Find research datasets worth reusing

opencc-by-4.0Oct 2020View details →

LCCSS: A Similarity Metric for Identifying Similar Test Code

Apresentação do artigo "LCCSS: A Similarity Metric for Identifying Similar Test Code" para o SBCARS 2020.

opencc-zeroNov 2020View details →

Data from: Natural disturbances can produce misleading bioassessment results: identifying metrics to detect anthropogenic impacts in intermittent rivers

Ecosystems experience natural disturbances and anthropogenic impacts that affect biological communities and ecological processes. When natural disturbance modifies anthropogenic impacts, current widely used bioassessment metrics can prevent accurate assessment of biological quality. Our aim was to assess the ability of biomonitoring metrics to detect anthropogenic impacts at both perennial and intermittent sites, and in the latter including both flowing and disconnected pool aquatic phases. Specifically, aquatic macroinvertebrates from 20 rivers were sampled along gradients of natural flow intermittence (natural disturbance) and anthropogenic impacts to investigate their combined effects on widely used river biomonitoring metrics (i.e. taxonomic richness and standard biological indices) and novel functional metrics, including functional redundancy (i.e. the number of taxa contributing similarly to an ecosystem function, here a trophic function) and response diversity (i.e. how functionally similar taxa respond to natural disturbance and anthropogenic impacts). Our results showed that natural flow intermittence can confound river bioassessment, and that a set of new functional metrics could be used as effective alternatives to standard metrics in naturally disturbed intermittent rivers.

opencc-by-4.0Dec 2020View details →

Computational code for CCV metrics and two empirical datasets (D. dichotoma and S. viridis)

The zipped file contains: 1) the self-explained R script for conducting multi-scale grid sampling and calculating various CCV metrics presented in the paper, 2) the users' guide for the R code, 3) abundance of D. dichotoma in  sampling quadrats of the Changjiang water reservoir in Zhongshan City of the Guangdong Province of China, and 4) S. viridis in  sampling quadrats of the highland barley cropland Rikaze City of Tibet, China.

opencc-by-4.0Dec 2020View details →

Metrics Recovering Dataset

Replication package data for Metrics Recovering project https://github.com/shavkunov/MLSE Includes data from https://doi.org/10.5281/zenodo.3547639

opencc-zeroJan 2021View details →

Macroevolution of dimensionless life history metrics in tetrapods

Life history traits represent organisms' strategies to navigate the fitness trade-offs between survival and reproduction. Eric Charnov developed three dimensionless metrics to quantify fundamental life history trade-offs. Lifetime reproductive effort (LRE), relative reproductive lifespan (RRL), and relative offspring size (ROS), together with body mass, can be used to classify life history strategies across the four major classes of tetrapods: amphibians, reptiles, mammals, and birds. First, we investigate how the metrics have evolved in concert with body mass. In most cases, we find evidence for correlated evolution between body mass and the three metrics. Second, we compare life history strategies across the four classes of tetrapods and find that LRE, RRL, and ROS delineate a space in which the major tetrapod classes occupy mostly unique subspaces. These distinct combinations of life history strategies provide us with a framework to understand the impact of major evolutionary transitions in energetics, physiology, and ecology.

opencc-by-4.0Dec 2020View details →

Replication package - The Mind Is a Powerful Place: How Showing Code Comprehensibility Metrics Influences Code Understanding

Replication package for: Marvin Wyrich, Andreas Preikschat, Daniel Graziotin and Stefan Wagner. The Mind Is a Powerful Place: How Showing Code Comprehensibility Metrics Influences Code Understanding. To appear in: Proceedings of the 43rd International Conference on Software Engineering (ICSE ’21), Madrid, Spain. - The `data` folder contains dataset, R analysis script, and figures for the paper - the `material` folder contains the snippets used for the experimental tasks (`code snippets` subfolder), the environment in which participants had to understand the code (`environment` subfolder) and the task sheet form to evaluate code comprehension. The R analysis script allows to reproduce all statistical analysis steps of the paper as well as its figures. We recommend calling `setwd()` before running the script contents, so that the dataset can be properly loaded. For ethics and privacy reasons, we had to drop the following potentially identifying fields from the openly released dataset, because the fields might enable participants to identify their peers: - Age - Gender - Subject (study plan) - Program - Semester no. These missed details will still allow full reproducibility of the study.

opencc-zeroDec 2014View details →

Data from: Relationships between spatial metrics and plant diversity in constructed freshwater wetlands

The diversity of plant species and their distribution in space are both thought to have important effects on the function of wetland ecosystems. However, knowledge of the relationships between plant species and spatial diversity remains incomplete. In this study, we investigated relationships between spatial pattern and plant species diversity over a five year period following the initial restoration of experimental wetland ecosystems. In 2003, six identical and hydrologically-isolated 0.18 ha wetland "cells" were constructed in former farmland in northeast Ohio. The systems were subjected to planting treatments that resulted in different levels of vascular plant species diversity among cells. Plant species diversity was assessed through annual inventories. Plant spatial pattern was assessed by digitizing low-altitude aerial photographs taken at the same time as the inventories. Diversity metrics derived from the inventories were significantly related to certain spatial metrics derived from the photographs, including cover type diversity and contagion. We found that wetlands with high cover type diversity harbor higher plant species diversity than wetlands with fewer types of patches. We also found significant relationships between plant species diversity and spatial patterning of patch types, but the direction of the effect differed depending on the diversity metric used. Links between diversity and spatial pattern observed in this study suggest that high-resolution aerial imagery may provide wetland scientists with a useful tool for assessing plant diversity.

opencc-zeroNov 2019View details →

Linking species-level network metrics to flower traits and plant fitness

1. Theoretical models indicate that the structure of plant-pollinator networks has important implications for species' reproduction and survival. However, despite the growing information on the mechanisms underlying such structure, we are still far from being able to predict the functional consequences of species' structural positions in such networks. From the plants' perspective, species position and roles in pollination networks might be related to traits describing flower attractiveness, availability, and dependence on pollinators. In turn, both, network metrics and species traits might influence plant fitness. 2. During two field seasons, we collected data of the 23 most abundant plant species from a rich coastal community in order to evaluate the association between population and floral traits (floral abundance at the population level and flowers/individual, flower shape and size, flowering length, nectar volume, pollinator dependence), species-level network metrics (linkage level, specialization –d'–, weighted closeness centrality, network roles related to modularity) and plant fitness (seeds/flower, seed weight). 3. Flowering length, flower size, flower abundance and pollinator dependence were positively related to increased generalization, as measured with different indices. More abundant species and those with larger flowers showed higher linkage levels (i.e. higher number of pollinator species), whereas longer flowering periods were negatively related to d' and positively related to closeness centrality and important roles in the network. Likewise, plants more dependent on pollinators occupied more central positions in the network. Furthermore, species' centrality in the networks was significantly associated with plant fitness. Specifically, central species in the network produced more and heavier seeds than the others. However, other plant traits, such as flower size and pollinator dependence had additional direct effects on seed production. 4. Synthesis. Our study highlights how population and floral traits define the positions and roles of species structuring the pollination communities. Moreover, the relationships between network metrics and plant reproduction indicate, for the first time, the functional implications of these structural positions at the inter-specific level of community assembly.

opencc-zeroDec 2014View details →

Data from: Investigating sensitivity of phylogenetic community structure metrics using North American desert bats

A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of bats from the 4 great desert regions of North America. We inferred a phylogeny of the regional species pool to calculate PCS metrics using community membership data delimited using 3 different methods. We also randomized our phylogeny to determine how reasonable changes to the tree affect PCS metrics. Overall, PCS metrics are quite robust to moderate changes in the phylogeny from which they are calculated. These metrics also are fairly insensitive to our 3 methods of delimiting communities. Additionally, we found that in general, communities are significantly phylogenetically clustered, suggesting habitat filtering has been important in community assembly.

opencc-zeroDec 2013View details →

Data from: Species traits and abundances predict metrics of plant–pollinator network structure, but not pairwise interactions

Plant–pollinator mutualistic networks represent the ecological context of foraging (for pollinators) and reproduction (for plants and some pollinators). Plant–pollinator visitation networks exhibit highly conserved structural properties across diverse habitats and species assemblages. The most successful hypotheses to explain these network properties are the neutrality and biological constraints hypotheses, which posit that species interaction frequencies can be explained by species relative abundances, and trait mismatches between potential mutualists respectively. However, previous network analyses emphasize the prediction of metrics of qualitative network structure, which may not represent stringent tests of these hypotheses. Using a newly documented temporally explicit alpine plant–pollinator visitation network, we show that metrics of both qualitative and quantitative network structure are easy to predict, even by models that predict the identity or frequency of species interactions poorly. A variety of phenological and morphological constraints as well as neutral interactions successfully predicted all network metrics tested, without accurately predicting species observed interactions. Species phenology alone was the best predictor of observed interaction frequencies. However, all models were poor predictors of species pairwise interaction frequencies, suggesting that other aspects of species biology not generally considered in network studies, such as reproduction for dipterans, play an important role in shaping plant–pollinator visitation network structure at this site. Future progress in explaining the structure and dynamics of mutualistic networks will require new approaches that emphasize accurate prediction of species pairwise interactions rather than network metrics, and better reflect the biology underlying species interactions.

opencc-zeroDec 2015View details →

Data from: Local and landscape metrics identify opportunities for conserving cavity-nesting birds in a rapidly urbanizing ecoregion

Urban centers are rapidly expanding globally, resulting in regional forest-cover transformations that shift from temperate forest biomes to a heterogeneous mix of urban development, forest patches, and agriculture. Data on habitat use within remaining forest patches embedded across land use types, particularly in urban land use, are needed to optimize conservation strategies as urban growth continues. In the rapidly urbanizing southern Piedmont, USA, small pine patches have become more frequent across the landscape and are found embedded within second-growth forest, agricultural, and urban land use matrices. We used point-count surveys and N-mixture models to determine the effect of patch- and landscape-scale drivers on cavity-nesting bird abundance, including the threatened Brown-headed Nuthatch (Sitta pusilla), in pine forest patches. Model-averaged estimates suggest Brown-headed Nuthatches are more abundant in large patches in a heterogeneous matrix that includes urban residential development. Three other cavity-nesting species declined in abundance as a function of reduced canopy cover. White-breasted Nuthatches increased and Tufted Titmice decreased in abundance in response to patch area. By identifying factors that predict abundance at local and landscape scales for ecologically sensitive and generalist species, we can more effectively contribute to regional conservation efforts in urban ecosystems, extending conservation in practice beyond protected areas.

opencc-zeroDec 2015View details →

Data from: Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks

Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for heterotrophic organisms within complex ecological networks. Here, we assemble data on avian traits across a global sample of mutualistic plant–frugivore networks to critically assess how the functional roles of frugivores are associated with their intrinsic traits, as well as their evolutionary and functional distinctiveness. We find strong evidence for niche complementarity, with phenotypically and phylogenetically distinct birds interacting with more unique sets of plants. However, interaction strengths—the number of plant species dependent on a frugivore—were unrelated to evolutionary or functional distinctiveness, largely because distinct frugivores tend to be locally rare, and thus have fewer connections across the network. Instead, interaction strengths were better predicted by intrinsic traits, including body size, gape width and dietary specialization. Our analysis provides general support for the use of traits in quantifying species ecological functions, but also highlights the need to go beyond simple metrics of functional or phylogenetic diversity to consider the multiple pathways through which traits may determine ecological processes.

opencc-zeroDec 2014View details →

Data from: A meta-analysis reveals a positive correlation between genetic diversity metrics and environmental status in the long-lived seagrass Posidonia oceanica

The seagrass Posidonia oceanica is a key engineering species structuring coastal marine systems throughout much of the Mediterranean basin. Its decline is of concern, leading to the search for short- and long-term indicators of seagrass health. Using ArcGIS maps from a recent, high-resolution (1–4 km) modelling study of 18 disturbance factors affecting coastal marine systems across the Mediterranean (Micheli et al. 2013, http://globalmarine.nceas.ucsb.edu/mediterranean/), we tested for correlations with genetic diversity metrics (allelic diversity, genotypic/clonal diversity and heterozygosity) in a meta-analysis of 56 meadows. Contrary to initial predictions, weak but significantly positive correlations were found for commercial shipping, organic pollution (pesticides) and cumulative impact. This counterintuitive finding suggests greater resistance and resilience of individuals with higher genetic and genotypic diversity under disturbance (at least for a time) and/or increased sexual reproduction under an intermediate disturbance model. We interpret the absence of low and medium levels of genetic variation at impacted locations as probable local extinctions of individuals that already exceeded their resistance capacity. Alternatively, high diversity at high-impact sites is likely a temporal artefact, reflecting the mismatch with pre-environmental impact conditions, especially because flowering and sexual recruitment are seldom observed. While genetic diversity metrics are a valuable tool for restoration and mitigation, caution must be exercised in the interpretation of correlative patterns as found in this study, because the exceptional longevity of individuals creates a temporal mismatch that may falsely suggest good meadow health status, while gradual deterioration of allelic diversity might go unnoticed.

opencc-zeroDec 2018View details →

Data from: Individuals' expected genetic contributions to future generations, reproductive value, and short-term metrics of fitness in free-living song sparrows (Melospiza melodia)

Appropriately defining and enumerating 'fitness' is fundamental to explaining and predicting evolutionary dynamics. Yet, general theoretical concepts of fitness are often hard to translate into quantities that can be measured in wild populations experiencing complex environmental, demographic, genetic and selective variation. While the 'fittest' entities might be widely understood to be those that ultimately leave most descendants at some future time, such long-term legacies can rarely be measured, impeding evaluation of the degree to which tractable short-term metrics of individual fitness could potentially serve as useful direct proxies. One opportunity for conceptual and empirical convergence stems from the principle of individual reproductive value (Vi), defined as the number of copies of each of an individual's alleles that is expected to be present in future generations given the individual's realised pedigree of descendants. Since Vi tightly predicts an individual's longer-term genetic contribution, quantifying Vi provides a tractable route to quantifying what, to date, has been an abstract theoretical fitness concept. We used complete pedigree data from free-living song sparrows (Melospiza melodia) to demonstrate that individuals' expected genetic contributions stabilise within an observed 20-year (i.e. ~8 generation) time period, allowing estimation of individual Vi. Considerable among-individual variation in Vi was evident in both sexes. Standard metrics of individual lifetime fitness, comprising lifespan, lifetime reproductive success and projected growth rate, typically explained less than half the variation. We thereby elucidate the degree to which fitness metrics observed on individuals concur with measures of longer-term genetic contributions, and consider the degree to which analyses of pedigree structure could provide useful complementary insights into evolutionary outcomes.

Data from: Individual growth as a non-dietary determinant of the isotopic niche metrics

1. Quantitative analytical approaches for isotopic niche analysis in the trophic diversity studies are proliferating rapidly; however, the assumptions behind the isotopic niche applications are rarely tested. One of the main assumptions is independence of the niche metrics and physiological status of the animals. The aim of this experimental study was to test the relationship between growth and Layman's metrics of isotopic niche in consumers eating the same food but in different quantities and growing at different rates. 2. Based on research indicating that individual variability in isotopic fractionation increases under suboptimal conditions, I hypothesized that a group of consumers originating from the same population and exposed to food limitation would have greater estimates of the niche breadth and diversity as a result of higher inter-individual variability in growth rate and stable isotope signatures than in non-limiting feeding conditions. This hypothesis was tested using Baltic mysids Neomysis integer fed isotopically uniform diet under laboratory conditions and analyzing individual growth and stable isotope signature in concert. 3. As hypothesized, mysid growth rate was a significant negative predictor of most niche metrics. These effects were related to both increased inter-individual variability and higher trophic fractionation in malnourished animals, whereas in actively growing mysids lower fractionation was observed together with lower values for niche size, isotopic range and trophic diversity. 4. These findings challenge how we interpret the intrapopulation isotopic variance and evaluate isotopic evidence of individual specialization and call for integrated approaches for isotopic niche and growth assessment.

Data from: Linking functional diversity and ecosystem processes: a framework for using functional diversity metrics to predict the ecosystem impact of functionally unique species

1.Functional diversity (FD) metrics are widely used to assess invasion ecosystem impacts, but we have limited theory to predict how FD should respond to invasion. A key challenge to effectively using FD metrics is the complexity of conceptualizing alterations to multi-dimensional trait space, making it difficult to select a priori the most appropriate metric for specific ecological questions. 2.Here, we provide expectations on how invasion should change four commonly used FD metrics—functional richness (FRic), evenness (FEve), divergence (FDiv), and dispersion (FDis)—and then test these expectations in a lab decomposition experiment. We simulate invasion of a forest by understory plants by adding leaf litter from 18 natives and nonnatives to a representative canopy tree litter mixture to test changes in FD and decomposition. 3.All four metrics changed predictably with invasion. Species that were more functionally unique or when added at greater proportions had larger impacts on FD. Overall, FRic, FEve, and FDiv were poor choices for understanding impacts of nonnative species. FDis was the only metric that both changed predictably with addition of understory litter and correlated intuitively with changes in carbon mineralization. Furthermore, ranking species based upon how much they changed FDis of the litter mixture provided a fair assessment of which species had the largest impact on decomposition. As such, functional dispersion may be a key tool for predicting a priori which nonnatives will have the greatest impact on ecosystem processes. 4.Synthesis: We highlight the need to assess the suitability of each FD metric for the specific ecological question at hand. Our work reveals the pitfalls of considering multiple metrics or randomly choosing a single metric without suitability assessments. At the same time, it suggests a framework for metric assessment that should help lead to selection of a metric or metrics that provide robust a priori insights into how invasion by nonnative species can impact ecosystem processes.

Data from: Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture

Different pathways of propagation and dispersal of non-native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure and larger estimates for the effective number of breeders (Nb) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue, and showed marked genetic structure and a significant isolation-by-distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, and habitat quality or quantity, may concomitantly explain contrasting genetic metrics and patterns for trout between lakes. We also discussed violations of assumptions that may lead to overestimating Nb . We contend that high propagule pressure from aquaculture may not only increase genetic diversity and Nb via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.

opencc-zeroOct 2019View details →

Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical-temperate congener pair

The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by "stronger" contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical-temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant-pollinator and plant-herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical-temperate range in one system. To test the prediction that lower-latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self-pollination ability (autogamy). To test the prediction that lower-latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north-temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young-leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north-temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young-leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination-related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study.

Data from: Sensitivity of functional diversity metrics to sampling intensity

1. Functional diversity (FD) metrics are increasingly used in ecological research, particularly in studies of community assembly and ecosystem functioning. However, studies using FD metrics vary greatly in the intensity by which ecological communities were sampled and it is largely unknown how sensitive these metrics are to low sampling intensity (undersampling). 2. Here, we used a combination of simulations with theoretically assembled communities and three comprehensive, independent, empirical datasets on plant, ground beetle and bird communities to investigate the sensitivity of nine commonly used FD metrics to undersampling. 3. Simulations with both theoretical communities and empirical data showed that in a wide range of contexts, the measurement of various FD metrics requires a much higher sampling effort to reach an 'adequate' precision (defined as an r2 of at least 0.7 between different subsets of the same population), than that required for commonly used taxonomic diversity metrics (e.g. species richness), although the 'accuracy' (their deviation from the diversity value of a completely sampled community) of their measurements is not more sensitive to undersampling than species richness. We also found that some FD metrics (e.g. Functional Dispersion) are consistently less sensitive to undersampling than others (e.g. nearest neighbour distance-metrics). Problems of undersampling were generally most severe in datasets with high overall species richness and low overall abundances. 4. We found that the precision of many FD metrics is highly sensitive to undersampling, and more so than commonly used taxonomic diversity metrics. Therefore, to ensure reproducible results in functional biodiversity research, we recommend that thorough sampling designs are used to sample communities and that datasets originally collected for studying taxonomic diversity should only be used for FD when it can be shown that undersampling is not a major issue. In cases where undersampling is suspected or logistically unavoidable, FD metrics that are relatively insensitive to its effects (e.g. Functional Dispersion) should be prioritized.