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LightLogR: Reproducible analysis of personal light exposure data.
Journal of open source software Pub Date : 2025-03-13 DOI: 10.21105/joss.07601
Johannes Zauner, Steffen Hartmeyer, Manuel Spitschan
{"title":"LightLogR: Reproducible analysis of personal light exposure data.","authors":"Johannes Zauner, Steffen Hartmeyer, Manuel Spitschan","doi":"10.21105/joss.07601","DOIUrl":"10.21105/joss.07601","url":null,"abstract":"<p><p>Light plays an important role in human health and well-being, which necessitates the study of the effects of personal light exposure in real-world settings, measured by means of wearable devices. A growing number of studies incorporate these kinds of data to assess associations between light and health outcomes. Yet with few or missing standards, guidelines, and frameworks, it is challenging setting up measurements, analysing the data, and comparing outcomes between studies. Overall, time series data from wearable light loggers are significantly more complex compared to controlled stimuli used in laboratory studies. In this paper, we introduce LightLogR, a novel resource to facilitate these research efforts. The package for R statistical software is open-source and permissively MIT-licenced. As part of a developing software ecosystem, LightLogR is built with common challenges of current and future datasets in mind. The package standardises many tasks for importing and processing personal light exposure data. It allows for quick as well as detailed insights into the datasets through summary and visualisation tools. Furthermore, LightLogR incorporates major metrics commonly used in the field (61 metrics across 17 metric families), all while embracing an inherently hierarchical, participant-based data structure.</p>","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"10 107","pages":"7601"},"PeriodicalIF":0.0,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617517/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
BART-Survival: A Bayesian machine learning approach to survival analyses in Python.
Journal of open source software Pub Date : 2025-01-28 DOI: 10.21105/joss.07213
Jacob Tiegs, Julia Raykin, Ilia Rochlin
{"title":"BART-Survival: A Bayesian machine learning approach to survival analyses in Python.","authors":"Jacob Tiegs, Julia Raykin, Ilia Rochlin","doi":"10.21105/joss.07213","DOIUrl":"10.21105/joss.07213","url":null,"abstract":"<p><p>BART-Survival is a Python package that allows time-to-event (survival) analyses in discrete-time using the non-parametric machine learning algorithm, Bayesian Additive Regression Trees (BART). BART-Survival combines the performance of the BART algorithm with the complementary data and model formatting required to complete the survival analyses. The library contains a convenient application programming interface (API) that allows a simple approach when using the library for survival analyses, while maintaining capabilities for added complexity when desired. The package is intended for analysts exploring use of flexible non-parametric alternatives to traditional (semi-)parametric survival analyses.</p>","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"10 105","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11848778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats. harmonize-wq：将水质门户网站的数据标准化、清理和整理成更易于分析的格式。
Journal of open source software Pub Date : 2024-10-22 DOI: 10.21105/joss.07305
Justin Bousquin, Cristina A Mullin
{"title":"harmonize-wq: Standardize, clean and wrangle Water Quality Portal data into more analytic-ready formats.","authors":"Justin Bousquin, Cristina A Mullin","doi":"10.21105/joss.07305","DOIUrl":"https://doi.org/10.21105/joss.07305","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"9 102","pages":"7305"},"PeriodicalIF":0.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142933878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other. primerForge：一个Python程序，用于识别能够区分基因组组的引物对。
Journal of open source software Pub Date : 2024-09-16 DOI: 10.21105/joss.06850
Joseph S Wirth, Lee S Katz, Grant M Williams, Jessica C Chen
{"title":"primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.","authors":"Joseph S Wirth, Lee S Katz, Grant M Williams, Jessica C Chen","doi":"10.21105/joss.06850","DOIUrl":"10.21105/joss.06850","url":null,"abstract":"<p><p>In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives. An \"ingroup\" refers to a group of microbes that are the primary focus of study or interest. Conversely, an \"outgroup\" consists of microbes that are closely-related to, but have evolved separately from, the ingroup. While whole genome sequencing and downstream phylogenetic analyses can be employed to do this, these techniques are often slow and can be resource intensive. Additionally, the laboratory would have to sequence the whole genome to use these tools to determine whether or not a new sample is part of the ingroup or outgroup. Alternatively, polymerase chain reaction (PCR) can be used to amplify regions of genetic material that are specific to the strain(s) of interest. PCR is faster, less expensive, and more accessible than whole genome sequencing, so having a PCR-based approach can accelerate the detection of specific strain(s) of microbes and facilitate diagnoses and/or population studies.</p>","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"9 101","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11611387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142775945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
small_gicp: Efficient and parallel algorithms for pointcloud registration small_gicp：点云注册的高效并行算法
Journal of open source software Pub Date : 2024-08-10 DOI: 10.21105/joss.06948
Kenji Koide
{"title":"small_gicp: Efficient and parallel algorithms for point\u0000cloud registration","authors":"Kenji Koide","doi":"10.21105/joss.06948","DOIUrl":"https://doi.org/10.21105/joss.06948","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141920298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
gollum: An intuitive programmatic and visual interfacefor precomputed synthetic spectral model grids 咕噜：预计算合成光谱模型网格的直观编程和视觉界面
Journal of open source software Pub Date : 2024-08-09 DOI: 10.21105/joss.06601
Sujay Shankar, M. Gully-Santiago, Caroline V. Morley, Jiayi Cao, Kyle F. Kaplan, Karina Kimani-Stewart, Diana Gonzalez-Argúeta
{"title":"gollum: An intuitive programmatic and visual interface\u0000for precomputed synthetic spectral model grids","authors":"Sujay Shankar, M. Gully-Santiago, Caroline V. Morley, Jiayi Cao, Kyle F. Kaplan, Karina Kimani-Stewart, Diana Gonzalez-Argúeta","doi":"10.21105/joss.06601","DOIUrl":"https://doi.org/10.21105/joss.06601","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"2 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
regional-mom6: A Python package for automaticgeneration of regional configurations for the Modular Ocean Model6 regional-mom6：用于自动生成模块海洋模式 6 区域配置的 Python 软件包
Journal of open source software Pub Date : 2024-08-09 DOI: 10.21105/joss.06857
Ashley J. Barnes, Navid C. Constantinou, A. Gibson, A. Kiss, Chris Chapman, John Reilly, Dhruv Bhagtani, Luwei Yang
{"title":"regional-mom6: A Python package for automatic\u0000generation of regional configurations for the Modular Ocean Model\u00006","authors":"Ashley J. Barnes, Navid C. Constantinou, A. Gibson, A. Kiss, Chris Chapman, John Reilly, Dhruv Bhagtani, Luwei Yang","doi":"10.21105/joss.06857","DOIUrl":"https://doi.org/10.21105/joss.06857","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"48 49","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ExoTiC-LD: thirty seconds to stellar limb-darkeningcoefficients ExoTiC-LD：30 秒恒星边缘致暗系数
Journal of open source software Pub Date : 2024-08-09 DOI: 10.21105/joss.06816
D. Grant, H. Wakeford
{"title":"ExoTiC-LD: thirty seconds to stellar limb-darkening\u0000coefficients","authors":"D. Grant, H. Wakeford","doi":"10.21105/joss.06816","DOIUrl":"https://doi.org/10.21105/joss.06816","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"4 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
XRTpy: A Hinode-X-Ray Telescope Python Package XRTpy：日冕-X 射线望远镜 Python 软件包
Journal of open source software Pub Date : 2024-08-09 DOI: 10.21105/joss.06396
Joy Velasquez, Nicholas Murphy, Katharine K. Reeves, Jonathan Slavin, Mark Weber, Will T. Barnes
{"title":"XRTpy: A Hinode-X-Ray Telescope Python Package","authors":"Joy Velasquez, Nicholas Murphy, Katharine K. Reeves, Jonathan Slavin, Mark Weber, Will T. Barnes","doi":"10.21105/joss.06396","DOIUrl":"https://doi.org/10.21105/joss.06396","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"49 42","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141923930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SIRITVIS: Social Interaction Research Insights TopicVisualisation SIRITVIS：社会互动研究洞察主题可视化
Journal of open source software Pub Date : 2024-08-08 DOI: 10.21105/joss.06243
Sagar Narwade, Gillian Kant, Benjamin Säfken, Benjamin Leiding
{"title":"SIRITVIS: Social Interaction Research Insights Topic\u0000Visualisation","authors":"Sagar Narwade, Gillian Kant, Benjamin Säfken, Benjamin Leiding","doi":"10.21105/joss.06243","DOIUrl":"https://doi.org/10.21105/joss.06243","url":null,"abstract":"","PeriodicalId":94101,"journal":{"name":"Journal of open source software","volume":"56 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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