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97 results for “code pattern”
Code and Data Repository for "Identifying microbiota community patterns important for plant protection using machine learning in synthetic community experiments"
<p>The repository includes data and R code necessary to reproduce all figures and analyses presented in the study titled "Identifying microbiota community patterns important for plant protection using machine learning in synthetic community experiments".</p>
Retrieving Data Constraint Implementations Using Fine-Grained Code Patterns
<p>Business rules are an important part of the requirements of software systems that are meant to support an organization. These rules describe the operations, definitions, and constraints that apply to the organization. Within the software system, business rules are often translated into constraints on the values that are required or allowed for data, called data constraints. Business rules are subject to frequent changes, which in turn require changes to the corresponding data constraints in the software. The ability to efficiently and precisely identify where data constraints are implemented in the source code is essential for performing such necessary changes.</p> <p>In this paper, we introduce Lasso, the first technique that automatically retrieves the method and line of code where a given data constraint is enforced. Lasso is based on traceability link recovery approaches and leverages results from recent research that identified line-of-code level implementation patterns for data constraints. We implement three versions of Lasso that can retrieve data constraint implementations when they are implemented with any one of 13 frequently occurring patterns. We evaluate the three versions on a set of 299 data constraints from 15 real-world Java systems, and find that they improve method-level link recovery by 30%, 70%, and 163%, in terms of true positives within the first 10 results, compared to their text-retrieval-based baseline. More importantly, the Lasso variants correctly identify the line of code implementing the constraint inside the methods for 68% of the 299 constraints.</p>
Versatile strategy for homogeneous drying patterns of dispersed particles: Matlab code
<p>Matlab code of "Versatile strategy for homogeneous drying patterns of dispersed particles"</p>
Typology of antipassive coding patterns and frequency effects of antipassives
<p><strong>Basic information about antipassives in languages with at least some ergative patterns.</strong></p>
Data and code for whole group tracking reveals that relatedness drives consistent subgrouping patterns in white-nosed coatis
<p>Three groups of wild white-nosed coatis were tracked with GPS collars between 2021 and 2023. Two groups (Galaxy and Trago) were tracked in Soberania National Park (SNP) (9° 12’ N, -79° 70’ W) and one group (Presidente) were tracked on Barro Colorado Island (BCI) (9° 16’ N, -79° 83’ W), Panama. Almost all group members were equipped with GPS collars that recorded one GPS fix every 10 minutes from 0600-1800 and 1 fix every hour from 1800-0600. Collars collected data for 15-21 days depending on the group. Adult males and one adult female from a different group were also collared during the Presidente collar period.</p> <p>Analysis was done in R, all scripts are in the coati_subgrouping_code folder, where there is a README file describing the code in more detail. Data are in the coati_subgrouping_data folder where there is a README describing the how the data are organised and structured. </p>
Data and figure production code for 'Hydrological cycle amplification imposes spatial pattern on climate change response of ocean pH and carbonate chemistry'
<p>Time mean data, and python code, used to create figures in 'Hydrological cycle amplification imposes spatial pattern on climate change response of ocean pH and carbonate chemistry', Biogeosciences, Hogikyan and Resplandy 2024</p>
Dataset and Code for "Mining Micro-Patterns of Issue Resolution Processes for Open Source Software Projects"
<p>Dataset and Code for "Mining Micro-Patterns of Issue Resolution Processes for Open Source Software Projects" with README included</p>
data and code for "Nest entrances, spatial fidelity, and foraging patterns in the red ant Myrmica rubra: a field and theoretical study"
<p>Data set and codes used for the results, figures and simulation of the paper "Nest entrances, spatial fidelity, and foraging patterns in the red ant <em>Myrmica rubra</em>: a field and theoretical study".</p>
Raw neural codes and binsizes for the paper 'Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus'
<p>Raw optimal spiking codes and binsizes that maximise information theoretic quantities for the figures of the paper 'Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus' (PLoS Comput Biol. 2024 Feb 20;20(2):e1010706) . Additional data will be added in the coming months.</p>
Diversity patterns and community structure of the macrofauna along the beach-inland transition zone of small tropical islands: supporting raw data and code
<p>Biodiversity follows distinct and observable patterns. Where to systems meet, biodiversity is often increased, due to overlapping occurrence ranges and the presence of specialized species that can tolerate the dynamic conditions of the transition zones. One of the most pronounced transition zones occurs at shores, where oceans and terrestrial habitat collide, forming the shore-inland transition zone. The relevance of this transition zone in shaping a system's community structure is particularly pronounced on small islands due to their high shore-to-inland-area ratio. However, the community structure of insular faunas along this transition zone is unknown. Here, we investigated the diversity patterns along the beach-inland transition zone of small islands and tested the hypothesis that species diversity increases towards the transition zone where beach and interior habitat meet. By measuring environmental parameters, resource availability, and macrofauna diversity along transects running across the beach-inland transition zone, we show that a gradual change in species composition from beach to the inland exists, but neither taxa richness, Shannon diversity, nor overall abundance change significantly. These findings give important insight into insular community structure at the transition zone from sea to land that are relevant to better understand the dynamic and unique characteristics of insular ecosystems.</p>
A Predictive Coding Approach to Modelling Perceived Drum Pattern Complexity
<p>Commented <em>R</em> script and matrices to carry out drum pattern complexity prediction.</p>
Detection of the Fire Drill anti-pattern: 15 real-world projects with ground truth, issue-tracking data, source code density, models and code
<p>This package contains artifacts for <strong>15</strong> real-world software projects. The data is supposed to aid the detection of the presence of the Fire Drill anti-pattern. We include original data, ground truth, code (experimental setups and models), and notebooks. The data supports two distinct methods of detecting the AP: a) through issue-tracking data, and b) through the underlying source code. This version of the dataset corresponds to <strong>v8</strong> of the <a href="https://arxiv.org/abs/2104.15090v8">technical report</a> and the <a href="https://github.com/MrShoenel/anti-pattern-models/releases/tag/arxiv-v8">GitHub repository</a>. The package includes the following:</p> <p>Original data:</p> <ul> <li>For each project, its <strong>original</strong> artifacts (e.g., wikis, meeting minutes, mentor's notes, etc.)</li> <li>Evaluation of raters' notes by the assessor</li> </ul> <p>Fire Drill in issue-tracking data:</p> <ul> <li><strong>Ground truth</strong> for whether and how strong each project exhibits the Fire Drill AP, on a scale from [0,10]. This was determined by two individual raters, who also reached a consensus.</li> <li>Coefficients for indicators for the first method, per project.</li> <li>Detailed issue-tracing data for each project: what occurred and when.</li> <li>Time logs for each project.</li> </ul> <p>Fire Drill in source-code data:</p> <ul> <li><strong>Four</strong> technical reports that document the developed method of how to translate a description into a detectable pattern, and to use the pattern to detect the presence and to score it (similar to the rating). Also includes a report for how activities were assigned to individual commits.</li> <li>Source code density data (metrics) for each commit in each of the nine projects as a separate dataset.</li> <li>Code: a snapshot of the repository that holds all code, models, notebooks, and pre-computed results, for utmost reproducibility (the code is written in R).</li> </ul>
Data and code related to the manuscript "Perceptual stability reflected in neuronal pattern similarities in human visual cortex" (Broday-Dvir et al.)
<p>This data set contains intracranial EEG data, analysis code and results associated with the manuscript "<strong>Perceptual stability reflected in neuronal pattern similarities in human visual cortex". </strong></p> <p>The code is written in Matlab R2019b. Matlab's Signal Processing Toolbox is required. </p> <p>Files ending with ".mat" are the data files, ".m" files are the associated scripts.</p> <p>Additional open-source toolboxes required to run the codes:</p> <ul> <li><strong>Mass Univariate ERP Toolbox</strong> (<a href="https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox">https://openwetware.org/wiki/Mass_Univariate_ERP_Toolbox</a>), version: "dmgroppe-Mass_Univariate_ERP_Toolbox-d1e60d4". D. M. Groppe, T. P. Urbach, M. Kutas, Mass univariate analysis of event-related brain potentials/fields I: A critical tutorial review. <em>Psychophysiology</em>. <strong>48</strong>, 1711–1725 (2011).</li> <li><strong>DRtoolbox </strong>(https://lvdmaaten.github.io/drtoolbox/), version: 0.8.1b. L.J.P. van der Maaten, E.O. Postma, and H.J. van den Herik. <strong>Dimensionality Reduction: A Comparative Review</strong>. Tilburg University Technical Report, TiCC-TR 2009-005, 2009.</li> </ul> <p> </p>
Serological dataset and R code for: Patterns and processes of pathogen exposure in gray wolves across North America
Open the record for dataset details and reuse information.
Data and code from: Bioacoustic monitoring reveals patterns of landscape use by migrating birds at a Great Lakes barrier crossing
Open the record for dataset details and reuse information.
Data and code for: Replay of innate vocal patterns during sleep in suboscines
Open the record for dataset details and reuse information.
Diversity patterns and community structure of the macrofauna along the beach-inland transition zone of small tropical islands: supporting raw data and code
Open the record for dataset details and reuse information.
A Large Scale Empirical Study of the Impact of Spaghetti Code and Blob Anti-patterns on Program Comprehension
<p>Dataset and scripts used for the paper.</p>
Replication package with data used in the study: "The effect of code smells on the relationship between design patterns and defects. An empirical study"
<p>This is a replication package with data used in a study by T. Alkhaeir and B. Walter "The effect of code smells on the relationship between design patterns and defects. An empirical study"</p> <p>This dataset contains the following folders:</p> <ul> <li> <p>"Analyzed systems" folder:</p> <ul> <li> <p>For each subject system (Ant-1.7, JEdit-4.2, Lucene-2.4, Camel-1.6, Log4j-1.2, Xalan-2.7, Poi-3.0, Ivy-2.0, Xerces-2.0, Velocity-1.6), we identify the following datasets: SDP, nSDP, SnDP, and nSnDP. Each dataset is represented by a separate csv file.</p> </li> <li> <p>Those csv files include raw data about every class in every release. Each file includes columns which represent:</p> <ul> <li> <p>System: The analyzed system</p> </li> <li> <p>className: A fully qualified class name</p> </li> <li> <p>Pattern: if the class is part of any pattern the cell contains the name of the pattern, and “null” otherwise</p> </li> <li> <p>Smell: if the class is part of affected by any smell the cell contains the name of the smell, and “null” otherwise</p> </li> <li> <p>Bugs: Number of defects reported inside the class (extracted from the PROMISE dataset)</p> </li> </ul> </li> </ul> </li> <li> <p>A "detailed analysis" folder:</p> <ul> <li> <p>For each pattern, we report all the classes which participate in it in all the analyzed systems. The csv files inside this folder follow the same structure as the other csv files reported above</p> </li> </ul> </li> </ul> <p><br> </p>
Replication package with data used in the study: The effect of code smells and design patterns on two change-related metrics: An exploratory study
<p>This is a replication package with data used in a study by T. Alkhaeir and B. Walter "The effect of code smells and design patterns on two change-related metrics: An exploratory study"</p> <p>This dataset contains the following folders:</p> <ul> <li>Aggregated Results Per System <ul> <li> For each subject system (AOI, Jedit, JHotDraw), we identify the following datasets: DP, nDP, S, nS ,SDP, nSDP, SnDP, and nSnDP. Each dataset is represented by a separate csv file.</li> <li> Those csv files include raw data about every class in every release, the csv files also include columns which represent: <ul> <li>- CHURN (CLPLPR(C)*100): defined as the sum of added and deleted lines in a class in a release, adjusted to the size of the class and to the number of revisions in the release;</li> <li>- and FREQ (MTPR(C)*100): defined as the average number of changes made to a class in a release, adjusted to the number of revisions in the release</li> </ul> </li> </ul> </li> <li>Detailed Results Per Smell Or Pattern <ul> <li> For each specific code smell (S) in each public release (Rel) of all subject systems, we identify SDP and SnDP datasets. Each dataset is in a separate .csv file</li> <li> For each specific design pattern (DP) in each public release (Rel) of all subject systems, we identify SDP and nSDP </li> </ul> </li> <li>Plots<br> We also include QQ plots for CHURN, FREQ values for every dataset in every system, that could serve as a supplementary data for the paper.</li> </ul>
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.