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260 results for “Empirical Study”
COVID-19 evidence syntheses with artificial intelligence: an empirical study of systematic reviews
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Data from: Behavioral thermoregulation of caterpillars is altered by temperature, but not parasitism: an empirical field study
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Assessing confidence in root placement on phylogenies: an empirical study using non-reversible models for Mammals
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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>
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>
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>
Data for: Gene tree estimation error with ultraconserved elements: An empirical study on Pseudapis bees
<p>Summarizing individual gene trees to species phylogenies using two-step coalescent methods is now a standard strategy in the field of phylogenomics. However, practical implementations of summary methods suffer from gene tree estimation error, which is caused by various biological and analytical factors. Greatly understudied is the choice of gene tree inference method and downstream effects on species tree estimation for empirical data sets. To better understand the impact of this method choice on gene and species tree accuracy, we compare gene trees estimated through four widely used programs under different model-selection criteria: PhyloBayes, MrBayes, IQ-Tree and RAxML. We study their performance in the phylogenomic framework of > 800 ultraconserved elements from the bee subfamily Nomiinae (Halictidae). Our taxon sampling focuses on the genus <i>Pseudapis</i>, a distinct lineage with diverse morphological features, but contentious morphology-based taxonomic classifications and no molecular phylogenetic guidance. We approximate topological accuracy of gene trees by assessing their ability to recover two uncontroversial, monophyletic groups, and compare branch lengths of individual trees using the stemminess metric (the relative length of internal branches). We further examine different strategies of removing uninformative loci and the collapsing of weakly supported nodes into polytomies. We then summarize gene trees with ASTRAL and compare resulting species phylogenies, including comparisons to concatenation-based estimates. Gene trees obtained with the reversible jump model search in MrBayes were most concordant on average and all Bayesian methods yielded gene trees with better stemminess values. The only gene tree estimation approach whose ASTRAL summary trees consistently produced the most likely correct topology, however, was IQ-Tree with automated model designation (MFP). We discuss these findings and provide practical advice on gene tree estimation for summary methods. Lastly, we establish the first phylogeny-informed classification for <i>Pseudapis</i> s. l. and map the distribution of distinct morphological features of the group.</p>
The geometry of resource constraint: an empirical study of the golden snub-nosed monkey
<p>1. Apposite conceptualization and measurement of resource variation is critical for understanding many issues in ecology, including ecological niches, persistence and distribution of populations, the structure of communities, and population resilience to perturbations.</p> <p>2. We apply the nutritional geometry framework to conceptualise and quantify the responses of a temperate-living primate, the golden snub-nosed monkey (<i>R</i><i>hinopithecus</i><i> roxellana</i>) to variation in resource quality and quantity and in nutrient requirements associated with seasonal environments.</p> <p>3. We present a geometric model distinguishing qualitative constraint, quantitative constraint, and "pseudo-constraint" whereby nutrient intakes resemble response to qualitative resource constraint but are in fact driven by variation in nutrient requirements. The model is applied to analyse nutrient intakes recorded in 164 full day observations of monkeys from two populations, one wild and the other captive, across seasons. Additionally, we recorded the diet of a single animal over 32 consecutive days in the wild.</p> <p>4. Despite considerable differences in available resources, the captive and wild populations showed marked similarities in nutrient intakes, including indistinguishable amounts and ratios of ingested macronutrients during summer and autumn and strong year-round maintenance of protein compared to seasonally variable fat and carbohydrate intakes. These similarities suggest homeostatically regulated nutritional targets and provide reference points to identify factors driving population differences in macronutrient intake in winter and spring.</p> <p>5. Our framework enabled us to distinguish examples of quantitative, qualitative, and "pseudo-constraint". We suggest that this approach can increase the resolution at which resource constraint is conceptualised and measured in ecological studies.</p>
Data from: Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications
Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.
An empirical evaluation of camera trap study design: how many, how long, and when?
1. Camera traps deployed in grids or stratified random designs are a well-established survey tool for wildlife but there has been little evaluation of study design parameters. 2. We used an empirical subsampling approach involving 2225 camera deployments run at 41 study areas around the world to evaluate three aspects of camera trap study design (number of sites, duration and season of sampling) and their influence on the estimation of three ecological metrics (species richness, occupancy, detection rate) for mammals. 3. We found that 25-35 camera locations were needed for precise estimates of species richness, depending on scale of the study. The precision of species-level estimates of occupancy was highly sensitive to occupancy level, with <20 camera sites needed for precise estimates of common (>0.75) species, but more than 150 sites likely needed for rare (<0.25) species. Species detection rates were more difficult to estimate precisely at the grid level due to spatial heterogeneity, presumably driven by unaccounted for habitat variability within the study area. Running a camera at a site for 2 weeks was most efficient for detecting new species, but 3-4 weeks were needed for precise estimates of local detection rate, with no gains in precision observed after 1 month. Metrics for all mammal communities were sensitive to seasonality, with 37-50% of the species at the sites we examined fluctuating significantly in their occupancy or detection rates over the year. This effect was more pronounced in temperate sites, where seasonally sensitive species varied in relative abundance by an average factor of 4-5, and some species were completely absent in one season due to hibernation or migration. 4. We recommend the following guidelines to efficiently obtain precise estimates of species richness, occupancy and detection rates with camera trap arrays: run each camera for 3-5 weeks across 40-60 sites per array. We recommend comparisons of detection rates be model-based and include local covariates to help account for small-scale variation. Furthermore, comparisons across study areas or times must account for seasonality, which had strong impacts on mammal communities in both tropical and temperate sites.
Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available. As their recommendation was mainly based on simulated data, we sought to replicate findings in two large-scale empirical studies. In our empirical data, SVA did not fully correct for cell-type effects, its performance was somewhat unstable, and it carried a risk of missing true signals caused by removing variation that might be linked to actual disease processes. By contrast, a reference-based correction method performed well and did not show these limitations. A disadvantage of this approach is that if reference methylomes are not (publicly) available, they will need to be generated once for a small set of samples. However, given the notable risk we observed for cell-type confounding, we argue that, to avoid introducing false-positive findings into the literature, it could be well worth making this investment.
Data from: Empirical and Bayesian approaches to fossil-only divergence times: a study across three reptile clades
Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.
Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)
Species tree methods are now widely used to infer the relationships among species from multi-locus datasets. Many methods have been developed, which differ in whether gene and species trees are estimated simultaneously or sequentially, and in how gene trees are used to infer the species tree. While these methods perform well on simulated data, less is known about what impacts their performance on empirical data. We used a dataset including five nuclear genes and one mitochondrial gene for 22 species of Batrachoseps to compare the effects of method of analysis, within-species sampling and gene sampling on species tree inferences. For this dataset, the choice of inference method had the largest effect on the species tree topology. Exclusion of individual loci had large effects in *BEAST and STEM, but not in MP-EST. Different loci carried the greatest leverage in these different methods, showing that the causes of their disproportionate effects differ. Even though substantial information was present in the nuclear loci, the mitochondrial gene dominated the *BEAST species tree. This leverage is inherent to the mtDNA locus and results from its high variation and lower assumed ploidy. This mtDNA leverage may be problematic when mtDNA has undergone introgression, as is likely in this dataset. By contrast, the leverage of RAG1 in STEM analyses does not reflect properties inherent to the locus, but rather results from a gene tree that is strongly discordant with all others, and is best explained by introgression between distantly related species. Within-species sampling was also important, especially in *BEAST analyses, as shown by differences in tree topology across 100 subsampled datasets. Despite the sensitivity of the species tree methods to multiple factors, five species groups, the relationships among these, and some relationships within them, are generally consistently resolved for Batrachoseps.
The spatiotemporal evolution and influencing factors of hotel industry in the metropolitan area: an empirical study based on China
Through the online booking platform, 10,543 big data of spatial and temporal distribution of Beijing hotel industry has been obtained in this paper. Then, the methods of GIS and the geographical detector are used to study the spatiotemporal evolution process and the influencing factors of Beijing hotel industry during 2003-2018. The results are as follows: a. During the period of 2003-2018, the hotel industry in Beijing maintained a high growth rate and had three growth peaks in 2008, 2010 and 2014. Meanwhile, major historical events, such as the Olympic Games had a significant influence on the development of the hotel industry. b. Between 2003 and 2018, the hotel industry in Beijing gradually developed from the centripetal agglomeration to aggregation + diffusion, and also from the single center to the multi-center. Besides, various hotels presented two characteristics of city orientation and scenic orientation. c. The natural geographical environment had shaped the overall pattern and characteristics of the spatial distribution of the hotel industry in Beijing, and the socio-economic factors such as commercial activities, public facilities, tourism services and traffic conditions significantly influenced the location selection of the hotel industry. Therefore, the urban center is the ideal area for the spatial layout of the hotel industry. d. Geographical detector research showed that the factors, such as administrative organs, road network density, leisure and recreational facilities, and companies have strong explanatory power for hotel location selection, which is an important reference index for hotels to select the micro location. This paper is a beneficial supplement to the existing research and has certain guiding significance for the sustainable development of Beijing hotel industry.
Dataset for the Paper: "How Do OSS Developers Reuse Architectural Solutions from Q&A Sites: An Empirical Study"
<p>This package contains the dataset of the paper "How Do OSS Developers Reuse Architectural Solutions from Q&A Sites: An Empirical Study":</p> <p><strong>(1) Commits and Issues.xlsx</strong></p> <p>This file includes 984 commits and issues for the mining study.</p> <p><strong>(2) Survey Questionnaire (Customized Invitation Email).docx</strong></p> <p>This file provides the customized email used to invite each survey participant.</p> <p><strong>(3) Survey Questionnaire.xlsx</strong></p> <p>This file includes 12 survey questions used to collect the responses from the participants.</p> <p><strong>(4) Survey Responses.</strong><strong>xlsx</strong></p> <p>This file includes 227 valid responses and the results of data extraction and analysis for the survey study.</p> <p><strong>(5) Data Extraction and Analysis.mx20</strong></p> <p>This file contains the results of data extraction and analysis for the mining study, which were analyzed by the MAXQDA tool. The file can be opened by MAXQDA 2020 or higher versions, which are available at https://www.maxqda.com/. You may also use the free 14 days trial version of MAXQDA 2020, which is available at https://www.maxqda.com/trial for download.</p>
Replication Package for the Paper: "How Do Users Revise Architectural Related Questions on Stack Overflow: An Empirical Study"
<p>This is the replication package for the paper: "How Do Users Revise Architectural Related Questions on Stack Overflow: An Empirical Study". In the following, we provide a brief description of the folders and files:</p> <p><strong>(1) raw data</strong></p> <p>The raw data folder contains the retrieved 36,417 posts and the SQL query used for retrieving ARPs from Stack Overflow through the query interface provided by Stack Exchange.</p> <p><strong>(2) filtered ARPs</strong></p> <p>The filtered ARPs folder contains 13,205 filtered candidates ARPs from the retrieved 36,417 posts and the results of data analysis for the first RQ (i.e., RQ1).</p> <p><strong>(3) randomly selected posts and labeling results</strong></p> <p>The randomly selected posts and labeling results folder contains 1,068 randomly selected posts and their labeling results (i.e., 21 ARPs, wherein 14.3%, 3 out of 21 ARPs, do not contain “architect*” terms and 85.7%, 18 out of 21 APRs, contain “architect*” terms).</p> <p><strong>(4) relevant ARPs for answering RQs</strong></p> <p>The relevant ARPs for answering RQs folder contains 4,114 ARPs with revision information for answering the last three RQs (i.e., RQ2, RQ3, and RQ4).</p> <p><strong>(5) interview responses</strong></p> <p>The interview responses folder contains 11 collected interview responses from software practitioners. These responses were gathered to evaluate the identified categories related to ARQ revisions.</p> <p><strong>(6) data extraction and analysis</strong></p> <p>The data extraction and analysis folder contains the MAXQDA file. Data Labeling & Encoding for RQs.mx20 is the results of data labeling and encoding for RQ2, RQ3, and RQ4, which were analyzed by the MAXQDA tool. This file can be opened by MAXQDA 2020 or higher versions, which are available at https://www.maxqda.com/ for download. You may also use the free 14 days trial version of MAXQDA 2020, which is available at https://www.maxqda.com/trial for download.</p>
ScienceDex guides
Understand access before you commit
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.