Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
547
datasets available to search
ShareScore release 0.9.0
Dataset results
547 results for “Model Tests”
Code from: Testing for normality in regression models: mistakes abound (but may not matter)
Open the record for dataset details and reuse information.
Data from: Conspicuous plumage does not increase predation risk: a continent-wide test using model songbirds
Open the record for dataset details and reuse information.
Data from: Context-dependence of maternal effects: testing assumptions of optimal egg size, differential- and sex-allocation models
Open the record for dataset details and reuse information.
Data from: Testing models of sex ratio evolution in a gynodioecious plant: female frequency covaries with the cost of male fertility restoration
Open the record for dataset details and reuse information.
Data for: The biomechanics of tooth strength: testing the utility of simple models for predicting fracture in geometrically complex teeth
Open the record for dataset details and reuse information.
Data from: Species richness, endemism, and abundance patterns: tests of two fractal models in a serpentine grassland
Open the record for dataset details and reuse information.
Model trees and associated simulated nucleotide sequences for testing phylogenetic inference methods
<p>This repository contains 142 tar.gz archive files, each containing nucleotide sequence data that have been simulated using <a href="http://abacus.gene.ucl.ac.uk/software/indelible/"><em>INDELible</em></a> for testing alignment-free phylogenetic inference methods. These datasets were generated by using the results (trees and model parameters) of 142 phylogenomic analyses of real-case data as model (available <a href="https://zenodo.org/record/4034261">here</a>). Initial sequence length was 5 Mbs, and an indel rate of 0.01 was set with indel length drawn from [1, 50000] according to a Zipf distribution with parameter 1.5 (see <em>INDELible</em> <a href="http://abacus.gene.ucl.ac.uk/software/indelible/manual/model.shtml">manual</a>).</p> <p>Each archive contains the following files/directories:</p> <ul> <li><code>GTR.params.trees.tsv </code> a tab-delimited file summarizing the real-case GTR+Γ model parameters and the phylogenetic tree used to simulate the sequence dataset (gathered from <a href="https://zenodo.org/record/4034261">https://zenodo.org/record/4034261</a>)</li> <li><code>tax.tsv </code> a tab-delimited file containing the initial (col 1) and simplified (col 2) taxon names</li> <li><code>model.nwk </code> a <a href="https://evolution.genetics.washington.edu/phylip/newicktree.html">Newick</a>-formatted file containing the initial model tree (gathered from <code>GTR.params.trees.tsv</code>) with simplified leaf names (following <code>tax.tsv</code>)</li> <li><code>control.txt </code> the <em>INDELible</em> input file used to simulate the evolution of a sequence along the tree in <code>model.nwk</code></li> <li><code>seq/ </code> a directory containing the simulated sequences (one FASTA file per leaf in the tree in <code>model.nwk</code>)</li> </ul> <p>___</p> <p>Criscuolo A (2020) <em>On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference</em>. F1000Research, 9:1309. <a href="https://doi.org/10.12688/f1000research.26930.1">doi:10.12688/f1000research.26930.1</a></p>
Using predictive models to evaluate the quality of a test suite at class and method level.
<p>Vídeo de apresentação para o Workshop de Teses e Dissertações do CBSoft (WTDSoft).</p>
Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island Southeast Asia (ISEA). A previous study revealed signatures of inter-specific admixture between these Sus species (Frantz et al. (2013) Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome biology, 14, R107). However, the timing, directionality and extent of this admixture remain unknown. Here we use a likelihood based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that inter-specific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
Data from: A test of genetic models for the evolutionary maintenance of same-sex sexual behaviour
The evolutionary maintenance of same-sex sexual behaviour (SSB) has received increasing attention because it is perceived to be an evolutionary paradox. The genetic basis of SSB is almost wholly unknown in non-human animals, though this is key to understanding its persistence. Recent theoretical work has yielded broadly applicable predictions centred on two genetic models for SSB: overdominance and sexual antagonism. Using Drosophila melanogaster, we assayed natural genetic variation for male SSB and empirically tested predictions about the mode of inheritance and fitness consequences of alleles influencing its expression. We screened 50 inbred lines derived from a wild population for male–male courtship and copulation behaviour, and examined crosses between the lines for evidence of overdominance and antagonistic fecundity selection. Consistent variation among lines revealed heritable genetic variation for SSB, but the nature of the genetic variation was complex. Phenotypic and fitness variation was consistent with expectations under overdominance, although predictions of the sexual antagonism model were also supported. We found an unexpected and strong paternal effect on the expression of SSB, suggesting possible Y-linkage of the trait. Our results inform evolutionary genetic mechanisms that might maintain low but persistently observed levels of male SSB in D. melanogaster, but highlight a need for broader taxonomic representation in studies of its evolutionary causes.
Data from: Modelling tooth–prey interactions in sharks: the importance of dynamic testing
The shape of shark teeth varies among species, but traditional testing protocols have revealed no predictive relationship between shark tooth morphology and performance. We developed a dynamic testing device to quantify cutting performance of teeth. We mimicked head-shaking behaviour in feeding large sharks by attaching teeth to the blade of a reciprocating power saw fixed in a custom-built frame. We tested three tooth types at biologically relevant speeds and found differences in tooth cutting ability and wear. Teeth from the bluntnose sixgill (Hexanchus griseus) showed poor cutting ability compared with tiger (Galeocerdo cuvier), sandbar (Carcharhinus plumbeus) and silky (C. falciformis) sharks, but they also showed no wear with repeated use. Some shark teeth are very sharp at the expense of quickly dulling, while others are less sharp but dull more slowly. This demonstrates that dynamic testing is vital to understanding the performance of shark teeth.
Data from: Effect of detection heterogeneity in occupancy-detection models: an experimental test of time-to-first-detection methods
Imperfect detection can bias estimates of site occupancy in ecological surveys but can be corrected by estimating detection probability. Time-to-first-detection (TTD) occupancy models have been proposed as a cost-effective survey method that allows detection probability to be estimated from single site visits. Nevertheless, few studies have validated the performance of occupancy-detection models by creating a situation where occupancy is known, and model outputs can be compared with the truth. We tested the performance of TTD occupancy models in the face of detection heterogeneity using an experiment based on standard survey methods to monitor koala (Phascolarctos cinereus) populations in Australia. Known numbers of koala faecal pellets were placed under trees, and observers, uninformed as to which trees had pellets under them, carried out a TTD survey. We fitted five TTD occupancy models to the survey data, each making different assumptions about detectability, to evaluate how well each estimated the true occupancy status. Relative to the truth, all five models produced strongly biased estimates, overestimating detection probability and underestimating the number of occupied trees. Despite this, goodness-of-fit tests indicated that some models fitted the data well, with no evidence of model misfit. Hence, TTD occupancy models that appear to perform well with respect to the available data may be performing poorly. The reason for poor model performance was unaccounted for heterogeneity in detection probability, which is known to bias occupancy-detection models. This poses a problem because unaccounted for heterogeneity could not be detected using goodness-of-fit tests and was only revealed because we knew the experimentally determined outcome. A challenge for occupancy-detection models is to find ways to identify and mitigate the impacts of unobserved heterogeneity, which could unknowingly bias many models.
Data from: Wolf in sheep's clothing: model misspecification undermines tests of the neutral theory for life histories
Understanding the processes behind change in reproductive state along life-history trajectories is a salient research program in evolutionary ecology. Two processes, state dependence and heterogeneity, can drive the dynamics of change among states. Both processes can operate simultaneously, begging the difficult question of how to tease them apart in practice. The Neutral Theory for Life Histories (NTLH) holds that the bulk of variations in life-history trajectories is due to state dependence and is hence neutral: Once previous (breeding) state is taken into account, variations are mostly random. Lifetime reproductive success (LRS), the number of descendants produced over an individual's reproductive life span, has been used to infer support for NTLH in natura. Support stemmed from accurate prediction of the population-level distribution of LRS with parameters estimated from a state dependence model. We show with Monte Carlo simulations that the current reliance of NTLH on LRS prediction in a null hypothesis framework easily leads to selecting a misspecified model, biased estimates and flawed inferences. Support for the NTLH can be spurious because of a systematic positive bias in estimated state dependence when heterogeneity is present in the data but ignored in the analysis. This bias can lead to spurious positive covariance between fitness components when there is in fact an underlying trade-off. Furthermore, neutrality implied by NTLH needs a clarification because of a probable disjunction between its common understanding by evolutionary ecologists and its translation into statistical models of life-history trajectories. Irrespective of what neutrality entails, testing hypotheses about the dynamics of change among states in life histories requires a multimodel framework because state dependence and heterogeneity can easily be mistaken for each other.
Data from: Using social parasitism to test reproductive skew models in a primitively eusocial wasp
Remarkable variation exists in the distribution of reproduction (skew) among members of cooperatively breeding groups, both within and between species. Reproductive skew theory has provided an important framework for understanding this variation. In the primitively eusocial Hymenoptera, two models have been routinely tested: concessions models, which assume complete control of reproduction by a dominant individual, and tug-of-war models, which assume on-going competition among group members over reproduction. Current data provide little support for either model, but uncertainty about the ability of individuals to detect genetic relatedness and difficulties in identifying traits conferring competitive ability mean that the relative importance of concessions versus tug-of-war remains unresolved. Here, we suggest that the use of social parasitism to generate meaningful variation in key social variables represents a valuable opportunity to explore the mechanisms underpinning reproductive skew within the social Hymenoptera. We present a direct test of concessions and tug-of-war models in the paper wasp Polistes dominulus by exploiting pronounced changes in relatedness and power structures that occur following replacement of the dominant by a congeneric social parasite. Comparisons of skew in parasitized and unparasitized colonies are consistent with a tug-of-war over reproduction within P. dominulus groups, but provide no evidence for reproductive concessions.
Data from: Sex-related online behaviors, perceived peer norms and adolescents' experience with sexual behavior: testing an integrative model
Research on the role of sex-related Internet use in adolescents' sexual development has often isolated the Internet and online behaviors from other, offline influencing factors in adolescents' lives, such as processes in the peer domain. The aim of this study was to test an integrative model explaining how receptive (i.e., use of sexually explicit Internet material [SEIM]) and interactive (i.e., use of social networking sites [SNS]) sex-related online behaviors interrelate with perceived peer norms in predicting adolescents' experience with sexual behavior. Structural equation modeling on longitudinal data from 1,132 Dutch adolescents (Mage T1 = 13.95; range 11-17; 52.7% boys) demonstrated concurrent, direct, and indirect effects between sex-related online behaviors, perceived peer norms, and experience with sexual behavior. SEIM use (among boys) and SNS use (among boys and girls) predicted increases in adolescents' perceptions of peer approval of sexual behavior and/or in their estimates of the numbers of sexually active peers. These perceptions, in turn, predicted increases in adolescents' level of experience with sexual behavior at the end of the study. Boys' SNS use also directly predicted increased levels of experience with sexual behavior. These findings highlight the need for multisystemic research and intervention development to promote adolescents' sexual health.
Incorporating evaporative water loss into bioenergetic models of hibernation to test for relative influence of host and pathogen traits on white-nose syndrome
<p class="Paragraph">Hibernation consists of extended durations of torpor interrupted by periodic arousals. The 'dehydration hypothesis' proposes that hibernating mammals arouse to replenish water lost through evaporation during torpor. Arousals are energetically expensive, and increased arousal frequency can alter survival throughout hibernation. Yet we lack a means to assess the effect of evaporative water loss (EWL), determined by animal physiology and hibernation microclimate, on torpor bout duration and subsequent survival. White-nose syndrome (WNS), a devastating disease impacting hibernating bats, causes increased frequency of arousals during hibernation and EWL has been hypothesized to contribute to this increased arousal frequency. WNS is caused by a fungus, which grows well in humid hibernaculum environments and damages wing tissue important for water conservation. Here, we integrated the effect of EWL on torpor expression in a hibernation energetics model, including the effects of fungal infection, to determine the link between EWL and survival. We collected field data for <i>Myotis lucifugus, </i>a species that experiences high mortality from WNS, to gather parameters for the model. In saturating conditions, we predicted healthy bats experience minimal mortality. Infected bats, however, suffer high fungal growth in highly saturated environments, leading to exhaustion of fat stores before spring. Our results suggest that host adaptation to humid environments leads to increased arousal frequency from infection, which drives mortality across hibernaculum conditions. Our modified hibernation model provides a tool to assess the interplay between host physiology, hibernaculum microclimate, and diseases such as WNS on winter survival.</p>
Testing the trade balance model_ raw data_NP
Open the record for dataset details and reuse information.
MUSDB18-HQ Test Set Inference Outputs for Models from "A Generalized Bandsplit Neural Network for Cinematic Audio Source Separation"
Open the record for dataset details and reuse information.
Female preference for colour-enhanced males: a test of the sensory bias model in medaka, a drab fish
<p>Sexual selection research has long focused on the evolution of female mate preferences. Most of the models that have been developed posit that mate preferences evolve in a mating context. In contrast, the sensory bias model proposes that mate choice preferences arise in a non-mating context, as a by-product of natural selection acting on a female's perceptual system. Recent research has shown that many species of fishes, from across a large clade including poeciliids, goodeids, and medaka, have a bias for long wavelength (LW) colors (yellow, orange, red) in a non-mating context. Even species that do not have LW-colored ornaments, apparently because they have been lost secondarily, retain this latent bias for LW colors. Here, we predicted that female <i>Oryzias latipes </i>(Japanese medaka), a drab species with a latent preference for LW colors, would show a mate choice preference for males with an artificial secondary sexual trait—a colored stripe added to their flank. We confirmed that females were more responsive to red and orange objects in a non-mating context than to other colors. We also showed that females were less resistant towards males with a LW-colored stripe than to those enhanced with a non-LW stripe and that, for many females, responses towards specific LW colors were consistent across these non-mating and mating contexts. Therefore, our results provide support for the sensory bias model by providing a link between a sensory bias in a non-mating context and a mate choice preference in a drab species like medaka.</p>
Dataset for training and testing the SCFNN model
<p>train_test_data.tar.gz contains the DFT calculation results of water cubic box under various strength of external electric field. This dataset is used to train and test the SCFNN model.</p> <p>HirshfeldMullikenCharges.tar.gz contains the DFT calculation results of Hirshfeld and Mulliken charges for the same water box. This dataset is used to train the 4G-HDNN model.</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.