Find research datasets worth reusing

opencc-byAug 2020View details →

On the use of real-time mortality data in modelling and analysis during an epidemic outbreak – extended data

This project contains extended data related to the journal article "On the use of real-time mortality data in modelling and analysis during an epidemic outbreak" by Per Liljenberg This project contains the following extended data: <ul> <li>Liljenberg2020_OGR_Appendix.pdf (Appendix to the main article)</li> <li>swedish_covid_deaths_OGR.R. (R-script to generate graphs and nowcasts in the paper.)</li> <li>MDAR author checklist.pdf (Completed MDAR reporting checklist)</li> </ul>

opencc-by-4.0Aug 2020View details →

Climate model data for "Atmosphere-ocean feedback from wind-driven sea spray aerosol production"

Data from atmosphere-only and coupled climate model simulations performed for "Atmosphere-ocean feedback from wind-driven sea spray aerosol production". Files are in netCDF format.

opencc-by-4.0Sep 2020View details →

Data, Code, Models, and Results for 'Empirical estimation of yield variability due to weather shocks using biophysical characteristics for U.S. rainfed and irrigated maize, soybeans, and winter wheat'

Data, Code, Models, and Results for 'Empirical estimation of yield variability due to weather shocks using biophysical characteristics for U.S. rainfed and irrigated maize, soybeans, and winter wheat'

opencc-by-4.0Apr 2020View details →

DATA for Land Surface Model influence on the simulated climatologies of temperature and precipitation extremes in the WRF v.3.9 model over North America

Code and daily temperature and precipitation outputs used to estimate climate extreme indices in García-García et al. 2020.   García-García A., Cuesta-Valero F.J., Beltrami H., González-Rouco J.F., García-Bustamante E., and Finnis J. "Land Surface Model influence on the simulated climatologies of temperature and precipitation extremes in the WRF v.3.9 model over North America" submitted to Geocientific Model Development. 2020.

opencc-by-4.0Apr 2020View details →

Data and code for GRL submission "Tropical rainfall linked to stronger future ENSO-NAO teleconnection in CMIP5 models"

Data and python code used to plot figures in GRL submission "Tropical rainfall linked to stronger future ENSO-NAO teleconnection in CMIP5 models".

Model data for "A hybrid dynamical-statistical model for advancing subseasonal tropical cyclone prediction over the western North Pacific"

The dataset is the potential predictors of the statistical forecast model based on the 4 methods. The files in the document named "Train" are the potential predictors and TC anomalous counts for C1-C7 and TCall in the training period of 1979-2002 with 480-time points. For example, "./data/Train/M1/prepar/Obs_C1_pre-data.txt" contains 7 potential predictors of OLR, SSTA, specific humidity at 700 hPa, omega at 500 hPa, divergence and vorticity at 850hPa defined with method 1, and TC anomalous for TC of C1 prediction. The files named "Model_Lead*_C*_pre-data_*.txt" in "Frcst" the document are the potential predictors in the forecast period of 2003-2013 at lead times of 10, 15, 20, 25, 30, and 35 days with 220-time points. For example, "./data/Frcst/M1/prepar/Model_Lead10_C1_pre-data_00.txt" contains 7 potential predictors from the output of the FLOR model at lead 10 days initialized at Z00 time defined with method 1. Besides, "./data/Frcst/M1/prepar/Obs_C1_pre-data.txt" contains 7 potential predictors from the observation, which is the result of lead 0 days.

opencc-by-4.0Dec 2019View details →

Subjective Test Dataset and Meta-data-based Models for 360° Streaming Video Quality

During the last years, the number of 360° videos available for streaming has rapidly increased, leading to the need for 360° streaming video quality assessment. In this paper, we report and publish results of three subjective 360° video quality tests, with conditions used to reflect real-world bitrates and resolutions including 4K, 6K and 8K, resulting in 64 stimuli each for the first two tests and 63 for the third. As playout device we used the HTC Vive for the first and HTC Vive Pro for the remaining two tests. Video-quality ratings were collected using the 5-point Absolute Category Rating scale. The 360° dataset provided with the paper contains the links of the used source videos, the raw subjective scores, video-related meta-data, head rotation data and Simulator Sickness Questionnaire results per stimulus and per subject to enable reproducibility of the provided results. Moreover, we use our dataset to compare the performance of state-of-the-art full-reference quality metrics such as VMAF, PSNR, SSIM, ADM2, WS-PSNR and WS-SSIM. Out of all metrics, VMAF was found to show the highest correlation with the subjective scores. Further, we evaluated a center-cropped version of VMAF ("VMAF-cc") that showed to provide a similar performance as the full VMAF. In addition to the dataset and the objective metric evaluation, we propose two new video-quality prediction models, a bitstream meta-data-based model and a hybrid no-reference model using bitrate, resolution and pixel information of the video as input. The new lightweight models provide similar performance as the full-reference models while enabling fast calculations.

Data for paper "Bayesian Model for HOPE Mass Spectrometers on Van Allen Probes"

Data set for paper "Bayesian Model for HOPE Mass Spectrometers on Van Allen Probes" to be published in Journal of Geophysical Research: Space Physics (Technical Methods). The uploaded files are CSV files for Data Set S1 through S7.

Data for tests of the NicheMapR transient heat budget modelling code

This data set and code is used to test the ability of the transient heat budget modelling code in the R package NicheMapR (functions 'onelump_var', 'twolump' and 'trans_behav') against inanimate objects (fruit, pipes) and real lizards (a small and a large lizard who's activity and body temperatures were observed on the same day at an arid locality in central Australia). It generates the figures and statistics reported as supplementary information for the paper: Kearney, M. R. et al. 2020. Modeling the joint effects of body size and microclimate on heat budgets and foraging opportunities of ectotherms. - Methods in Ecology and Evolution in press. See the latter paper for more details. To run the code the package NicheMapR must be installed.

Cross-correlation functions, dispersion data, and 3D velocity models of the Chao lake

We obtained a 3-D isotropic and azimuthal anisotropic model beneath the Chao Lake. These datasets contain the cross-correlation functions, dispersion data we picked, and the models we obtained.

opencc-by-4.0Nov 2020View details →

Data from ROMS-CoSiNE-Fe model outputs at Station S1

ROMS-CoSiNE-Fe model outputs at Station S1. Standard ROMS averaged files.

Cross-Node Federated Graph Neural Network for Spatio-Temporal Data Modeling

Dataset for ICLR 2021 submission "Cross-Node Federated Graph Neural Network for Spatio-Temporal Data Modeling".

opencc-by-4.0Nov 2020View details →

Data supplement for "Efficient calculation of phase coexistence and phase diagrams: application to a binary phase-field crystal model"

This dataset contains the data and source files for the diagrams of the following publication: Holl, M. P., Archer, A.J., & Thiele, U. Efficient calculation of phase coexistence and phase diagrams: application to a binary phase-field crystal model arXiv preprint <a href="https://arxiv.org/abs/2009.02946">arXiv:2009.02946</a>, 2020 We provide the data and sources necessary to generate figures 10-14 of the manuscript. Additionally we provide the MATLAB codes to run all the continuations for the results in sections 4.2 and 5.  For more information, please see the included README.md

opencc-by-4.0Jan 2021View details →

MicN model calibration and calibration data

MicN model calibration and validation data, including concentrations of ammonium and nitrate and N2O emission.

opencc-zeroDec 2008View details →

Data from: Mixture modeling of transcript abundance classes in natural populations

BACKGROUND: Populations diverge in genotype and phenotype under the influence of such evolutionary processes as genetic drift, mutation accumulation, and natural selection. Because genotype maps onto phenotype by way of transcription, it is of interest to evaluate how these evolutionary factors influence the structure of variation at the level of transcription. Here, we explore the distributions of cis-acting and trans-acting factors and their relative contributions to expression of transcripts that exhibit two or more classes of abundance among individuals within populations. RESULTS: Expression profiling using cDNA microarrays was conducted in Drosophila melanogaster adult female heads for 58 nearly isogenic lines from a North Carolina population and 50 from a California population. Using a mixture modeling approach, transcripts were identified that exhibit more than one mode of transcript abundance across the samples. Power studies indicate that sample sizes of 50 individuals will generally be sufficient to detect divergent transcript abundance classes. The distribution of transcript abundance classes is skewed toward low frequency minor classes, which is reminiscent of the typical skew in genotype frequencies. Similar results are observed in reported data on gene expression in human lymphoblast cell lines, in which analysis of association with linked polymorphisms implies that cis-acting single nucleotide polymorphisms make only a modest contribution to bimodal distributions of transcript abundance. CONCLUSION: Population surveys of gene expression may complement genetical genomics as a general approach to quantifying sources of transcriptional variation. Differential expression of transcripts among individuals is due to a complex interplay of cis-acting and trans-acting factors.

opencc-zeroDec 2017View details →

Data from: Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling

Detecting all species in a given survey is challenging, regardless of sampling effort. This issue, more commonly known as imperfect detection, can have negative impacts on data quality and interpretation, most notably leading to false absences for rare or difficult‐to‐detect species. It is important that this issue be addressed, as estimates of species richness are critical to many areas of ecological research and management. In this study, we set out to determine the impacts of imperfect detection, and decisions about thresholds for inclusion in occupancy, on estimates of species richness and community structure. We collected data from a stream fish assemblage in Algonquin Provincial Park to be used as a representation of ecological communities. We then used multispecies occupancy modeling to estimate species‐specific occurrence probabilities while accounting for imperfect detection, thus creating a more informed dataset. This dataset was then compared to the original to see where differences occurred. In our analyses, we demonstrated that imperfect detection can lead to large changes in estimates of species richness at the site level and summarized differences in the community structure and sampling locations, represented through correspondence analyses.

opencc-zeroDec 2017View details →

Data from: A unified model for optimizing riverscape conservation

1.Spatial prioritization tools provide a means of finding efficient trade-offs between biodiversity protection and the delivery of ecosystem services. Although a large number of prioritization approaches have been proposed in the literature, most are specifically designed for terrestrial systems. When applied to river ecosystems, they often fail to adequately account for the essential role that landscape connectivity plays in maintaining both biodiversity and ecosystem services. This is particularly true of longitudinal connectivity, which in many river catchments is highly altered by the presence of dams, stream-road crossings, and other artificial structures. 2.We propose a novel framework for coordinating river conservation and connectivity restoration. As part of this, we formulate an optimization model for deciding which subcatchments to designate for ecosystem services and which to include in a river protected area (RPA) network, while also deciding which existing river barriers to remove in order to maximize longitudinal connectivity within the RPA network. In addition to constraints on the size and makeup of the RPA network, the model also considers the suitability of sites for conservation, based on a biological integrity index, and connectivity to multiple habitat types. We demonstrate the usefulness of our approach using a case study involving four managed river catchments located in Hungary. 3.Results show that large increases in connectivity-weighted habitat can be achieved through targeted selection of barrier removals and that the benefits of barrier removal are strongly depend on RPA network size. We find that (i) highly suboptimal solutions are produced if habitat conservation planning and connectivity restoration are done separately and (ii) RPA acquisition provides substantially greater marginal benefits than barrier removal given limited resources. 4.Synthesis and applications. Finding a balance between conservation and ecosystem services provision should give more consideration to connectivity restoration planning, especially in multi-use riverscapes. We present the first modelling framework to directly integrate and optimize river conservation and connectivity restoration planning. This framework can help conservation managers to account better for connectivity, resulting in more effective catchment scale maintenance of biological integrity and ecosystem services delivery.

opencc-zeroDec 2016View details →

Data from: Plant water potential improves prediction of empirical stomatal models

Climate change is expected to lead to increases in drought frequency and severity, with deleterious effects on many ecosystems. Stomatal responses to changing environmental conditions form the backbone of all ecosystem models, but are based on empirical relationships and are not well-tested during drought conditions. Here, we use a dataset of 34 woody plant species spanning global forest biomes to examine the effect of leaf water potential on stomatal conductance and test the predictive accuracy of three major stomatal models and a recently proposed model. We find that current leaf-level empirical models have consistent biases of over-prediction of stomatal conductance during dry conditions, particularly at low soil water potentials. Furthermore, the recently proposed stomatal conductance model yields increases in predictive capability compared to current models, and with particular improvement during drought conditions. Our results reveal that including stomatal sensitivity to declining water potential and consequent impairment of plant water transport will improve predictions during drought conditions and show that many biomes contain a diversity of plant stomatal strategies that range from risky to conservative stomatal regulation during water stress. Such improvements in stomatal simulation are greatly needed to help unravel and predict the response of ecosystems to future climate extremes.

opencc-zeroDec 2018View details →

Data from: High-frequency sampling and piecewise models reshape dispersal kernels of a common reef coral

Models of dispersal potential are required to predict connectivity between populations of sessile organisms. However, to date, such models do not allow for time‐varying rates of acquisition and loss of competence to settle and metamorphose, and permit only a limited range of possible survivorship curves. We collect high‐resolution observations of coral larval survival and metamorphosis, and apply a piecewise modeling approach that incorporates a broad range of temporally‐varying rates of mortality and loss of competence. Our analysis identified marked changes in competence loss and mortality rates, whose timing implicates developmental failure and depletion of energy reserves. Asymmetric demographic rates suggest more intermediate‐range dispersal, less local retention, and less long‐distance dispersal than predicted by previously‐employed non‐piecewise models. Because vital rates are likely temporally asymmetric, at least for non‐feeding broadcast‐spawned larvae, piecewise analysis of demographic rates will likely yield more reliable predictions of dispersal potential.