%,表明?兹分量是实验中多通道LFPs同步的特征频段;多通道LFPs的?兹分量频谱相干值随时间变化,行为事件点前后1 s的相干值具有显著差别（P＜0.05）,表明多通道LFPs的?兹频段时变频谱相干有效地编码了这一行为事件。     

Snapshot of an early Paleoproterozoic ecosystem: Two diverse microfossil communities from the Turee Creek Group,Western Australia

Eighteen microfossil morphotypes from two distinct facies of black chert from a deep‐water setting of the c. 2.4 Ga Turee Creek Group, Western Australia, are reported here. A primarily in situ, deep‐water benthic community preserved in nodular black chert occurs as a tangled network of a variety of long filamentous microfossils, unicells of one size distribution and fine filamentous rosettes, together with relatively large spherical aggregates of cells interpreted as in‐fallen, likely planktonic, forms. Bedded black cherts, in contrast, preserve microfossils primarily within, but also between, rounded clasts of organic material that are coated by thin, convoluted carbonaceous films interpreted as preserved extracellular polymeric substance (EPS). Microfossils preserved within the clasts include a wide range of unicells, both much smaller and larger than those in the nodular black chert, along with relatively short, often degraded filaments, four types of star‐shaped rosettes and umbrella‐like rosettes. Large, complexly branching filamentous microfossils are found between the clasts. The grainstone clasts in the bedded black chert are interpreted as transported from shallower water, and the contained microfossils thus likely represent a phototrophic community. Combined, the two black chert facies provide a snapshot of a microbial ecosystem spanning shallow to deeper‐water environments, and an insight into the diversity of life present during the rise in atmospheric oxygen. The preserved microfossils include two new, distinct morphologies previously unknown from the geological record, as well as a number of microfossils from the bedded black chert that are morphologically similar to—but 400–500 Ma older than—type specimens from the c. 1.88 Ga Gunflint Iron Formation. Thus, the Turee Creek Group microfossil assemblage creates a substantial reference point in the sparse fossil record of the earliest Paleoproterozoic and demonstrates that microbial life diversified quite rapidly after the end of the Archean.     

老龄化对内源性注意的影响研究

目的:观察老年人和年轻人的内源性注意行为学及事件相关电位(ERP)表现,探讨老龄化对内源性注意的影响及其机制。方法:参考Posner的经典的"cue-target"范式设计内源性注意任务,分别记录和分析年轻人和老年人行为学和事件相关电位波形P1、N1,比较老年人和年轻人在内源性注意任务中的不同表现。结果:在内源性注意条件下,年轻人的反应时明显短于老年人(P0.05),对于N1成分的波幅,年龄主效应显著(P0.05),年轻人较老年人诱发更大的N1波幅。对于N1成分的潜伏期,年龄主效应显著(P0.05),年轻人潜伏期明显短于老年人。结论:老龄化对内源性注意的早期阶段有影响,在提高老年人注意力时应当对注意的不同类型进行评估和分类以采取合适的治疗策略。     

Dynamic analysis of recurrent event data using the additive hazard model

We propose a method for analysis of recurrent event data using information on previous occurrences of the event as a time-dependent covariate. The focus is on understanding how to analyze the effect of such a dynamic covariate while at the same time ensuring that the effects of treatment and other fixed covariates are unbiasedly estimated. By applying an additive regression model for the intensity of the recurrent events, concepts like direct, indirect and total effects of the fixed covariates may be defined in an analogous way as for traditional path analysis. Theoretical considerations as well as simulations are presented, and a data set on recurrent bladder tumors is used to illustrate the methodology.     

Dynamic analysis of multivariate failure time data

We present an approach for analyzing internal dependencies in counting processes. This covers the case with repeated events on each of a number of individuals, and more generally, the situation where several processes are observed for each individual. We define dynamic covariates, i.e., covariates depending on the past of the processes. The statistical analysis is performed mainly by the nonparametric additive approach. This yields a method for analyzing multivariate survival data, which is an alternative to the frailty approach. We present cumulative regression plots, statistical tests, residual plots, and a hat matrix plot for studying outliers. A program in R and S-PLUS for analyzing survival data with the additive regression model is available on the web site http://www.med.uio.no/imb/stat/addreg. The program has been developed to fit the counting process framework.