Find research datasets worth reusing

opencc-by-4.0Oct 2020View details →

Dataset for "Recursive Input and State Estimation: A General Framework for Learning from Time Series with Missing Data"

Dataset for "Recursive Input and State Estimation: A General Framework for Learning from Time Series with Missing Data"   Missing values in the blood glucose datasets are represented with -2.

Supplementary material 1 from: Wilson JRU, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM (2020) Frameworks used in invasion science: progress and prospects. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 1-30. https://doi.org/10.3897/neobiota.62.58738

Details of the workshop, the invitation, list of attendees, the programme, ground rules, form for highlighting case-studies, and the process for compiling the special issue

Supplementary material 1 from: Brock KC, Daehler CC (2020) Applying an invasion and risk framework to track non-native island floras: a case study of challenges and solutions in Hawai'i. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 55-79. https://doi.org/10.3897/neobiota.62.52764

Guidance on the status confidence rating and adapting a regional checklist to track invasion statuses

Supplementary material 2 from: Kumschick S, Wilson JRU, Foxcroft LC (2020) A framework to support alien species regulation: the Risk Analysis for Alien Taxa (RAAT). In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 213-239. https://doi.org/10.3897/neobiota.62.51031

Risk Analysis for Alien Taxa framework, adapted to South African NEMBA A&IS Regulations (v.1.2) (Appendix S2)

Supplementary material 1 from: Kumschick S, Wilson JRU, Foxcroft LC (2020) A framework to support alien species regulation: the Risk Analysis for Alien Taxa (RAAT). In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 213-239. https://doi.org/10.3897/neobiota.62.51031

How the Risk Analysis Framework covers Section 6, Regulation 14-17, in the NEM:BA A&IS Regulations of 2014 (Appendix S1)

opencc-by-4.0Oct 2020View details →

On the (Un-)Adoption of JavaScript Front-end Frameworks

DBR

opencc-zeroNov 2020View details →

Data from: Plotting for change: an analytic framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

A recent study argued that coalescent-based models of species delimitation mostly delineate population structure not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable, or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (a) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles, and to hold aside individuals involved in contemporary admixture for independent consideration; (b) apply phylogenetic techniques to identify lineages; (c) assess diagnosability of those lineages as potential candidate species; (d) interpret the diagnosable lineages in a geographic context (sympatry, parapatry, allopatry); (e) assess significance of difference or trends in the context of sampling intensity; and (f) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We use this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not explicitly discussed in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.

Model Validation Framework Evaluation Result

CSV Files with the results of the Model Validation Framework Evaluation

Framework for performing experiments on IBM Quantum Computers

The data used in my B.Sc. thesis.

Scholarly publications reported by the projects funded by the European Union under the 7th Framework Programme.

N.B:  An updated dataset has been published by CORDIS on the European Union Open Data Portal  It can be found under the following link : <a href="https://data.europa.eu/data/datasets/cordisfp7projects">CORDIS - EU research projects under FP7 (2007-2013)</a> The documentation of the data quality process has been also updated  Mugabushaka, A,M, (2020). Linking Publications to Funding at Project Level: A curated dataset of publications reported by FP7 projects.  <a href="https://arxiv.org/abs/2011.07880">https://arxiv.org/abs/2011.07880</a> ------- Here we release the first version of a complete and curated dataset of scholarly publications reported by the projects funded by the European Union under the 7th Framework Programme.  For the creation of the dataset, we not only consolidated data from different reporting channels, we also undertook extensive quality assurance steps to:  <ol> <li> to validate reported records by systematically matching them to external authoritative sources and </li> <li>to assign them external identifiers, most notably digital object identifiers. </li> </ol> The process is described in the following ArXiv preprint:  Mugabushaka, A,M, (2020). Linking Publications to Funding at Project Level: A curated dataset of publications reported by FP7 projects. <a href="https://arxiv.org/abs/2011.07880">ArXiv 2011.07880 </a>   Dataset Description This version is provided as a csv file and contains 18 fields. id_project : project/grant identifier it corresponds to the project id (grant agreement number) provided in the project dataset in the European Open data portal     https://data.europa.eu/euodp/en/data/dataset/cordisfp7projects id_record : unique identifier of the records, created by the European Commission services id_dataset: initial reporting channel (please refer to the <a href="https://arxiv.org/abs/2011.07880">ArxIv pre-print </a>for explanations) the fields with the pre-fix "reported_" refer to the entries as provided by the Grant Holders in reporting systems the fields with the pre-fix "qa_" refer the links between the records and external authoritative sources . They are the results of the data quality process as described in the <a href="https://arxiv.org/abs/2011.07880">ArXiv pre-print</a>

Supporting dataset: A framework to quantify flow through coral reefs of varying coral cover and morphology

This dataset contains the STL files and data from the numerical and laboratory models used in the related publication.

opencc-by-4.0Dec 2020View details →

A Conceptual Model Framework for Analyzing, Simulating, Planning and Controlling of Supply-Demand Matching of Ecosystem Services in Agricultural Landscapes

The video gives an explanation of our conceptual approach for the investigation of the adaptation of societal demands for ecosystem services in agricultural landscapes.

opencc-by-4.0Dec 2020View details →

Tracing the origin of the South Asian summer monsoon precipitation and its variability using a novel Lagrangian framework

moc.zip: This dataset was used to calculate the meridional overturning water-mass stream function (Fig.2) and net evaporation which are responsible for net precipitation over the South Asian landmass during June to September months (Fig.3). track_amp.zip: The vertically integrated horizontal water-mass flux was computed from this data (Fig.4). bob_path.zip: Net precipitation (Fig.5) and net evaporation (Fig.6) calculated from Lagrangian water-mass trajectories that have crossed over the Bay of Bengal at least once and fallen down over the South Asian landmass. Also, Table 2 was prepared using this data. evap_precip_basins.zip: This file contain datasets that were used to compute the contribution of separate basins to the South Asian summer monsoon precipitation (Table 1) and also how the spatial distribution related to each basin (Fig.7) interannual.zip: Interannual precipitation variability was obtained from this dataset.

opencc-zeroDec 2016View details →

Data from: Telomere attrition and growth: a life-history framework and case study in common terns

The relationship between growth and age-specific telomere length, as a proxy of somatic state, is increasingly investigated, but observed patterns vary and a predictive framework is lacking. We outline expectations based on the assumption that telomere maintenance is costly and argue that individual heterogeneity in resource acquisition is predicted to lead to positive covariance between growth and telomere length. However, canalization of resource allocation to the trait with a larger effect on fitness, rendering that trait relatively invariant, can cause the absence of covariance. In a case study of common tern (Sterna hirundo) chicks, in which hatching order is the main determinant of variation in resource acquisition within broods, we find that body mass, but not telomere length or attrition, varies with hatching order. Moreover, body mass and growth positively predict survival to fledging, whereas telomere length and attrition do not. Using a novel statistical method to quantify standardized variance in plasticity, we estimate between-individual variation in telomere attrition to be only 12% of that of growth. Consistent with the relative invariance of telomere attrition, we find no correlation between age-specific body mass or growth and telomere attrition. We suggest that common tern chicks prioritize investment in long-term somatic state (as indicated by canalization of telomere maintenance) over immediate survival benefits of growth as part of an efficient brood reduction strategy that benefits the parents. As such, inter-specific variation in the growth-telomere length relationship may be explained by the extent to which parents benefit from rapid mortality of excess offspring.

Data from: A framework for analysing colour pattern geometry: adjacent colours

The analysis of colour pattern geometry is not as well advanced as the analysis of colour, although this reflects a lack of an analytical framework. The present study proposes an approach based on a consideration of which colours are adjacent to each other. Both vertebrate and invertebrate eyes do not take static images of the world but move across the field of view. As a consequence, the eye takes transects across the field of view responding to the colours and luminances within patches and to the colour and/or luminance transitions between patches. The framework and methods suggested here are based upon transects across colour patterns and make it possible to estimate colour pattern parameters that capture not only the relative areas of each patch class, but also the relative frequencies of colour/luminance transitions or adjacency. This allows tests of new hypotheses about colour patterns at the same time as including colour, pattern, and texture. Eleven groups of predictions are made with respect to the often conflicting needs of communication with conspecifics, avoiding predation, and finding food. New phenomena may be discovered as a result of these methods and predictions. For example, certain colour transitions may be used for species recognition even though the same colours are used by all species.

Data from: A statistical framework to explore ontogenetic growth variation among individuals and populations: a marine fish example

Growth is a fundamental biological process, driven by a multitude of intrinsic (within-individual) and extrinsic (environmental) factors, that underpins individual fitness and population demographics. Focussing on the comprehensive information stored in aquatic and terrestrial organism hard parts, we develop a series of increasingly complex hierarchical models to explore spatial and temporal sources of growth variation, ranging in resolution from within individuals to across a species. We apply this modelling framework to an extensive data set of otolith increment measurements from tiger flathead (Platycephalus richardsoni), a demersal commercially exploited fish that inhabits the warming waters of south-east Australia. We recreated growth histories (biochronology) up to four decades in length from seven fishing areas spanning this species' range. The dominant pattern in annual growth was an age-dependent, allometric decline that varied amongst individuals, sexes, fishing areas, years and cohorts. We found evidence for among-area differences in growth rate selectivity whereby younger fish at capture were generally faster growers. Temporal growth variation was partitioned into two main sources: extrinsic year-to-year annual fluctuations in environmental conditions and persistent cohort-specific growth differences, reflecting density dependence and/or juvenile experience. Despite low levels of among-individual growth synchrony within areas, we detected a regionally coherent signal of increasing average growth rate through time, a trend related to oceanic warming. At the southerly (poleward) range limit, growth was only weakly related to temperature, but further north in warmer waters this relationship strengthened until at the species' equatorward range limit, growth declined with increasing temperatures. We partitioned these species-wide and area-specific phenotypic responses into within and among-individual components using a reaction norm approach. Individual tiger flathead likely possess sufficient growth plasticity to successfully adapt to warming waters across much of their range, but increased future warming in the north will continue to depress growth, affecting individual fitness and even population persistence. Our modelling framework is directly applicable to other long-term, individual-based, data sets such as those derived from tree rings, corals, and tag-recapture studies, and provides an unprecedented level of resolution into the drivers of growth variation and the ecological and evolutionary implications of environmental and climatic change.

Data from: A preliminary framework for DNA barcoding, incorporating the multispecies coalescent

The capacity to identify an unknown organism using the DNA sequence from a single gene has many applications. These include the development of biodiversity inventories (Janzen et al. 2005), forensics (Meiklejohn et al. 2011), biosecurity (Armstrong and Ball 2005), and the identification of cryptic species (Smith et al. 2006). The popularity and widespread use (Teletchea 2010) of the DNA barcoding approach (Hebert et al. 2003), despite broad misgivings (e.g., Smith 2005; Will et al. 2005; Rubinoff et al. 2006), attest to this. However, one major shortcoming to the standard barcoding approach is that it assumes that gene trees and species trees are synonymous, an assumption that is known not to hold in many cases (Pamilo and Nei 1988; Funk and Omland 2003). Biological processes that violate this assumption include incomplete lineage sorting and interspecific hybridization (Funk and Omland 2003). Indeed, simulation studies indicate that the concatenation approach (in which these two processes are ignored) can lead to statistically inconsistent estimation of the species tree (Kubatko and Degnan 2007). However, recent developments make a barcoding approach that utilizes a single locus outdated. The cost of sequencing multiple gene fragments is no longer inhibitory, but more importantly, a range of analytical approaches have been developed that account for incomplete lineage sorting (Degnan and Salter 2005; Edwards et al. 2007; Liu et al. 2008; Kubatko et al. 2009; Heled and Drummond 2010; Yang and Rannala 2010). These approaches incorporate coalescent theory into the analysis of species trees and species delimitation (Fujita et al. 2012) and are conveniently accessible as software programs (e.g., BEST, BPP, *BEAST, MrBayes v. 3.2, STEM, and COAL). Although the general mixed Yule coalescent (GMYC) approach has also been developed for species delimitation (Pons et al. 2006), we do not consider it further here. It operates quite differently to the approaches outlined above (i.e., BEST, BPP, *BEAST, MrBayes v. 3.2, STEM, and COAL). The GMYC approach seeks to identify the shift in the rate of lineage branching that should be evident when interspecific evolutionary processes switch to population-level processes (Pons et al. 2006). Both empirical (Esselstyn et al. 2012) and simulation studies (Esselstyn et al. 2012; Fujisawa and Barraclough 2013) report that it performs poorly when effective population sizes and speciation rates are high, but within biologically relevant ranges. Ideally, a "next-generation" barcoding approach would (1) identify a minimal set of barcoding genes (perhaps specific to certain lineages), (2) generate a large and cladistically divergent database for comparisons, and (3) identify species using species delimitation approaches that incorporate the multispecies coalescent. The first two of these conditions are straightforward and require only discussion (requirement 1) and resources (requirement 2). However, the third requirement is much more problematic. Some of the recently developed approaches for species delimitation could not be used alone; for example, BPP requires a user-specified guide tree (Yang and Rannala 2010). All of the recently developed approaches are computationally intensive (Degnan and Rosenberg 2009), with many having practical limitations on the number of individuals that can be compared. By contrast, the current barcoding approach is able to compare enormous numbers of sequences in a very short time, primarily because the approach is analytically simple; a single sequence is compared with all sequences in the database by calculating all possible pairwise K2P distances. As long as exemplars exist within the database that have K2P distances below some predetermined threshold (usually 4%), the species is considered identified. The speed of analysis is due primarily to the use of distance-based measures. The purpose of this article is to initiate the development of a framework for "next-gen barcoding": one that incorporates the multispecies coalescent, but does so by comparing multiple gene sequences from an unknown taxon with a database of sequences.

Data from: A framework for developing ecosystem-specific nutrient criteria: integrating biological thresholds with predictive modeling

We present a novel ecosystem-specific framework for developing nutrient criteria from biological thresholds and predictive modeling (BTPM) and an application of this framework to lakes in Michigan, U.S. The four main components for the BTPM framework are: (1) to predict each ecosystem s expected nutrient concentration in the absence of human effects using a predictive model, (2) to identify important biological thresholds along a nutrient gradient (i.e., biological [BIO] benchmarks), (3) to determine each ecosystem s current nutrient concentration, and (4) to use the above information to derive a nutrient criterion for each ecosystem using the BTPM algorithm. The BTPM framework is extremely flexible in that it can be applied to any aquatic ecosystem type or nutrient and the four components can be implemented in a variety of ways. Our BTPM framework has two additional features: it recognizes that prior to human disturbance, ecosystems varied in their natural nutrient concentrations, and it incorporates risk into the decision-making process. In the simplest scheme, a nutrient criterion is set at a BIO benchmark greater than the expected nutrient concentration. However, to protect ecosystems more conservatively, a criterion is set at current lake nutrient concentrations if current is less than the BIO benchmark. In our application of the BTPM framework, we developed total phosphorus (TP) criteria for a diverse set of 374 lakes in MI. The expected lake TP concentrations in the absence of human effects ranged from 3 µg L-1 to 24 µg L-1, suggesting that a single criterion approach would not be appropriate.We found two predominant benchmarks in the biological data along the TP gradient, one for zooplankton metrics at 8 µg L-1, and one for phytoplankton metrics at 18 µg L-1. We present the sequence of analyses and decisions that could be used to apply this approach in a management context using Michigan lakes as an example.

opencc-zeroDec 2019View details →

Data from: A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity

Phylogenetics is a powerful tool for understanding the diversification dynamics of viral pathogens. Here we present an extension of the spectral density profile of the modified graph Laplacian, which facilitates the characterization of within-host molecular evolution of viruses and the direct comparison of diversification dynamics between hosts. This approach is non-parametric and therefore fast and model-free. We used simulations of within-host evolutionary scenarios to evaluate the efficiency of our approach and to demonstrate the significance of interpreting a viral phylogeny by its spectral density profile in terms of diversification dynamics. The key features that are captured by the profile are positive selection on the viral gene (or genome), temporal changes in substitution rates, mutational fitness, and time between sampling. Using sequences from individuals infected with HIV-1, we showed the utility of this approach for characterizing within-host diversification dynamics, for comparing dynamics between hosts, and for charting disease progression in infected individuals sampled over multiple years. We furthermore propose a heuristic test for assessing founder heterogeneity, which allows us to classify infections with single and multiple HIV-1 founder viruses. This non-parametric approach can be a valuable complement to existing parametric approaches.