Find research datasets worth reusing

Fig. 3 in The history of the Botanic Garden of Brera during the Restoration of the Austrian Empire and the early years of the Kingdom of Italy

Fig. 3 - Ilex ×cornuta Lindl. & Paxton pro sp. (Aquifoliaceae) (Lemaire Ch. (redigÉ par), 1854 - L'illustration horticole, Gand, 1, tav. 10).

Fig. 1 - Begonia veitchii Hook. f in The history of the Botanic Garden of Brera during the Restoration of the Austrian Empire and the early years of the Kingdom of Italy

Fig. 1 - Begonia veitchii Hook. f. (Begoniaceae) (Lemaire Ch. (redigÉ par), 1868 - L'illustration horticole, Gand, 15, tav. 553).

Fig. 2 in The history of the Botanic Garden of Brera during the Restoration of the Austrian Empire and the early years of the Kingdom of Italy

Fig. 2 - Camellia 'M.me Ambroise Verschaffelt' (Theaceae) (Lemaire Ch. (redigÉ par), 1868 - L'illustration horticole, Gand, 15, tav. 546).

Fig. 6 in The history of the Botanic Garden of Brera during the Restoration of the Austrian Empire and the early years of the Kingdom of Italy

Fig. 6 - Psychilis purpurea (Willd.) Sauleda 'Rosea' (Orchidaceae) (Lemaire Ch. (redigÉ par), 1868 - L'illustration horticole, Gand, 15, tav. 544).

opencc-zeroJul 2021View details →

Source code for R tutorials and dataset for empirical case study on Malurus elegans (red-winged fairy wren)

Biological processes exhibit complex temporal dependencies due to the sequential nature of allocation decisions in organisms' life-cycles, feedback loops, and two-way causality. Consequently, longitudinal data often contain cross-lags: the predictor variable depends on the response variable of the previous time-step. Although statisticians have warned that regression models that ignore such covariate endogeneity in time series are likely to be inappropriate, this has received relatively little attention in biology. Furthermore, the resulting degree of estimation bias remains largely unexplored. We use a graphical model and numerical simulations to understand why and how regression models that ignore cross-lags can be biased, and how this bias depends on the length and number of time series. Ecological and evolutionary examples are provided to illustrate that cross-lags may be more common than is typically appreciated and that they occur in functionally different ways. We show that routinely used regression models that ignore cross-lags are asymptotically unbiased. However, this offers little relief, as for most realistically feasible lengths of time series conventional methods are biased. Furthermore, collecting time series on multiple subjects–such as populations, groups or individuals—does not help to overcome this bias when the analysis focusses on within-subject patterns (often the pattern of interest). Simulations (R tutorial 1 & 2), a literature search and a real-world empirical example on fairy wrens (data archived here with analyses presented in R-tutorial 3) together suggest that approaches that ignore cross-lags are likely biased in the direction opposite to the sign of the cross-lag (e.g. towards detecting density-dependence of vital rates and against detecting life history trade-offs and benefits of group living). Next, we show that multivariate (e.g. structural equation) models can dynamically account for cross-lags, and simultaneously address additional bias induced by measurement error, but only if the analysis considers multiple time series. We provide guidance on how to identify a cross-lag and subsequently specify it in a multivariate model, which can be far from trivial. Our tutorials with data and R code of the worked examples provide step‐by‐step instructions on how to perform such analyses. Our study offers insights into situations in which cross-lags can bias analysis of ecological and evolutionary time series and suggests that adopting dynamical models can be important, as this directly affects our understanding of population regulation, the evolution of life histories and cooperation, and possibly many other topics. Determining how strong estimation bias due to ignoring covariate endogeneity has been in the ecological literature requires further study, also because it may interact with other sources of bias.

opencc-by-4.0Aug 2021View details →

How Do I Refactor This? An Empirical Study on Refactoring Trends and Topics in Stack Overflow

This is the dataset that accompanies the study: "How Do I Refactor This? An Empirical Study on Refactoring Trends and Topics in Stack Overflow." This study has been accepted for publication in the software engineering journal Empirical Software Engineering.   Following is the abstract of the study: An essential part of software maintenance and evolution, refactoring is performed by developers, regardless of technology or domain, to improve the internal quality of the system, and reduce its technical debt. However, choosing the appropriate refactoring strategy is not always straightforward, resulting in developers seeking assistance. Although research in refactoring is well-established, with several studies altering between the detection of refactoring opportunities and the recommendation of appropriate code changes, little is known about their adoption in practice. Analyzing the perception of developers is critical to understand better what developers consider to be problematic in their code and how they handle it. Additionally, there is a need for bridging the gap between refactoring, as research, and its adoption in practice, by extracting common refactoring intents that are more suitable for what developers face in reality. In this study, we analyze refactoring discussions on Stack Overflow through a series of quantitative and qualitative experiments. Our results show that Stack Overflow is utilized by a diverse set of developers for refactoring assistance for a variety of technologies. Our observations show five areas that developers typically require help with refactoring-- Code Optimization, Tools and IDEs, Architecture and Design Patterns, Unit Testing, and Database. We envision our findings better bridge the support between traditional (or academic) aspects of refactoring and their real-world applicability, including better tool support. Manuscript DOI: <a href="https://doi.org/10.1007/s10664-021-10045-x">https://doi.org/10.1007/s10664-021-10045-x</a>

opencc-by-4.0Mar 2019View details →

INSYDE model - Testing empirical and synthetic flood damage models: the case of Italy

This repository contains the R code for <a href="http://www.nat-hazards-earth-syst-sci.net/16/2577/2016/">INSYDE, a synthetic, probabilistic flood damage model based on explicit cost analysis</a>. Correspondence to: Rui Figueiredo (<a href="mailto:rui.figueiredo@iusspavia.it">rui.figueiredo@iusspavia.it</a>)

opencc-by-4.0Sep 2021View details →

Empirical Research on Requirements Quality: A Systematic Mapping Study - Dataset

We conducted a systematic mapping study on the empirical research into the quality of requirements titled "Empirical Research on Requirements Quality: A SystematicMapping Study" in the Requirements Engineering Journal. This is our replication package. Full Abstract: Research has repeatedly shown that high quality requirements are essential for the success of development projects. While the term “quality” is pervasive in the field of requirements engineering and while the body of research on requirements quality is large, there is no meta study of the field that overviews and compares the concrete quality attributes addressed by the community. To fill this knowledge gap, we conducted a systematic mapping study of the scientific literature. We retrieved 6,905 articles from six academic databases, which we filtered down to our 105 relevant primary studies: explicitly defining, improving, or evaluating quality attributes while including an empirical research component. We found that research on requirements quality focuses on improvement techniques, with very few primary studies addressing evidence-based definitions and evaluations of quality attributes. Among the 12 quality attributes identified, the most prominent in the field are ambiguity, completeness, consistency, and correctness. We identified 111 sub-types of quality attributes such as “template conformance” for consistency or “passive voice” for ambiguity. Ambiguity has the largest share of these sub-types. The artefacts being studied are mostly referred to in the broadest sense as “requirements,” while little research targets quality attributes in specific types of requirements such as use cases or user stories. We present and discuss our detailed analysis along the various quality attributes. Our findings highlightthe need to conduct more grounded research aimed at “definitions,” to use more diverse research methods, and to address a more diverse set of requirements types.

opencc-by-4.0Nov 2022View details →

Raw videos of the empirical observations performed studying large shoals of sulphur mollies (P. sulphuraria).

Data acquired between April 6th and April 11th 2018 in Teapa, Tabasco, Mexico. These dataset was obtained for the study of the spontaneous wave activity observed in large shoals of sulphur mollies. Details on the analysis can be found in DOI: XX.XXXX/XXX (currently under review). The file called <a href="https://zenodo.org/api/files/3278318f-de77-4ee2-b1f2-0e7b6c6178aa/data_ALL_clusters.csv?versionId=e11e17f5-ac27-421c-bc83-09a2ea08dd1e">data_ALL_clusters.csv</a> contains four columns with the following information: <ol> <li>cluster ID</li> <li>cluster area</li> <li>cluster volume</li> <li>cluster time duration</li> <li>cluster speed</li> </ol> The h5 files contain the same information separated by acquisition day. In these h5 files, the areas, volumes and times are given in number of pixels and/or number of frames. Thus, they have to be re-scaled with the scaling factor dx=0.02 and dt=1/50.

opencc-by-4.0Feb 2023View details →

A multi-lab experimental assessment reveals that replicability can be improved by using empirical estimates of genotype-by-lab interaction

Raw data sets, curated data sets and R code underlying the paper "A multi-lab experimental assessment reveals that replicability can be improved by using empirical estimates of genotype-by-lab interaction"  https://doi.org/10.1101/2021.12.05.471264

opencc-zeroMar 2023View details →

Data for: Does the evolution of ontogenetic niche shifts favor species coexistence? An empirical test in Trinidadian streams

A major question in ecology is how often competing species evolve to reduce competitive interactions and facilitate coexistence. One untested route for a reduction in competitive interactions is through ontogenetic changes in the trophic niche of one or more of the interacting species. In such cases, theory predicts that two species can coexist if the weaker competitor changes its resource niche to a greater degree with increased body size than the superior competitor. We tested this prediction using stable isotopes that yield information about the trophic position (δ15N) and carbon source (δ13C) of two coexisting fish species: Trinidadian guppies (Poecilia reticulata) and killifish (Rivulus hartii). We examined fish from locations representing three natural community types: 1) where killifish and guppies live with predators; 2) where killifish and guppies live without predators; and 3) where killifish are the only fish species. We also examined killifish from communities in which we had introduced guppies, providing a temporal sequence of the community changes following the transition from a killifish only to a killifish-guppy community. We found that killifish, which are the weaker competitor, had a much larger ontogenetic niche shift in trophic position than guppies in the community where competition is most intense (killifish-guppy only). This result is consistent with theory for size-structured populations, which predicts that these results should lead to stable coexistence of the two species. Comparisons with other communities containing guppies, killifish and predators and ones where killifish live by themselves revealed that these results are caused primarily by a loss of ontogenetic niche changes in guppies, even though they are the stronger competitor. Comparisons of these natural communities with communities in which guppies were translocated into sites containing only killifish showed that the experimental communities were intermediate between the natural killifish-guppy community and the killifish-guppy-predator community, suggesting contemporary evolution in these ontogenetic trophic differences. These results provide comparative evidence for ontogenetic niche shifts in contributing to species coexistence and comparative and experimental evidence for evolutionary or plastic changes in ontogenetic niche shifts following the formation of new communities.

openmit-licenseMar 2023View details →

An Empirical Evaluation of Quasi-Static Executable Slices

This artifact contains the dataset and scripts used to reproduce the experiments of the article "An Empirical Evaluation of Quasi-Static Executable Slices"

opencc-zeroMar 2023View details →

Data for: Predicting age and mass at maturity from feeding behavior and diet in M. sexta: An empirical test of a life history model

Feeding for most animals involves bouts of active ingestion alternating with bouts of no ingestion. In insects, the temporal patterning of bouts varies widely with resource quality and is known to affect growth, development time, and fitness. However, the precise impacts of resource quality and feeding behavior on insect life history traits is poorly understood. To explore and better understand the connections between feeding behavior, resource quality and insect life history traits, we combined laboratory experiments with a recently proposed mechanistic model of insect growth and development for a larval herbivore, Manduca sexta. We ran feeding trials for 4th and 5th instar larvae across different diet types (two hostplants and artificial diet) and used these data to parameterize a joint model of age and mass at maturity that incorporates both insect feeding behavior and hormonal activity. We found that the estimated durations of both feeding and non-feeding bouts were significantly shorter on low- than on high-quality diets. We then explored how well the fitted model predicted historical out-of-sample data on age and mass of M. sexta. We found that the model accurately described qualitative outcomes for the out-of-sample data, notably that a low-quality diet results in reduced mass and later age at maturity compared to high-quality diets. Our results clearly demonstrate the importance of diet quality on multiple components of insect feeding behavior (feeding and non-feeding), and partially validate a joint model of insect life history. We discuss the implications of these findings with respect to insect herbivory and discuss ways in which our model could be improved or extended to other systems.

opencc-by-4.0Mar 2023View details →

Accompanying empirical data for Kirchherr et al., 2023, "Bayesian multilevel hidden Markov models identify stable state dynamics in longitudinal recordings from macaque primary motor cortex"

This repository contains data accompanying: Kirchherr et al., 2023, "Bayesian multilevel hidden Markov models identify stable state dynamics in longitudinal recordings from macaque primary motor cortex". Data collection methods: Two adult female rhesus macaques (Macaca mulatta) trained on a reaching, and grasping, and placing task served as the subjects. The animal handling as well as surgical and experimental procedures complied with European guideline (2010/63/UE) and authorized by the French Ministry for Higher Education and Research (project # 2016112713202878) in force on the care and use of laboratory animals, and were approved by the ethics committee CELYNE (comité d’éthique Lyonnais pour les neurosciences expérimentale, C2EA 42). After initial training, we performed a sterile surgery to implant six floating multielectrode arrays (FMA, Microprobes for Life Science, Gaithersburg, MD, USA) in the right (monkey 1) or left (monkey 2) cortical hemisphere. Each array was comprised of 32 platinum/iridium electrodes (impedance 0.5 MΩ at 1 kHz) with lengths ranging from 1 to 6 mm, and with an inter-electrode spacing of 400 μm. One electrode array was implanted in the primary motor cortex (M1), two were implanted in the ventral premotor cortex (F5), one in the dorsal premotor cortex (F2), and two in the prefrontal cortex (45a and 46/12r), as estimated according to a previous magnetic resonance imaging scan. For the purposes of this study, we analyzed data from the M1 array of each monkey. The wideband neural signal (bandpass filtered at 0.1 to 7500 kHz) was recorded at 30 kS/s, and amplified and digitized (16-bit; 0.192 μV resolution) with an Intan Tech-based (Intan Technologies, Los Angeles, CA, USA) open source acquisition system (Open Ephys; Siegle et al. 2017). This system uses a 256-channel Intan RHD2000 series acquisition board and 32-channel headstages (RHD2132). Spike detection was performed offline using Trisdesclous (Garcia & Pouzat,2015). The common reference was removed to reduce ambient noise. Spikes were then detected from each electrode using a threshold of 2 times the median absolute deviation (MAD), and analyzed as multi-unit activity (MUA) in 10 ms bins. All electrodes in which at least one well-isolated spike waveform was detected were selected for the following analyses. We thus used a sample of 21 electrodes out of 32 for monkey 1, and 25 out of 32 electrodes for monkey 2. Custom made detection panels were used to record the moments when the monkey’s hand released the handle, the hand contacted the target object, and when the object was placed in the groove. An Omniplex 16-channel recording system (Plexon, Dallas, TX, USA) was used to simultaneously record these behavioral events. Trials were discarded if the response time (time between the go signal and handle release) was less than 100 or greater than 1500 ms, the reach duration (time between handle release and object contact) was less than 100 or greater than 1000 ms, or the placing duration (time between object contact and placing the object in the groove) was less than 100 or greater than 1200 ms, leaving 19 - 68 trials per day for monkey 1 (M = 43.9, SD = 15.46, N = 439; left: M = 14.8, SD = 5.74; center: M = 14.4, SD = 5.15; right: M = 14.7, SD = 7.73), and 23 - 49 per day for monkey 2 (M = 38.3, SD = 9.87, N = 383; left: M = 14.2, SD = 3.91; center: M = 10.8, SD = 3.55; right: M = 13.3, SD = 3.37). Abstract: Neural populations, rather than single neurons, may be the fundamental unit of cortical computation. Analyzing chronically recorded neural population activity is challenging not only because of the high dimensionality of activity in many neurons, but also because of changes in the recorded signal that may or may not be due to neural plasticity. Hidden Markov models (HMMs) are a promising technique for analyzing such data in terms of discrete, latent states, but previous approaches have either not considered the statistical properties of neural spiking data, have not been adaptable to longitudinal data, or have not modeled condition specific differences. We present a multilevel Bayesian HMM which addresses these shortcomings by incorporating multivariate Poisson log-normal emission probability distributions, multilevel parameter estimation, and trial-specific condition covariates. We applied this framework to multi-unit neural spiking data recorded using chronically implanted multi-electrode arrays from macaque primary motor cortex during a cued reaching, grasping, and placing task. We show that the model identifies latent neural population states which are tightly linked to behavioral events, despite the model being trained without any information about event timing. We show that these events represent specific spatiotemporal patterns of neural population activity and that their relationship to behavior is consistent over days of recording. The utility and stability of this approach is demonstrated using a previously learned task, but this multilevel Bayesian HMM framework would be especially suited for future studies of long-term plasticity in neural populations.

opencc-zeroApr 2023View details →

Data from: How important are functional and developmental constraints on phenotypic evolution? An empirical test with the stomatal anatomy of flowering plants

Quantifying the relative contribution of functional and developmental constraints on phenotypic variation is a longstanding goal of macroevolution, but it is often difficult to distinguish different types of constraints. Alternatively, selection can limit phenotypic (co)variation if some trait combinations are generally maladaptive. The anatomy of leaves with stomata on both surfaces (amphistomatous) presents a unique opportunity to test the importance of functional and developmental constraints on phenotypyic evolution. The key insight is that stomata on each leaf surface encounter the same functional and developmental constraints, but potentially different selective pressures because of leaf asymmetry in light capture, gas exchange, and other features. Independent evolution of stomatal traits on each surface implies that functional and developmental constraints alone likely do not explain trait covariance. Packing limits on how many stomata can fit into a finite epidermis and cell-size-mediated developmental integration are hypothesized to constrain variation in stomatal anatomy. The simple geometry of the planar leaf surface and knowledge of stomatal development makes it possible to derive equations for phenotypic (co)variance caused by these constraints and compare them with data. We analyzed evolutionary covariance between stomatal density and length in amphistomatous leaves from 236 phylogenetically independent contrasts using a robust Bayesian model. Stomatal anatomy on each surface diverges partially independently, meaning that packing limits and developmental integration are not sufficient to explain phenotypic (co)variation. Hence, (co)variation in ecologically important traits like stomata arises in part because there is a limited range of evolutionary optima. We show how it is possible to evaluate the contribution of different constraints by deriving expected patterns of (co)variance and testing them using similar but separate tissues, organs, or sexes.

opencc-by-4.0Apr 2023View details →

Measurements of type 3 non-uniqueness between 660 °C and 960 °C for 18SIB02 EMPIR project "Real-K"

Dataset coming from type 3 non uniqueness investigation at INRiM, for project Real-K. The dataset has been collected by 5 test HT-SPRTs, inserted into a sodium heat pipe, calibrated at the fixed points of water, tin, zinc, silver and aluminium. The measurements have been performed at 760, 780, 800, 820, 840 and 860 °C. RPTW_Polito.xlsx are measurements taken on 6 probes at the triple point of water.  MAP-HP-SODIO.txt contains measurements performed with 2 reference sensors in order to evaluate the uniformity among the HP wells. note-durante.xlsx contains notes taken during the "MAP-HP-SODIO" measurements 760-SODI-2.txt contains the actual measurements of the 5 probes + 1 control probe (in channel 4). calibrations_2023.xlsx contains the calibration measurements and calculations of the test HT-SPRTs

opencc-by-4.0Oct 2020View details →

Quality Attributes Assessment in Self-Adaptive Systems: An Empirical Evaluation

Self-adaptive Systems (SAS) can monitor themselves and their context. They can detect changes and react to unexpected conditions with minimal human supervision during their execution. One of the challenges behind developing SAS is dealing with the decision-making process while analyzing the tradeoff points among the multiple quality attributes (QA). In Software Engineering, a widely accepted method of evaluating QA goals in software projects is the Architecture Tradeoff Analysis Method (ATAM). However, despite its importance and wide acceptance, there are few reports of empirical studies on analyzing QA tradeoffs in SAS. In this sense, the present investigation proposes an adapted version of ATAM called ATAM-4SAS to deal with the particularities of SAS. To achieve the research goal, we employed the UPPAAL SMC (statistical verification model) to analyze a set of QA. To evaluate the feasibility of the proposed method, we performed an empirical study on the execution of the ATAM-4SAS in a SAS developed according to the MAPE-K model. This model encompasses the Monitoring, Analysis, Planning, and Execution phases. Such steps share a knowledge base (K), which is fundamental in supporting decision-making. We complemented the empirical evaluation by conducting a focus group, which sought to assess the perceived ease of use and the perceived usefulness of the ATAM-4SAS to support the strategic choice of QA in a SAS. As a result, we observed that most participants agreed that ATAM-4SAS provides adequate support for the strategic choice of QA in SAS.

opencc-by-4.0Nov 2022View details →

An Empirical Comparison of Pre-Trained Models of Source Code

The replication package of the paper "An Empirical Comparison of Pre-Trained Models of Source Code". For the source code, please refer to <a href="https://github.com/NougatCA/FineTuner">https://github.com/NougatCA/FineTuner</a>.

opencc-by-4.0Jun 2023View details →

Empirical Study on Test Generation Using GitHub Copilot --- Replication Package

This replication package contains the data and scripts used in the "Empirical Study on Test Generation Using GitHub Copilot" thesis.