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spsurvey: Spatial Sampling Design and Analysis in R. spsurvey:R 中的空间抽样设计与分析。
IF 5.8 2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-18 DOI: 10.18637/jss.v105.i03
Michael Dumelle, Tom Kincaid, Anthony R Olsen, Marc Weber

spsurvey is an R package for design-based statistical inference, with a focus on spatial data. spsurvey provides the generalized random-tessellation stratified (GRTS) algorithm to select spatially balanced samples via the grts() function. The grts() function flexibly accommodates several sampling design features, including stratification, varying inclusion probabilities, legacy (or historical) sites, minimum distances between sites, and two options for replacement sites. spsurvey also provides a suite of data analysis options, including categorical variable analysis (cat_analysis()), continuous variable analysis cont_analysis()), relative risk analysis (relrisk_analysis()), attributable risk analysis (attrisk_analysis()), difference in risk analysis (diffrisk_analysis()), change analysis (change_analysis()), and trend analysis (trend_analysis()). In this manuscript, we first provide background for the GRTS algorithm and the analysis approaches and then show how to implement them in spsurvey. We find that the spatially balanced GRTS algorithm yields more precise parameter estimates than simple random sampling, which ignores spatial information.

spsurvey 提供广义随机分层(GRTS)算法,通过 grts() 函数选择空间平衡样本。grts() 函数可灵活适应多种抽样设计特征,包括分层、不同的包含概率、遗留(或历史)站点、站点之间的最小距离以及两个替换站点选项。spsurvey 还提供了一套数据分析选项,包括分类变量分析 (cat_analysis())、连续变量分析 cont_analysis())、相对风险分析 (relrisk_analysis())、可归因风险分析 (attrisk_analysis())、风险差异分析 (diffrisk_analysis())、变化分析 (change_analysis()) 和趋势分析 (trend_analysis())。在本手稿中,我们首先介绍了 GRTS 算法和分析方法的背景,然后展示了如何在 spsurvey 中实现它们。我们发现,与忽略空间信息的简单随机抽样相比,空间平衡 GRTS 算法能得到更精确的参数估计。
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引用次数: 0
hdpGLM: An R Package to Estimate Heterogeneous Effects in Generalized Linear Models Using Hierarchical Dirichlet Process 用层次Dirichlet过程估计广义线性模型中的异质效应的R包
2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v107.i10
Diogo Ferrari
The existence of latent clusters with different responses to a treatment is a major concern in scientific research, as latent effect heterogeneity often emerges due to latent or unobserved features - e.g., genetic characteristics, personality traits, or hidden motivations - of the subjects. Conventional random- and fixed-effects methods cannot be applied to that heterogeneity if the group markers associated with that heterogeneity are latent or unobserved. Alternative methods that combine regression models and clustering procedures using Dirichlet process are available, but these methods are complex to implement, especially for non-linear regression models with discrete or binary outcomes. This article discusses the R package hdpGLM as a means of implementing a novel hierarchical Dirichlet process approach to estimate mixtures of generalized linear models outlined in Ferrari (2020). The methods implemented make it easy for researchers to investigate heterogeneity in the effect of treatment or background variables and identify clusters of subjects with differential effects. This package provides several features for out-of-the-box estimation and to generate numerical summaries and visualizations of the results. A comparison with other similar R packages is provided.
对治疗有不同反应的潜在集群的存在是科学研究中的一个主要问题,因为潜在效应的异质性往往是由于潜在的或未观察到的特征(例如,受试者的遗传特征、人格特征或隐藏的动机)而出现的。如果与该异质性相关的群体标记是潜在的或未观察到的,则传统的随机效应和固定效应方法不能应用于该异质性。使用Dirichlet过程结合回归模型和聚类过程的替代方法是可用的,但这些方法实现起来很复杂,特别是对于具有离散或二元结果的非线性回归模型。本文讨论了R包hdpGLM作为实现一种新的分层狄利克雷过程方法的手段,该方法用于估计法拉利(2020)中概述的广义线性模型的混合物。所采用的方法使研究人员易于调查治疗效果或背景变量的异质性,并识别具有差异效应的受试者群。这个包为开箱即用的估计提供了几个特性,并生成数值摘要和结果的可视化。提供了与其他类似R包的比较。
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引用次数: 0
Application of Equal Local Levels to Improve Q-Q Plot Testing Bands with R Package qqconf. 等局部水平在R包qconf改进Q-Q地块测试波段中的应用。
IF 5.8 2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v106.i10
Eric Weine, Mary Sara McPeek, Mark Abney

Quantile-Quantile (Q-Q) plots are often difficult to interpret because it is unclear how large the deviation from the theoretical distribution must be to indicate a lack of fit. Most Q-Q plots could benefit from the addition of meaningful global testing bands, but the use of such bands unfortunately remains rare because of the drawbacks of current approaches and packages. These drawbacks include incorrect global Type I error rate, lack of power to detect deviations in the tails of the distribution, relatively slow computation for large data sets, and limited applicability. To solve these problems, we apply the equal local levels global testing method, which we have implemented in the R Package qqconf, a versatile tool to create Q-Q plots and probability-probability (P-P) plots in a wide variety of settings, with simultaneous testing bands rapidly created using recently-developed algorithms. qqconf can easily be used to add global testing bands to Q-Q plots made by other packages. In addition to being quick to compute, these bands have a variety of desirable properties, including accurate global levels, equal sensitivity to deviations in all parts of the null distribution (including the tails), and applicability to a range of null distributions. We illustrate the use of qqconf in several applications: assessing normality of residuals from regression, assessing accuracy of p values, and use of Q-Q plots in genome-wide association studies.

分位数-分位数(Q-Q)图通常很难解释,因为不清楚与理论分布的偏差有多大才能表明缺乏拟合。大多数Q-Q图都可以从增加有意义的全局测试波段中受益,但不幸的是,由于当前方法和封装的缺点,这种波段的使用仍然很少。这些缺点包括不正确的全局I型错误率,缺乏检测分布尾部偏差的能力,对大型数据集的计算相对较慢,以及有限的适用性。为了解决这些问题,我们应用了我们在R Package qqconf中实现的等局部水平全局测试方法,这是一个多功能工具,可以在各种设置中创建Q-Q图和概率-概率(P-P)图,并使用最新开发的算法快速创建同步测试波段。qqconf可以很容易地将全局测试带添加到其他包制作的Q-Q图中。除了快速计算之外,这些波段具有各种理想的特性,包括准确的全局电平,对零分布的所有部分(包括尾部)的偏差具有相同的灵敏度,以及对零分布范围的适用性。我们举例说明了qqconf在以下几个应用中的使用:评估回归残差的正态性,评估p值的准确性,以及在全基因组关联研究中使用Q-Q图。
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引用次数: 3
drda: An R Package for Dose-Response Data Analysis Using Logistic Functions 使用逻辑函数进行剂量-反应数据分析的R包
2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v106.i04
Alina Malyutina, Jing Tang, Alberto Pessia
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引用次数: 2
REndo: Internal Instrumental Variables to Address Endogeneity REndo:解决内生性的内部工具变量
2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v107.i03
Raluca Gui, Markus Meierer, Patrik Schilter, René Algesheimer
Endogeneity is a common problem in any causal analysis. It arises when the independence assumption between an explanatory variable and the error in a statistical model is violated. The causes of endogeneity are manifold and include response bias in surveys, omission of important explanatory variables, or simultaneity between explanatory and response variables. Instrumental variable estimation provides a possible solution. However, valid and strong external instruments are difficult to find. Consequently, internal instrumental variable approaches have been proposed to correct for endogeneity without relying on external instruments. The R package REndo implements various internal instrumental variable approaches, i.e., latent instrumental variables estimation (Ebbes, Wedel, Boeckenholt, and Steerneman 2005), higher moments estimation (Lewbel 1997), heteroscedastic error estimation (Lewbel 2012), joint estimation using copula (Park and Gupta 2012) and multilevel generalized method of moments estimation (Kim and Frees 2007). Package usage is illustrated on simulated and real-world data.
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引用次数: 1
ARCHModels.jl: Estimating ARCH Models in Julia ARCHModels。[j]: Julia中ARCH模型的估计
2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v107.i05
Simon A. Broda, Marc S. Paolella
This paper introduces ARCHModels.jl, a package for the Julia programming language that implements a number of univariate and multivariate autoregressive conditional heteroskedasticity models. This model class is the workhorse tool for modeling the conditional volatility of financial assets. The distinguishing feature of these models is that they model the latent volatility as a (deterministic) function of past returns and volatilities. This recursive structure results in loop-heavy code which, due to its just-in-time compiler, Julia is well-equipped to handle. As such, the entire package is written in Julia, without any binary dependencies. We benchmark the performance of ARCHModels.jl against popular implementations in MATLAB, R, and Python, and illustrate its use in a detailed case study.
本文介绍了ARCHModels。jl,一个用于Julia编程语言的包,实现了许多单变量和多变量自回归条件异方差模型。这个模型类是对金融资产的条件波动进行建模的主要工具。这些模型的显著特征是,它们将潜在波动率建模为过去收益和波动率的(确定性)函数。这种递归结构会导致循环繁重的代码,由于Julia的即时编译器,它可以很好地处理这些代码。因此,整个包是用Julia编写的,没有任何二进制依赖项。我们对ARCHModels的性能进行基准测试。在MATLAB, R和Python中比较流行的实现,并在详细的案例研究中说明其使用。
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引用次数: 0
netmeta: An R Package for Network Meta-Analysis Using Frequentist Methods netmeta:一个使用频率方法进行网络元分析的R包
IF 5.8 2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v106.i02
S. Balduzzi, G. Rücker, A. Nikolakopoulou, T. Papakonstantinou, G. Salanti, O. Efthimiou, G. Schwarzer
Network meta-analysis compares different interventions for the same condition, by combining direct and indirect evidence derived from all eligible studies. Network meta-analysis has been increasingly used by applied scientists and it is a major research topic for methodologists. This article describes the R package netmeta , which adopts frequentist methods to fit network meta-analysis models. We provide a roadmap to perform network meta-analysis, along with an overview of the main functions of the package. We present three worked examples considering different types of outcomes and different data formats to facilitate researchers aiming to conduct network meta-analysis with netmeta
网络荟萃分析通过结合来自所有符合条件的研究的直接和间接证据,对相同条件下的不同干预措施进行比较。网络元分析已被越来越多的应用科学家所使用,也是方法学家的一个重要研究课题。本文介绍了R软件包netmeta,该软件包采用频域方法拟合网络元分析模型。我们提供了执行网络元分析的路线图,以及软件包主要功能的概述。我们提出了三个考虑不同类型结果和不同数据格式的工作示例,以方便研究人员使用netmeta进行网络元分析
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引用次数: 23
RecordTest: An R Package to Analyze Non-Stationarity in the Extremes Based on Record-Breaking Events RecordTest:一个基于破纪录事件分析极端事件非平稳性的R包
IF 5.8 2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v106.i05
Jorge Castillo-Mateo, A. Cebrián, J. Asín
The study of non-stationary behavior in the extremes is important to analyze data in environmental sciences, climate, finance, or sports. As an alternative to the classical extreme value theory, this analysis can be based on the study of record-breaking events. The R package RecordTest provides a useful framework for non-parametric analysis of non-stationary behavior in the extremes, based on the analysis of records. The underlying idea of all the non-parametric tools implemented in the package is to use the distribution of the record occurrence under series of independent and identically distributed continuous random variables, to analyze if the observed records are compatible with that behavior. Two families of tests are implemented. The first only requires the record times of the series, while the second includes more powerful tests that join the information from different types of records: upper and lower records in the forward and backward series. The package also offers functions that cover all the steps in this type of analysis such as data preparation, identification of the records, exploratory analysis, and complementary graphical tools. The applicability of the package is illustrated with the analysis of the effect of global warming on the extremes of the daily maximum temperature series in Zaragoza, Spain.
研究极端情况下的非平稳行为对于分析环境科学、气候、金融或体育领域的数据非常重要。作为经典极值理论的替代,这种分析可以基于对破纪录事件的研究。R包RecordTest基于对记录的分析,为极端情况下的非平稳行为的非参数分析提供了一个有用的框架。包中实现的所有非参数工具的基本思想是使用记录在一系列独立和同分布的连续随机变量下的分布,来分析观察到的记录是否与该行为兼容。实现了两类测试。第一种方法只需要序列的记录时间,而第二种方法包含更强大的测试,可以连接来自不同类型记录的信息:向前和向后序列中的上记录和下记录。该软件包还提供了涵盖此类分析的所有步骤的功能,例如数据准备、记录识别、探索性分析和补充图形工具。通过分析全球变暖对西班牙萨拉戈萨日最高温度系列极端值的影响,说明了该方案的适用性。
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引用次数: 1
Additive Bayesian Network Modeling with the R Package abn 基于R包的加性贝叶斯网络建模
IF 5.8 2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v105.i08
Gilles Kratzer, F. Lewis, A. Comin, M. Pittavino, R. Furrer
The R package abn is designed to fit additive Bayesian network models to observational datasets and contains routines to score Bayesian networks based on Bayesian or information theoretic formulations of generalized linear models. It is equipped with exact search and greedy search algorithms to select the best network, and supports continuous, discrete and count data in the same model and input of prior knowledge at a structural level. The Bayesian implementation supports random effects to control for one-layer clustering. In this paper, we give an overview of the methodology and illustrate the package’s functionality using a veterinary dataset concerned with respiratory diseases in commercial swine production.
R包abn旨在将加性贝叶斯网络模型拟合到观测数据集,并包含基于广义线性模型的贝叶斯或信息论公式对贝叶斯网络进行评分的例程。它采用精确搜索和贪婪搜索算法来选择最佳网络,支持同一模型中的连续、离散和计数数据,并在结构层面上输入先验知识。贝叶斯实现支持随机效应来控制单层聚类。在本文中,我们概述了该方法,并使用与商业养猪生产中呼吸道疾病有关的兽医数据集说明了该包装的功能。
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引用次数: 0
jumpdiff: A Python Library for Statistical Inference of Jump-Diffusion Processes in Observational or Experimental Data Sets jumpdiff:一个Python库,用于在观测或实验数据集中对跳跃扩散过程进行统计推断
IF 5.8 2区 计算机科学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Pub Date : 2023-01-01 DOI: 10.18637/jss.v105.i04
L. R. Gorjão, D. Witthaut, P. Lind
We introduce a Python library, called jumpdiff , which includes all necessary functions to assess jump-diffusion processes. This library includes functions which compute a set of non-parametric estimators of all contributions composing a jump-diffusion process, namely the drift, the diffusion, and the stochastic jump strengths. Having a set of measurements from a jump-diffusion process, jumpdiff is able to retrieve the evolution equation producing data series statistically equivalent to the series of measurements. The back-end calculations are based on second-order corrections of the conditional moments expressed from the series of Kramers-Moyal coefficients. Additionally, the library is also able to test if stochastic jump contributions are present in the dynamics underlying a set of measurements. Finally, we introduce a simple iterative method for deriving second-order corrections of any Kramers-Moyal coefficient.
我们介绍一个名为jumpdiff的Python库,它包含评估跳跃扩散过程所需的所有函数。该库包括计算组成跳跃-扩散过程的所有贡献的一组非参数估计量的函数,即漂移,扩散和随机跳跃强度。有了一组来自跳跃-扩散过程的测量值,jumpdiff能够检索演化方程,产生与一系列测量值统计等效的数据序列。后端计算基于从Kramers-Moyal系数序列中表达的条件矩的二阶修正。此外,该库还能够测试随机跳跃贡献是否存在于一组测量的动态中。最后,我们介绍了一种简单的迭代方法来推导任何Kramers-Moyal系数的二阶修正。
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引用次数: 3
期刊
Journal of Statistical Software
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