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Python Battery Mathematical Modelling (PyBaMM) Python电池数学建模（PyBaMM）
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2020-02-06 DOI: 10.1149/osf.io/5npy8
V. Sulzer, S. Marquis, R. Timms, Martin Robinson, S. J. Chapman
As the UK battery modelling community grows, there is a clear need for software that uses modern software engineering techniques to facilitate cross-institutional collaboration and democratise research progress. The Python package PyBaMM aims to provide a flexible platform for implementation and comparison of new models and numerical methods. This is achieved by implementing models as expression trees and processing them in a modular fashion through a pipeline. Comprehensive testing provides robustness to changes and hence eases the implementation of model extensions. PyBaMM is open source and available on GitHub at https://github.com/pybamm-team/PyBaMM.
随着英国电池建模社区的发展，显然需要使用现代软件工程技术来促进跨机构合作和民主化研究进展的软件。Python包PyBaMM旨在为新模型和数值方法的实现和比较提供一个灵活的平台。这是通过将模型实现为表达式树，并通过管道以模块化方式对其进行处理来实现的。全面的测试提供了对更改的健壮性，从而简化了模型扩展的实现。PyBaMM是开源的，可在GitHub上获得，网址为https://github.com/pybamm-team/PyBaMM.
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引用次数: 107
Moirai Version 3: A Data Processing System to Generate Recent Historical Land Inputs for Global Modeling Applications at Various Scales Moirai版本3:一个数据处理系统，用于在各种尺度上为全球建模应用程序生成最近的历史土地输入
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2020-01-15 DOI: 10.5334/jors.266
A. Vittorio, C. Vernon, Shijie Shu
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引用次数: 9
Using SAS Macros for Multiple Mediation Analysis in R. 在R中使用SAS宏进行多重中介分析。
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2020-01-01 Epub Date: 2020-10-07 DOI: 10.5334/jors.277
Paige Fisher, Wentao Cao, Qingzhao Yu

Mediation analysis refers to the process of making inferences on effects of third variables that intervene in the relationship between an exposure and response variable. The relationships among variables can be modelled by generalized linear models (GLM). However, GLM are not sufficient to describe relationships among variables when there are nonlinear relationships and potential interaction effects. A general mediation analysis method was developed using not only GLMs, but also multiple additive regression trees and smoothing splines by Yu and Li (2017). The method is implemented in the R package, mma. In this paper, we developed SAS macros so that functions in the mma package can be called and the mediation analysis performed in the SAS environment.

中介分析是指对第三个变量的影响进行推断的过程，这些第三个变量干预了暴露变量和反应变量之间的关系。变量之间的关系可以用广义线性模型(GLM)来建模。然而，当存在非线性关系和潜在的相互作用时，GLM不足以描述变量之间的关系。Yu和Li(2017)不仅使用glm，还使用多元加性回归树和平滑样条开发了一种通用的中介分析方法。该方法是在R包mma中实现的。在本文中，我们开发了SAS宏，以便在SAS环境中调用mma包中的函数并执行中介分析。
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引用次数: 0
A Figure One Web Tool for Visualization of Experimental Designs. 用于实验设计可视化的图一网络工具。
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2020-01-01 Epub Date: 2020-03-30 DOI: 10.5334/jors.243
Foo Cheung

This manuscript introduces a user-friendly, point and click open source and platform-independent software tool that aids the graphical representation of experimental studies. A graphical summary can give a high-level view of a study and represent in one illustration the important features of the data. Examples include sample collections, the time of each data collection, perturbations, and analysis performed. Graphical summaries can be useful in clarifying and documenting the complex relationships within an experiment by breaking down the component parts and expressing them visually. Commonly used cases for this tool include generating summary figures for presentation and publications. This tool was used either alone or in conjunction with other tools to generate schematic diagrams for talks and publications on several different on-going research projects.

这篇手稿介绍了一个用户友好的，点和点击开源和平台无关的软件工具，有助于实验研究的图形表示。图形摘要可以提供研究的高级视图，并在一个插图中表示数据的重要特征。示例包括样本收集、每次数据收集的时间、扰动和执行的分析。通过分解组成部分并可视化地表达它们，图形摘要在澄清和记录实验中的复杂关系方面非常有用。此工具的常用案例包括为演示文稿和出版物生成摘要数据。这个工具可以单独使用，也可以与其他工具结合使用，为几个不同的正在进行的研究项目的演讲和出版物生成示意图。
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引用次数: 1
SnappySonic: An Ultrasound Acquisition Replay Simulator. SnappySonic：超声波采集回放模拟器
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2020-01-01 Epub Date: 2020-03-30 DOI: 10.5334/jors.289
Stephen Thompson, Thomas Dowrick, Goufang Xiao, João Ramalhinho, Maria Robu, Mian Ahmad, Dan Taylor, Matthew J Clarkson

SnappySonic provides an ultrasound acquisition replay simulator designed for public engagement and training. It provides a simple interface to allow users to experience ultrasound acquisition without the need for specialist hardware or acoustically compatible phantoms. The software is implemented in Python, built on top of a set of open source Python modules targeted at surgical innovation. The library has high potential for reuse, most obviously for those who want to simulate ultrasound acquisition, but it could also be used as a user interface for displaying high dimensional images or video data.

SnappySonic 是一款超声采集回放模拟器，专为公众参与和培训而设计。它提供了一个简单的界面，用户无需专业硬件或声学兼容的模型即可体验超声采集。该软件用 Python 实现，建立在一套针对外科创新的开源 Python 模块之上。该库具有很高的重复使用潜力，最明显的是，它适用于想要模拟超声采集的用户，但也可用作显示高维图像或视频数据的用户界面。
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引用次数: 0
A Grid for Multidimensional and Multivariate Spatial Representation and Data Processing 一种用于多维和多变量空间表示和数据处理的网格
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2019-11-11 DOI: 10.31223/osf.io/9szfp
Tobias Stål, A. Reading
Researchers use 2D and 3D spatial models of multivariate data of differing resolutions and formats. It can be challenging to work with multiple datasets, and it is time consuming to set up a robust, performant grid to handle such spatial models. We share ‘agrid’, a Python module which provides a framework for containing multidimensional data and functionality to work with those data. The module provides methods for defining the grid, data import, visualisation, processing capability and export. To facilitate reproducibility, the grid can point to original data sources and provides support for structured metadata. The module is written in an intelligible high level programming language, and uses well documented libraries as numpy, xarray, dask and rasterio.
研究人员使用不同分辨率和格式的多元数据的2D和3D空间模型。使用多个数据集可能很有挑战性，而且建立一个健壮、高性能的网格来处理这样的空间模型也很耗时。我们共享“agrid”，这是一个Python模块，它提供了一个包含多维数据的框架和处理这些数据的功能。该模块提供了定义网格、数据导入、可视化、处理能力和导出的方法。为了便于再现，网格可以指向原始数据源，并为结构化元数据提供支持。该模块是用一种可理解的高级编程语言编写的，并使用了大量文档库，如numpy、xarray、dask和rasterio。
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引用次数: 8
Analysing Noisy Driver Physiology Real-Time Using Off-the-Shelf Sensors: Heart Rate Analysis Software from the Taking the Fast Lane Project 使用现成的传感器实时分析噪声驾驶员生理:来自快速通道项目的心率分析软件
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2019-10-29 DOI: 10.5334/jors.241
P. van Gent, Haneen Farah, N. van Nes, B. van Arem
This paper describes the functioning and development of HeartPy: a heart rate analysis toolkit designed for photoplethysmogram (PPG) data. Most openly available algorithms focus on electrocardiogram (ECG) data, which has very different signal properties and morphology, creating a problem with analysis. ECG-based algorithms generally don’t function well on PPG data, especially noisy PPG data collected in experimental studies. To counter this, we developed HeartPy to be a noise-resistant algorithm that handles PPG data well. It has been implemented in Python and C. Arduino IDE sketches for popular boards (Arduino, Teensy) are available to enable data collection as well. This provides both pc-based and wearable implementations of the software, which allows rapid reuse by researchers looking for a validated heart rate analysis toolkit for use in human factors studies.
本文描述了HeartPy的功能和开发：这是一个为光体积描记图（PPG）数据设计的心率分析工具包。大多数公开可用的算法都专注于心电图（ECG）数据，这些数据具有非常不同的信号特性和形态，这给分析带来了问题。基于ECG的算法通常不能很好地处理PPG数据，尤其是在实验研究中收集的有噪声的PPG数据。为了应对这种情况，我们开发了HeartPy作为一种抗噪声算法，可以很好地处理PPG数据。它已经在Python和C.中实现。流行板（Arduino，Teensy）的Arduino IDE草图也可以用于数据收集。这提供了该软件的基于pc和可穿戴实现，研究人员可以快速重复使用该软件，以寻找用于人为因素研究的经验证的心率分析工具包。
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引用次数: 64
DataDeps.jl: Repeatable Data Setup for Reproducible Data Science DataDeps。可复制数据科学的可重复数据设置
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2019-10-29 DOI: 10.5334/jors.244
Lyndon White, R. Togneri, Wei Liu, Bennamoun
We present DataDeps.jl: a julia package for the reproducible handling of static datasets to enhance the repeatability of scripts used in the data and computational sciences. It is used to automate the data setup part of running software which accompanies a paper to replicate a result. This step is commonly done manually, which expends time and allows for confusion. This functionality is also useful for other packages which require data to function (e.g. a trained machine learning based model). DataDeps.jl simplifies extending research software by automatically managing the dependencies and makes it easier to run another author’s code, thus enhancing the reproducibility of data science research.
我们介绍DataDeps。Jl:一个Julia包，用于可再现地处理静态数据集，以增强数据和计算科学中使用的脚本的可重复性。它用于自动运行软件的数据设置部分，该软件随论文一起复制结果。这一步通常是手动完成的，这会花费时间并导致混乱。此功能对于其他需要数据才能运行的包也很有用(例如，基于训练有素的机器学习模型)。DataDeps。Jl通过自动管理依赖关系简化了研究软件的扩展，并使运行其他作者的代码变得更容易，从而增强了数据科学研究的可再现性。
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引用次数: 3
gcamland v1.0 – An R Package for Modelling Land Use and Land Cover Change gcamland v1.0 -一个模拟土地利用和土地覆盖变化的R包
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2019-10-22 DOI: 10.5334/jors.233
K. Calvin, R. Link, M. Wise
gcamland v1.0 is an open source R package that was built to allocate land across a variety of uses based on changes in agricultural yield and commodity price. The land allocation algorithm is based on the one included in the Global Change Assessment Model (GCAM). gcamland v1.0 includes the ability to run in a historical mode, enabling model validation and parameter estimation, or in a future mode, simulating changes in land use/land cover in the future. For both modes, gcamland v1.0 can run a single simulation or a large ensemble of simulations with different parameters. When ensembles are generated in the historical mode, gcamland v1.0 calculates the likelihood of a given parameter set by comparing to observational data. gcamland v1.0 is publicly available via GitHub and has can be adjusted to represent alternative scenarios or configured to different regions and land types.
gcamland v1.0是一个开源的R包，用于根据农业产量和商品价格的变化分配不同用途的土地。土地分配算法基于全球变化评估模型(GCAM)中的土地分配算法。Gcamland v1.0包括在历史模式下运行的能力，支持模型验证和参数估计，或者在未来模式下，模拟未来土地利用/土地覆盖的变化。对于这两种模式，gcamland v1.0都可以运行单个模拟或具有不同参数的大型模拟集合。当在历史模式下生成集合时，gcamland v1.0通过与观测数据进行比较来计算给定参数集的可能性。gcamland v1.0可以通过GitHub公开获得，并且可以调整以表示替代方案或配置为不同的区域和土地类型。
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引用次数: 2
A Multilingual Copy Task: Measuring Typing and Motor Skills in Writing with Inputlog 多语言复制任务:用输入日志测量打字和写作运动技能
Q1 Social Sciences
Journal of Open Research Software
Pub Date : 2019-10-16 DOI: 10.5334/jors.234
L. Van Waes, M. Leijten, Tom Pauwaert, Eric Van Horenbeeck
Keyboarding is an essential mode of text production. In the context of typing courses, instruments have been developed to gauge typing skills but to our knowledge there is no computerized typing test measuring both motor skills and the influence of different levels of lexicality on typing fluency. That is why, we developed a strictly controlled copy task guiding participants through seven modules in which different prompts are presented, each dealing with complementary levels of lexicality. Fine-grained keystroke logging allows for a range of analyses with Inputlog [16]. The copy task can be used in writing process studies: research shows that typing fluency has an impact in the quality of text production [1, 24]. In previous writing research studies copy tasks have been used to study the relation between writing fluency and text composition (Wallot and Grabowski, 2013). The Inputlog copy task allows researchers to investigate different levels of lexicality in more detail. At the moment the copy task has been developed in ten different languages. The software is open-access and allows researchers to adapt the tasks to their specific needs.
键盘是文本生成的一种重要模式。在打字课程中，已经开发了测量打字技能的仪器，但据我们所知，还没有计算机化的打字测试来测量运动技能和不同程度的词汇对打字流利性的影响。这就是为什么，我们开发了一个严格控制的复制任务，指导参与者完成七个模块，在这些模块中呈现不同的提示，每个模块都涉及互补的词汇水平。细粒度的击键记录允许使用Inputlog[16]进行一系列分析。复制任务可用于写作过程研究：研究表明，打字流畅性对文本制作质量有影响[1，24]。在以往的写作研究中，复制任务被用来研究写作流畅性与文本构成之间的关系（Wallot和Grabowski，2013）。输入日志复制任务使研究人员能够更详细地调查不同级别的词汇。目前，复制任务已经用十种不同的语言开发。该软件是开放访问的，允许研究人员根据自己的具体需求调整任务。
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