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1,034 results for “Empirical”
Data from: The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander
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The departure between constant-rate birth-death and empirically inferred diversification processes
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Data from: Does pH matter for ecosystem multifunctionality? An empirical test in a semi-arid grassland on the Loess Plateau
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Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies
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An Empirical Study on the Use and Misuse of Java 8 Streams
<p>Streaming APIs allow for big data processing of native data structures by providing MapReduce-like operations over these structures. However, unlike traditional big data systems, these data structures typically reside in shared memory accessed by multiple cores. Although popular, this emerging hybrid paradigm opens the door to possibly detrimental behavior, such as thread contention and bugs related to non-execution and non-determinism. This study explores the use and misuse of a popular streaming API, namely, Java 8 Streams. The focus is on how developers decide whether or not to run these operations sequentially or in parallel and bugs both specific and tangential to this paradigm. Our study involved analyzing 34 Java projects and 5.53 million lines of code, along with 719 manually examined code patches. Various automated, including interprocedural static analysis, and manual methodologies were employed. The results indicate that streams are pervasive, stream parallelization is not widely used, and performance is a crosscutting concern that accounted for the majority of fixes. We also present coincidences that both confirm and contradict the results of related studies. The study advances our understanding of streams, as well as benefits practitioners, programming language and API designers, tool developers, and educators alike.</p>
Data - An Empirical Study of Method Chaining in Java
<p><strong>THERE ARE PROBLEMS WITH THIS DATASET. SEE <a href="https://tomokinakamaru.github.io/msr2020/">HERE</a> FOR MORE INFORMATION.</strong></p> <p>The collected method chains and the results of our manual inspections presented in "An Empirical Study of Method Chaining in Java.", which will be published in MSR 2020. The archive file contains the following materials:</p> <ul> <li><code>data.txt</code>: List of all the collected chains</li> <li><code>metadata.txt</code>: List of files and the number of lines for each file</li> <li><code>rq1_{short,long,extlong}_201{0,8}.md</code>: Sampled chains for RQ1</li> <li><code>rq1_201{0,8}.csv</code>: Result of our manual inspections in RQ1</li> <li><code>rq2.md</code>: Sampled chains for RQ2</li> <li><code>rq2.csv</code>: Result of our manual inspections in RQ2</li> </ul>
Dataset of Empirical MOOC Research 2016 - 2017
<p>Dataset of Empirical MOOC Research 2016 - 2018 </p>
A Large-scale Data Set and an Empirical Study of Docker Images Hosted on Docker Hub
<p>The data set schema, fields description, and analysis scripts are in the GitHub artifact repository.</p> <p>https://github.com/linncy/icsme2020-docker-study</p> <p> </p> <p>@inproceedings{LinICSME20,<br>author={Changyuan Lin and Sarah Nadi and Hamzeh Khazaei},<br>title={A Large-scale Data Set and an Empirical Study of Docker Images Hosted on Docker Hub},<br>booktitle={Proceedings of the 36th IEEE International Conference on Software Maintenance and Evolution (ICSME)},<br>year={2020},<br>url_Paper={https://www.dropbox.com/s/3bktcmdr7rlw1ic/LinICSME20.pdf}<br>}</p>
"An Empirical Study of i18n Collateral Changes and Bugs in GUIs of Android apps" Complementary Material
<p>Study results for the paper: "An Empirical Study of i18n Collateral Changes and Bugs in GUIs of Android apps"</p>
Heating Rates for Protons and Electrons in Polar Coronal Holes: Empirical Constraints from UVCS/SOHO (Associated Data)
<p>The accompanying files provide some "data behind the figures," as well as some supplementary data (e.g., properties of Monte Carlo trial models), for the paper titled "Heating Rates for Protons and Electrons in Polar Coronal Holes: Empirical Constraints from the Ultraviolet Coronagraph Spectrometer" (by Steven R. Cranmer), which was submitted to the Astrophysical Journal on 25 May 2020, and is currently undergoing revision in response to the referee's report as of 25 June 2020. All files ought to be in standard "Machine Readable Table" format.</p> <p>v1.1 note: The paper has been published as ApJ, vol. 900, paper number 105.<br> ADS link: https://ui.adsabs.harvard.edu/abs/2020ApJ...900..105C/abstract<br> </p>
SMartyMetrics Empirical Evaluation
<p>SMartyMetrics Empirical Evaluation</p>
Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards
<p>Genomic datasets generated by next-generation sequencing are increasingly prevalent in phylogenetics, but morphological data are required to phylogenetically place fossils, corroborate molecular hypotheses, and date phylogenies. Combined-evidence analyses provide an integrative assessment of tree topology. However, no attempt has been made to simultaneously analyze next-generation genomic datasets and morphological data, and the future of morphology in the context of genomic data is uncertain. I conducted combined-evidence analyses that include genomic and morphological datasets, specifically, with ultraconserved elements and two morphological matrices. In unweighted maximum likelihood and Bayesian combined-evidence analyses, morphological signal was dwarfed by the ultraconserved elements, and some node support values were reduced relative to ultraconserved element-only analyses. Increasing the weight of morphological characters allowed those data to influence the tree, but weighting subjectivity should be considered in future analyses. More attempts should be made to simultaneously analyze genomic and morphological datasets.</p>
The Brokers in a Dependency Ecosystem: An Empirical Study on using Package Managers
<p>A package manager (PM) is crucial to most technology stacks, acting as a broker to ensure that a verified dependency package is correctly installed, configured, or removed from an application. Diversity in technology stacks has led to dozens of PMs with various features. While recent studies have shown that developers struggle to migrate their dependencies, the common assumption is that PMs broker dependencies without any issues. In this paper, we would like to explore issues faced by developers when using PMs through an empirical study of content on Stack Overflow (SO). Through a quantitative analysis of 470,806 posts related to 16 PMs, we first determine the importance of PM-related posts and extract topics contained in these posts. We then carry out a qualitative analysis of 1,131 posts related to the Maven, npm, and NuGet dependency ecosystems to analyze questions, underlying causes and their resolutions. Our results confirm that developers tend to struggle with PMs. The choice of PM affects their user experience, as questions are likely to arise from lack of instructions and error messages. We find that PM-related posts are not likely to get resolved, with only 40% to 50% having an accepted answer. Our work further lays out a road-map to investigate the trade-off between design features to understand what an ideal PM would look like.</p>
Data from: Finding clarity in ecological outcomes using empirical integrated social-ecological systems: a case study of agriculture-dependent grassland birds
<p>1. Efforts to monitor and conserve populations and ecosystems in human-dominated landscapes can benefit from an empirical social-ecological systems approach.<br> 2. Here we illustrate how latent variable structural equation modelling of regional time series data can effectively describe interconnected drivers of population fluctuations in dynamic landscapes and can help to reveal previously unknown system drivers.<br> 3. Using a declining farmland-dependent bird species (Ammodramus savannarum) in the eastern United States (1994-2015) as a case study, our analysis reveals how farm management decisions drive population fluctuations (R<sup>2</sup> = 20%), while management is in turn highly influenced by climate (R<sup>2</sup> = 23-51%), but not by regional conservation spending.<br> 4. Synthesis and applications. Structural equation modelling revealed potential social-ecological pathways for halting regional population declines in a grassland bird, the Grasshopper Sparrow. Lower population growth rates followed years of higher hay yields (~4 percentage points per metric ton increase in hay yield) and later harvests (~2 percentage points per 10-day delay in harvest). Thus, one pathway for stabilising regional populations could involve compensating farmers for reducing hay harvests, potentially requiring a six-fold increase in current annual agri-environmental conservation spending.</p>
Dataset of "Test-Driven Code Review: An Empirical Study"
<p>Dataset of "Test-Driven Review: An Empirical Study"<br> This appendix material refers to the paper "Test-Driven Review: An Empirical Study" published in the Proceedings of the 41st International Conference on Software Engineering (ICSE 2019)</p>
DO THE TERRORISTS VERITABLY THE DEPRIVED SOULS? EXPLORING THE BITTER TRUTH EMPIRICALLY
<p>This dataset is related to the research conducted by the Authors on the topic "<strong>DO THE TERRORISTS VERITABLY THE DEPRIVED SOULS? EXPLORING THE BITTER TRUTH EMPIRICALLY".</strong></p>
Equatorial pitch angle distributions of 1 – 50 keV electrons in Earth's inner magnetosphere: an empirical model based on the Van Allen Probes observations
<p>This dataset contains the parameters of the pitch angle distribution model of 1 – 50 keV electrons, constructed using data from the HOPE instrument on the Van Allen Probes A using method described in the manuscript, along with the example IDL programs to read in model coefficients and plot out the model PADs.</p>
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
<p>A dye-sensitized solar cell was solvated by RTILs; using optimized empirical potentials, a molecular dynamics simulation was applied to compute vibrational properties. The obtained vibrational spectra were compared with experiment and ab initio molecular dynamics; various empirical potential spectra show how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction.</p>
BreakingVane/Defining-resilience-empirically_UCM: Defining resilience empirically_UCM
<p>Database with our main variables to perform multinomial logistic regression analyses used to determine which health-related, psychological, interpersonal and socio-demographic variables predicted the four psychological response patterns over time of resilience. Health-related variables (i.e., pre-existing health condition, pregnancy, SARS-CoV-2 infection and history of mental health difficulties), psychological variables (i.e. anxiety about the COVID-19 pandemic, economic threat due to COVID-19, increased substance use during confinement, intolerance to uncertainty, death anxiety, well-being, openness to the future and self-reported resilience), interpersonal variables (i.e. loneliness, perception of belonging, suspiciousness of others, religious identity, goodness of the world beliefs and identification with humanity) and demographic and living conditions variables (i.e. sex, age, education, employment, income, urbanicity, living with children and housing conditions).</p>
Empirical and methodological challenges to the model-based inference of diversification rates in extinct clades
<p>Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs, and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with (PyRate) or without (BAMM) a steep diversification drop, and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to hinder inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations, and suggest how the latter may be mitigated.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.