Find research datasets worth reusing

opencc-by-4.0Feb 2022View details →

Datasets and R source code of manuscript "Parasites make hosts more profitable but less available to predators"

Data about experimentations of DIV-1 (virus) infection on Daphnia magna. Linked article: Parasites make hosts more profitable but less available to predators

opencc-by-4.0Jun 2022View details →

Books of hours as codified compilations of compilations: dataset and code

Dataset, code to produce the figures, additional figures and visualizations for the following contribution: Stutzmann, Dominique, and Chevalier, Louis, "Books of hours as codified compilations of compilations Textual networks and hybrid liturgical uses", Journal of Historical Network Research 9 (2023) 146 – 199, doi:10.25517/jhnr.v9i1.139 <pre><code>@article{stutzmann_books_2023, title = {Books of hours as codified compilations of compilations {Textual} networks and hybrid liturgical uses}, volume = {9}, doi = {10.25517/jhnr.v9i1.139}, language = {en}, journal = {Journal of Historical Network Research}, author = {Stutzmann, Dominique and Chevalier, Louis}, year = {2023}, pages = {146--199}, } </code></pre> Books of hours were the medieval best-seller. The referenced article aims to change how we study the textual content of books of hours by tackling the most common texts at a large scale. Intended for lay people and imitating the model of liturgical books, books of hours contain a core of votive offices and appear to have a very standardized content. The choice and the order of the chants, readings and orations may vary within the offices according to not only the liturgical destination, but also the place of production, the target export market, and the choices of the client. Variations are therefore difficult to characterize and analyze. Here, we focus on an analysis of the Hours of the Virgin and the Office of the Dead as both compilations and networks of compilations. At the level of texts and liturgical uses, we highlight and study textual commonalities based on geography or other historical links (e.g. Germany, the Dominican order and Southern France for the Hours of the Virgin, Flanders and Scandinavia, Poitiers and Bordeaux, Auxerre and Bayeux for the Office of the Dead). Since patrons or copyists could also modify the expected contents, our last part analyses the uses by Utrecht and Bruges, and how uses specific to one institution may either be faithfully reproduced or give way to hybridization. This phenomenon is characterized, for example, by changes between pieces from another use into a well-identified set.

opencc-by-4.0Sep 2023View details →

MATLAB codes for : "Diagnosis and Prognosis of Faults in High-Speed Aeronautical Bearings with a Collaborative Selection Incremental Deep Transfer Learning Approach".

The package contains all the materials needed to reproduce the findings of our paper. The paper is published by MDPI Applied Sciences journal and its details are as follow. Berghout, T.; Benbouzid, M. Diagnosis and Prognosis of Faults in High-Speed Aeronautical Bearings with a Collaborative Selection Incremental Deep Transfer Learning Approach. Appl. Sci. 2023, 13, 10916. https://doi.org/10.3390/app131910916 1) Please you need to download the dataset from original link provided by introductory paper (Please read the above paper to find out about the datset used). 2) Put the data in folders "RawData" for both experments. 3) Please run the files for each experiment as provided, in alphabetical order.

opencc-by-4.0Oct 2022View details →

Deliverable 2.3 Design Load Case Database for Code-to-Code Comparison

In work package 2 of FLOATECH a detailed validation and verification of the capabilities of QBlade-Ocean was performed. Thereby, three wind turbine models mounted on floating substructures with differing characteristics serve as the means for the validation.This  dataset contains Floating Offshore Wind Turbine (FOWT) calculations in various design situations, computed with three different codes. In more detail, three floating platform archetypes are used in the code-to-code comparison ongoing in work package 2: a semi-submersible-type floater and a spar-type floater as well as the Hexafloat® concept recently proposed by Saipem®. The three test-cases are the NREL 5MW RWT mounted on the DeepCwind semi-submersible platform, the DTU 10MW RWT mounted on the SOFTWIND spar-type platform and the DTU 10MW RWT mounted on the Hexafloat® platform.  More details regarding the dataset structure and the testcases can be found in the accompanying document.    Changelog:  Version 5.0.0 <ul> <li>Changed structural damping ratio (increased) in OpenFAST results (SOFTWIND and Hexafloat models) to match structural damping ratios in QBlade</li> <li>Added wave time series at platform undisplaced position</li> <li>Added TurbSim input files for wind field generation. TurbSim v2.0.0 (https://www.nrel.gov/wind/nwtc/turbsim.html - National Renewable Energy Laboratory)</li> <li>Added detailed DLC and simulation information in "DLC&SimulationList.xlsx"</li> </ul> Version 4.0.0 <ul> <li>Correction of bugs in QB 5MWOC4 and 10MWSOFT models: wind shear exponent in wind fields (0.11 -> 0.14)</li> <li>Update of hydrodynamic database used in OpenFAST and QBlade results of 10MWSOFT model </li> </ul>   <pre><code>Data in version 5.0.0 is used in WES publication: Papi, F., Troise, G., Behrens de Luna, R., Saverin, J., Perez-Becker, S., Marten, D., Ducasse, M.-L., and Bianchini, A.: A Code-to-Code Comparison for Floating Offshore Wind Turbine Simulation in Realistic Environmental Conditions: Quantifying the Impact of Modeling Fidelity on Different Substructure Concepts, Wind Energ. Sci. Discuss. [preprint], https://doi.org/10.5194/wes-2023-107, in review, 2023.</code></pre>

openCC (other)Feb 2022View details →

Everglades Landscape Model (ELM) Code and Documentation

The Everglades Landscape Model (ELM) is an application instance of the generalized Ecological Landscape Modeling code package. For applications within the Florida Coastal Everglades (FCE) LTER, the ELM is one of the simulation modeling tools used to a) explore hypotheses of ecosystem processes in heterogenous spatial landscapes, b) extrapolate field-scale research findings across space and time, and c) predict the evolution of the Everglades landscape in response to plausible future scenarios. For ELM v.2.8.3-4, the 2 zip-archive packages here contains 1a) all (C) source code and unix (Bourne) shell scripts used to build and run the ELM (& includes Doxygen-generated hyperlinked source code documentation of every file/function/struct/parameter), 1b) all Everglades-specific input data used in historical (1981-2000) simulations; and 2) a complete documentation report with chapters including the Introduction&Goals, Model Data, Model Structure, Model Performance, and Model User's Guide. The ELM is being applied and updated routinely. Such updated information can be found at http://www.ecolandmod.com .

openCC (other)Nov 2023View details →

Data and code from "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" Kaiser et al. 2023 Behavioral Ecology and Sociobiology

This dataset is published in support of "No evidence of sex ratio manipulation by black-throated blue warblers in response to food availability" by Kaiser et al. 2023 in Behavioral Ecology and Sociobiology. Data and code to test the assumptions and key predictions of the Trivers-Willard hypothesis, which proposes that females produce more sons or daughters depending on food availability, in the black-throated blue warbler at the Hubbard Brook Experimental Forest, NH, 2007-2012. Datasets support analyses of sex ratio bias at both the nest and nestling levels. Data tables support the comparison of the ratio of variances in the scaled pre-fledging mass of male and female nestlings using an F test and reproduction of Figures 2a and 2b. Figures are those used in the published manuscript. Code supports the calculation of offspring sex ratio bias at the population level, and considering separately both low- and high-quality habitats, using the Neuhäuser test, statistical models testing the assumptions of the Trivers-Willard hypothesis, effects of food availability and parental provisioning on offspring sex ratio, and effects of food availability on pre-fledging nestling mass of sons and daughters, and a power analysis to determine the power to detect an effect of food supplementation on sex ratio. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the US Forest Service, Northern Research Station.

openCC (other)Aug 2025View details →

Data and Code in support of Nitrogen and phosphorus co-limitation of forest growth in northern hardwood forests; Blumenthal et al. 2025

The Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE) project studies N and P acquisition and limitation of forest productivity through a series of nutrient manipulations in northern hardwood forests. This data set is published in support of a manuscript titled "Nitrogen and phosphorus co-limitation of forest growth in northern hardwood forests" and includes data and code used in the analysis. The primary diameter breast height dataset can be found in: Fisk, M.C., R.D. Yanai, and T.J. Fahey. 2025. Tree DBH response to nitrogen and phosphorus fertilization in the MELNHE study, Hubbard Brook Experimental Forest, Bartlett Experimental Forest, and Jeffers Brook ver 2. Environmental Data Initiative. https://doi.org/10.6073/pasta/fb8f8d5b903627bee9ad6aa4c32f2289. Additional detail on the MELNHE project, including a datatable of site descriptions and a pdf file with the project description and diagram of plot configuration can be found in this data package: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-hbr&identifier=344 These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station.

openCC (other)Sep 2024View details →

Data and code from "Black-throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability" Kaiser et al. 2024 Ecology and Evolution

Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing ‘green’ season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black-throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a two-week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long-legged cobweaver), and Philodromus rufus (white-striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black-throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate-induced changes in insect communities with longer green seasons. These data were gathered as part of the Hubbard Brook Ecosystem Study (HB

openCC (other)Dec 2025View details →

Limno run codes, dates, and locations associated with vertical lake profile data collected in the McMurdo Dry Valleys, Antarctica (1991-2025, ongoing)

This data package provides a summary of "limno runs" performed each season in lakes located throughout the McMurdo Dry Valleys of Antarctica as part of the McMurdo Dry Valleys Long Term Ecological Research program. Each limno run is identified by unique code that allows one to compile a complete set of limnological data from a particular lake and location at specific time points. There are usually two or three limno runs performed per lake per austral summer field season, although the number of runs may vary by lake and by season depending on site access, site conditions, and other external factors.

opencc-by-4.0Jan 2020View details →

German ZIP codes, Kreisschlüssel (Administration Unit), Kreis, Inhabitant per ZIP, City Names, responsible Arbeitsagentur (Social Agency

This dataset from 2019 contains all German ZIP codes, city names associated with it, Kreisschlüssel (Administration Unit ID) Kreis, (Administration Unit), Bundesland (State), Inhabitants, responsible Arbeitsagentur (Social Agency). Note that especially the PLZ ZIP Codes and the responsible Arbeitsagentur change from time to time due to administrative reasons.

opencc-by-4.0Jan 2020View details →

Preprocessed Java Code Corpus

A preprocessed code corpus for the Java programming language. The corpus was used for the experiments in the paper Big Code != Big Vocabulary: Open-Vocabulary Models for Source Code. It contains preprocessed-tokenized files for training, validation, testing, and BPE encoding learning. The BPE segmented versions of the above files are also included for three different encoding sizes i,e., 2000, 5000, and 10000 BPE merge operations as well as the learned BPE encodings. Similar versions are also contained for splitting compound identifiers on camelCase and snake_case as in (Allamanis et al., 2015) as well as the corresponding subtoken maps.

opencc-by-4.0Feb 2020View details →

Data and R Code from "A novel approach to sustainability assessment of food supply chains using networks of ecosystem services"

Data and R code from this paper applying network analysis (iGraph) to two case studies pre and post agroecological transitions in Central America and Tanzania, Africa from the IPES-Food report. Further descriptions of this data and code can be found within the extended manuscript. R Code relies on the data from the scenarios (e.g., Nodes and Relations CSVs) and creates the output network metrics (e.g., Node Metric CSVs).

openmit-licenseMay 2020View details →

liampshaw/Pathogen-host-range: Pathogen-host-range initial code release

Release of code and dataset for publication of associated paper: "The phylogenetic range of bacterial and viral pathogens of vertebrates" (doi: 10.1111/mec.15463).

opencc-by-4.0May 2020View details →

CodiEsp corpus: gold standard Spanish clinical cases coded in ICD10 (CIE10) - eHealth CLEF2020

Introduction These are the train, development and test sets of the CodiEsp corpus. Train, development and test have gold standard annotations. In addition, the unannotated background set is also distributed. All documents are released in the context of the CodiEsp track for CLEF ehealth 2020 (<a href="http://temu.bsc.es/codiesp/">http://temu.bsc.es/codiesp/</a>). The CodiEsp corpus contains manually coded clinical cases. All documents are in Spanish language and CIE10 is the coding terminology (it is the Spanish version of ICD10-CM and ICD10-PCS). The CodiEsp corpus has been randomly sampled into three subsets: the train, the development, and the test set. The train set contains 500 clinical cases, and the development and test set 250 clinical cases each. CodiEsp participants must submit predictions for the test and background set, but they will only be evaluated on the test set.   Please cite if you use this dataset: Antonio Miranda-Escalada, Aitor Gonzalez-Agirre, Jordi Armengol-Estapé and Martin Krallinger. Overview of automatic clinical coding: annotations, guidelines, and solutions for non-English clinical cases at CodiEsp track of CLEF eHealth 2020. In CLEF (Working Notes). 2020 <pre><code>@inproceedings{miranda2020overview, title={Overview of automatic clinical coding: annotations, guidelines, and solutions for non-english clinical cases at codiesp track of CLEF eHealth 2020}, author={Miranda-Escalada, Antonio and Gonzalez-Agirre, Aitor and Armengol-Estap{\'e}, Jordi and Krallinger, Martin}, booktitle={Working Notes of Conference and Labs of the Evaluation (CLEF) Forum. CEUR Workshop Proceedings}, year={2020} }</code></pre>   Annotation quality Inter-annotator agreement: 88.6% for diagnosis coding, 88.9% for procedure coding and 80.5% for the textual reference annotation. For more information, see the <a href="http://ceur-ws.org/Vol-2696/paper_263.pdf">paper</a>. Zip structure Four folders: train, dev, test and background. Each one of them contains the files for the train, development, test and background corpora, respectively. <ul> <li>train, dev and test folders have: <ul> <li>3 tab-separated files with the annotation information relevant for each of the 3 sub-tracks of CodiEsp. </li> <li>A subfolder named text_files with the plain text files of the clinical cases.</li> <li>A subfolder named text_files_en with the plain text files machine-translated to English. Due to the translation process, the text files are sentence-splitted.</li> </ul> </li> <li>The background folder has only text_files and text_files_en subfolders with the plain text files.</li> </ul> Format The CodiEsp corpus is distributed in plain text in UTF8 encoding, where each clinical case is stored as a single file whose name is the clinical case identifier. Annotations are released in a tab-separated file. Since the CodiEsp track has 3 sub-tracks, every set of documents (train and test) has 3 tab-separated files associated with it.  For the sub-tracks CodiEsp-D and CodiEsp-P, the file has the following fields: <pre>articleID ICD10-code </pre> Tab-separated files for the sub-track CodiEsp-X contain extra fields that provide the text-reference and its position: <pre>articleID label ICD10-code text-reference reference-position</pre> Corpus summary statistics The final collection of 1000 clinical cases that make up the corpus had a total of 16504 sentences, with an average of 16.5 sentences per clinical case. It contains a total of 396,988 words, with an average of 396.2 words per clinical case.   Resources: <ul> <li><a href="https://temu.bsc.es/codiesp/">Web</a></li> <li><a href="http://ceur-ws.org/Vol-2696/paper_263.pdf">Citation</a>: Antonio Miranda-Escalada, Aitor Gonzalez-Agirre, Jordi Armengol-Estapé and Martin Krallinger. Overview of automatic clinical coding: annotations, guidelines, and solutions for non-English clinical cases at CodiEsp track of CLEF eHealth 2020. In CLEF (Working Notes). 2020</li> <li><a href="https://doi.org/10.5281/zenodo.3859869">Silver Standard corpus</a></li> <li><a href="https://doi.org/10.5281/zenodo.3730566">Annotation guidelines</a></li> <li><a href="https://www.youtube.com/playlist?list=PL5uSCzf1azhA0crlSVCYMPqMUWd4mXc4x">YouTube presentations</a></li> <li><a href="https://temu.bsc.es/codiesp/index.php/participants-systems/">Participant codes</a></li> </ul>   For more information, visit the track webpage: http://temu.bsc.es/codiesp/ or email us at encargo-pln-life@bsc.es   Copyright (c) 2019 Secretaría de Estado para el Avance Digital

opencc-by-4.0May 2020View details →

Data and code for the analysis in "Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland"

Data and code used for the analysis in Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland (Lemaitre et al., Swiss Medial Weekly 2020).

opencc-by-4.0May 2020View details →

Data and code to perform the"Target deformation" workflow in R: virtual reconstruction of the Equus stenonis holotype skulll

Data and code to perform the"Target deformation" workflow in R: virtual reconstruction of the Equus stenonis holotype skulll. TargetDeformation.R: R code with for the Target Deformation procedure. IGF560.ply: 3D mesh of the holotype IGF560 in ply extension. IGF560_set.txt: landmark set of the holotype IGF560. Dm. 5/154.3/4.A4.5.ply: 3D mesh of Dm 5/154.3/4.A4.5 in .ply extension. Dm_set.txt: landmark set of the Dm 5/154.3/4.A4.5 sample. IGF11023: 3D mesh of IGF11023 in.ply extension. IGF11023_set.txt: landmark set on the IGF11023 sample. IGF560R: 3D mesh of IGF560R in.ply extension. IGF560W: 3D mesh of IGF560W in.ply extension. IGF560R-s: 3D mesh of IGF560R-s in.ply extension. IGF560W-s: 3D mesh of IGF560W-s in.ply extension. IGF560_IGF560R_IGF560W.html: file that contain WebGL code to reproduce the 3D meshes of IGF560, IGF560R and IGF560W in a browser. IGF560Rs_IGF560Ws.html: file that contain WebGL code to reproduce the 3D meshes of IGF560R-S and IGF560W-S in a browser. IGF560W Mesh area variation.html: file that contain WebGL code to reproduce two 3d meshes of IGF560W using localmeshDist() and meshdist() in a browser.

opencc-by-4.0Jul 2020View details →

Matlab code for a multipolar decomposition of optical forces

This dataset supplements Figure 5 from the publication "Multipolar Origin of the Unexpected Transverse Force Resulting from Two-Wave Interference*" by Karim Achouri, Andrei Kiselev, and Olivier J. F. Martin. Here, we provide the code for the multipolar analysis of the optical force based on the vector spherical harmonic decomposition. Based on the Mie solution, electric fields can be obtained numerically in the far-field by using the software developed by Dr. Karim Achouri https://github.com/kachourim/MieScatteringPEC. This code analyzes the far-field scattered by a perfect electric conductor sphere placed in vacuum for different sphere radii. In the framework of the Maxwell stress tensor, we find the optical force acting on a sphere along the z-direction in the illumination configuration presented in Figure 1*. The use of the vector spherical decomposition allows to observe contributions from different multipolar interactions. In this code,we analyze the force appearing as a result of the interaction between electric dipole aligned along x, px, and electric quadrupole with components xz, Qexz and compare it with the total force along the z-axis appearing as a result of interaction between all multipoles supported by the sphere with given radius.

opencc-by-4.0Sep 2020View details →

SHAPE-ID Literature Review dataset: journal occurrences with ASJC codes

Background and methodology: The dataset consists of a list of 2202 journal titles represented in the <a href="https://doi.org/10.5281/zenodo.4034507">SHAPE-ID Literature Review bibliography</a>, prepared for the purposes of quantitative analysis. The list of journals is based on 3955 journal articles in the bibliography dataset that had an International Standard Serial Number (ISSN). To each journal title the project team attributed: - a weight factor based on how many articles from the given journal  featured in bibliography dataset - at least one <a href="https://service.elsevier.com/app/answers/detail/a_id/15181/supporthub/scopus/">All Science Journal Classification</a> (ASJC) code, representing different scientific disciplines - a country of publication.  In case of 1853 of those journal titles, the attribution was automatised (we matched the ISSNs of journal titles in our sample against the Scopus Sources list from February 2019). In case of the remaining 349 titles the attribution was accomplished manually, based on the information available in SCOPUS, Web of Science, JSTOR, Information Matrix for the Analysis of Journals (MIAR) and ISSN databases. Description of the file: This is a csv file containing a list of 2202 journal titles represented in the SHAPE-ID Literature Review bibliography, with country of publication and ASJC codes assigned.  The file is formatted as follows: Column A: ISSN of the journal Column B: information on how country and ASJC codes were attributed. Value “N” indicates automatic attribution based on match with Scopus list of sources. Other values indicate manual attribution. Values WOS, SCOPUS, JSTOR indicate source of information. Valu “Y” indicates that information was compiled based on multiple sources.  Column C: numeric values correspond to the weight factor, i.e. number of time articles from each journal featured in the SHAP-ID Literature Review bibliography.  Column D: SHAPE-ID Zotero bibliography identifier. Column E: Journal title Column F: The country of publication Columns G-AD: ASJC codes (numeric and word values) associated with journal entries.

opencc-by-4.0Jul 2020View details →

Effect of net direct current on the properties of radio frequency sheaths: simulation and cross-code comparison

The accompanying files contain digital data for figures in the article "Effect of net direct current on the properties of radio frequency sheaths: simulation and cross-code comparison" by J. R. Myra, M.T. Elias, D. Curreli, and T. G. Jenkins, submitted to the journal Nucl. Fusion. Abstract In order to understand, predict and control ion cyclotron range of frequency (ICRF) interactions with tokamak scrape-off layer plasmas, computational tools which can model radio frequency (RF) sheaths are needed. In particular, models for the effective surface impedance and DC rectified sheath potentials may be coupled with full wave RF simulation codes to predict self-consistent wave fields near surfaces and the resulting power dissipation and plasma-material interactions from ion sputtering. In this study, previous work assuming zero net DC current flow through the sheath is generalized to allow the surface to collect net positive or negative current, as is often observed in experiments. The waveforms, DC potential and RF admittance are investigated by means of analytical theory, nonlinear fluid and particle-in-cell (PIC) codes. Cross-code comparisons provide detailed model verification and elucidate the roles of ion and electron kinetics. When the sheath draws negative (positive) DC current, the voltage rectification is reduced (increased) compared with the zero-current case, and both the real and imaginary parts of the admittance are increased (reduced).  A previous four-input parametrization of the sheath rectification and admittance properties is generalized to include a fifth parameter describing the DC sheath current.