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317 results for “R code”
Sexual dimorphism in subterranean amphipod crustaceans covaries with subterranean habitat type: data and R code
<p>The data and R code used for data analyses in the manuscript titled "Sexual dimorphism in <em>Niphargus </em>amphipods is predicted by surface-subterranean environmental gradient". The collection contains:</p> <ol> <li>A zipped folder "videos", where raw videos used in the study are stored.</li> <li>A zipped folder "tracking_results", where video-tracking results obtained from the raw videos are stored, along with supporting files and R code (Rscript_extract_behavior.Rmd) with custom functions (Behavior_custom_functions.Rmd) needed to analyze tracking results and retrieve final behavioral data.</li> <li>A README file with details on how the data and code is organized.</li> <li>Supplementary Material file including all raw data used in the main data analysis (SupplementaryMaterial.xlsx)</li> <li>A supporting file with data from another study used in the main data analysis (sex_ratio.xlsx, results from https://onlinelibrary.wiley.com/doi/full/10.1111/jeb.13917; https://zenodo.org/records/5175861)</li> <li>Two files containing phylogenetic trees: one complete phylogenetic tree of<em> Niphargus </em>(consensus_tree)<em> </em>and 100 randomly drawn phylogenetic trees from the stationary phase of the Bayesian analysis, pruned to focal species (100_pruned_trees), which were used in the main data analysis.</li> <li>The Rcode containing the code of the main data analysis to reproduce the reported results (RScript_data_analysis.Rmd), as well as some additional analyses not included in the manuscript.</li> </ol>
Dataset and R code used in "Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes"
<p>Dataset and R code used for the manuscript:</p> <p>Von Eggers, J. M., Wisnoski, N. I., Calder, J. W., Capo, E., Groff, D. V., Krist, A. C., & Shuman, B. (2024). Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. <em>Environmental Microbiology</em>, 26(3), e16607.</p> <p>This dataset and code are also available on GitHub (<a href="https://github.com/jvoneggers/WYLakeSedMicrobes">https://github.com/jvoneggers/WYLakeSedMicrobes</a>).</p>
Apathy, motivation, and physical activity behavior: Material, data and R code
<p>This new release includes updates to the code and additional material following the peer review process conducted by Communications in Kinesiology.</p>
Datasets and R codes used for the analyses in "Seasonal variation in home range size of White-Backed Woodpeckers"
<p><strong>Abstract</strong></p> <p>Knowing a species’ area requirements is fundamental for species conservation. For the nominate subspecies of the White-backed Woodpecker<em> Dendrocopos leucotos</em>, a species of high conservation concern in Europe, estimates of the seasonal and year-round area requirements based on telemetry are missing. In the present study, we radio-tracked adult White-backed Woodpeckers in Central Europe and investigated bi-monthly home range sizes based on three home range estimators in relation to season, sex, body weight, and year. Home range size of 49 radio-tracked individuals varied depending on the used home range estimator, with minimum convex polygons (MCP) and autocorrelated kernel density estimation (AKDE) producing 1.6 – 1.8 and 2 – 3.3 times larger seasonal home ranges than traditional kernel density estimation (KDE). Moreover, home range sizes varied between seasons. Home ranges were smallest in February/March (predicted median home range sizes ranged from 35 ha with KDE to 88 ha with AKDE) and April/May (KDE: 30 ha, AKDE: 55 ha) and larger during the rest of the year (KDE: 48 – 67 ha, AKDE: 136 – 184 ha). The mean home range size of six individuals tracked in all seasons (calculated with all locations per individual) was 116 ha with KDE, 304 ha with MCP and 350 ha with AKDE. Our results highlight the importance of considering the full annual cycle when addressing area requirements of White-backed Woodpeckers and likely also of other species. Furthermore, our study shows that using multiple methods for home range estimation may be useful to obtain results that are both comparable with those of other studies and capture the range in which the true home range size is likely to be. For the conservation of the White-backed Woodpecker, we conclude that at least 116 to 350 ha of forest should be present for a pair.</p>
Supplementary datasets, data analysis code, and R tutorials for: Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs
<p>Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require collecting data from many species, a challenge when data collection is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework—the Ornstein-Uhlenbeck process—that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate use of the model through studying the evolution of thermal physiology in treefrogs. Frogs of the family Hylidae have twice colonized the temperate zone from the tropics, and such colonization likely involved a fundamental change in physiology due to colder and more seasonal temperatures. However, which traits changed to allow colonization is unclear. We measured cold-temperature tolerance and characterized thermal performance curves in jumping for twelve species of treefrogs distributed from the Neotropics to temperate North America. We then conducted phylogenetic comparative analyses to examine how tolerances and performance curves evolved and to test whether that evolution was adaptive. We found that tolerance to low temperatures increased with the transition to the temperate zone. In contrast, jumping well at colder temperatures was unrelated to biogeography and thus did not adapt during dispersal. Overall, our paper shows how comparative phylogenetic methods can be leveraged in biomechanics and physiology to test the evolutionary drivers of variation among species.</p>
Affective, physiological, and attention restoration at a wooden desk: A pilot study (Datasets and R analysis code)
<p>This entry contains datasets and R processing and analysis code for the article <em>Affective, physiological, and attention restoration at a wooden desk: A pilot study.</em><br> <br> The analysis primarily investigates how people respond to the Mental Arithmetic Task (MAT) in terms of their affective states and physiological arousal, and how their cognitive performance changes between two task administrations. The analysis also checks whether affective, physiological, and cognitive responses differ between settings furnished with or without wood. We base our analysis on self-reported affective states, captured physiological (electrodermal and cardiovascular) activity, and results on the cognitive task (i.e., MAT).</p>
Data and R code from: Relics of beavers past: time and population density drive scale-dependent patterns of ecosystem engineering
<p><span>Like many ecological processes, natural disturbances exhibit scale-dependent dynamics that are largely a function of the magnitude, frequency, and scale at which they are assessed. Ecosystem engineers create patch-scale disturbances that affect ecological processes, yet we know little about how these effects scale across space or vary through time. Here, we investigate how patch disturbances by beavers (<i>Castor canadensis</i>), ecosystem engineers renowned for their pond-creation behavior, affect ecological processes across space and time. We evaluated how beaver population recovery influenced surface water dynamics in relation to population density over 70 years across multiple spatial scales (pond, watershed, and regional) in northern Minnesota. Surface water area was positively related to population density at the watershed scale; however, despite variation in beaver densities (and therefore surface water area) at the watershed scale, regional-scale surface water area was stable through time. This stability appears to have been driven by asynchronous beaver density fluctuations among watersheds, combined with the increasing importance of abandoned ponds. Beavers initially created and occupied larger ponds with greater surface water area, but through time shifted towards occupying smaller ponds. As ponds accumulated on the landscape proportionally more surface water was stored within abandoned ponds, which offset the smaller size of occupied ponds. Beaver engineering—driven by density-dependent mechanisms and the legacy effects from abandoned ponds—not only follows general patterns of patch disturbance dynamics by creating a spatial mosaic of patches, but the organism-created mosaic also appears to generate ecological stability at greater spatial scales. We suggest restoring beavers to landscapes is a viable method for increasing surface water storage and will ultimately help advance numerous conservation and rewilding objectives. Our study demonstrates that ecosystem engineering effects can be scale-dependent, indicating researchers should evaluate the ecological impact of engineers across diverse spatiotemporal scales to fully understand their functional roles in ecosystems.</span></p>
Datasets and R code for: Brood as booty: The effect of colony size and resource value in social insect contests
<p><strong>From the Manuscript: </strong>Animals engage in contests for access to resources like food, mates, and space. Intergroup contests between groups of organisms have received little attention, and it remains unresolved what information groups might use collectively to make contest decisions. We staged whole-colony contests using ant colonies (<em>Temnothorax rugatulus</em>), which perceive conspecific colonies as both a threat and resource from which to steal brood. We recorded individual behaviors and used demographic characteristics as proxies for resource value (number of brood items) and fighting ability (number of workers). We found that ants altered their fighting effort depending on the relative number of workers of their opponent. While the proximate mechanism for this ability remains uncertain, we found that colonies increased fighting when their opponent had relatively more brood, but not if opposing colonies had relatively many more workers. This suggests that ant colonies can use information about opposing colonies that shapes contest strategies. Further, the behavior of opposing colonies were strongly correlated with each other despite colony size differences ranging from 4-51%, consistent with the hypothesis that colonies can use opponent information. The behavior of a distributed, collective system of many individuals, like a eusocial insect colony, thus fits several predictions of contest models designed for individuals if we consider the gain and loss of worker ants analogous to energetic costs accrued during typical dyadic contests.</p>
Data and R codes: species range-size variation in oaks
<p>We used occurrence data of 183 oak species (<em>Quercus </em>spp.) in North and South America to test how niche breadth and niche position affect the amount of suitable habitat area, and how colonization ability and post-glacial migration lags affect range filling. This dataset includes the data and R files related to the analyses. </p>
Datasets and R-codes complementing the Opinion of the Norwegian Scientific Committee for Food and Environment (VKM) "Risk-Benefit Assessment of Sunscreen"
<p>These datasets complement the Opinion of the Norwegian Scientific Committee for Food and Environment (VKM) "Risk-Benefit Assessment of Sunscreen". They contain:</p> <p>i) data on concentration of the UV filters bis-ethyl-hexyloxyphenol methoxyphenyl triazine (BEMT), butyl methoxydibenzoyl methane (BMDBM), 2-ethylhexyl salicylate (EHS), ethylhexyl triazone (EHT), octocrylene (OC), and titanium dioxide in nanoform (NP-TiO<sub>2</sub>) in commercially available sunscreens,</p> <p>ii) data on amount sunscreen used, and</p> <p>iii) data on dermal absorption of the UV filters bis-ethyl-hexyloxyphenol methoxyphenyl triazine (BEMT), butyl methoxydibenzoyl methane (BMDBM), 2-ethylhexyl salicylate (EHS), ethylhexyl triazone (EHT), octocrylene (OC), and titanium dioxide in nanoform (NP-TiO<sub>2</sub>).</p> <p>The data are used in the probabilistic exposure estimations in the Opinion. The data were retrieved from open sources.</p> <p>In addition, the R-codes used to perform the exposure estimation, are included.</p>
Dataset and R code: Effects of temperature and air pollution on emergency ambulance dispatches: a time series analysis in a medium-sized city in Germany
<p>Dataset and R script to replicate results in the manuscript "Effects of temperature and air pollution on emergency ambulance dispatches: a time series analysis in a medium-sized city in Germany", currently under review.</p>
R_JAGS code for estimation and analysis of species-area-relationship (SAR) parameters from NEON (National Ecological Observatory Network) data on plant surveys
<p><span>Invasive species science is heavily geared toward the invasive agent. </span>However, management to protect native species also requires a proactive approach focused on understanding the features affecting community vulnerability to invasion impacts<span>. </span><span>Vulnerability </span><span>is likely the result of </span><span>factors acting across spatial scales, from </span><span>local to regional, and it is the combined effects of these factors that will determine the magnitude of vulnerability.</span><span> We introduce an analytical framework that quantifies the scale-dependent impact of biological invasions from the shape of the native species-area-relationship (SAR). We leverage newly available, biogeographically extensive vegetation data from the US National Ecological Observatory Network to assess plant community vulnerability to invasion impact as a function of factors acting across scales. We analyzed more than 1000 SARs widely distributed across the USA along environmental gradients and under different levels of invasion. </span>Results show that a decrease in native richness is consistently associated with invasive species cover<span>, but it is only at relatively high levels of invasion that native richness is compromised. After accounting for variation in baseline ecosystem diversity, net primary productivity, and human modification, ecoregions that are colder and wetter seem to be most vulnerable to losses of native plant species at the local level, while warmer and wetter areas seem most susceptible at the landscape level. We also document how the combined effects of cross-scale factors result in a heterogenous spatial pattern of vulnerability. </span><span>This pattern </span><span>cannot be predicted by analyses at any single scale, underscoring the importance of accounting for factors acting across scales. Simultaneously assessing differences in vulnerability between distinct plant communities at local, landscape and regional scales provided outputs that can be used to inform policy and management aimed at reducing vulnerability to the impact of plant invasions.</span></p>
Data and R code used for the GLMM and NBDA analyses in 'Captive Asian short-clawed otters (Aonyx cinereus) learn to exploit unfamiliar natural prey'
<p>Foraging plays a vital role in animal life histories, learning whether unfamiliar food items are palatable is a key part of this process. Animals that engage in extractive foraging must also learn how to overcome the protective measures of their prey. While otters (subfamily Lutrinae) are a taxon known for their extractive foraging behaviour, how they learn about prey palatability and acquire extractive foraging techniques remains poorly understood. Here we investigated: (i) how captive Asian short-clawed otters (<em>Aonyx cinereus</em>) learned to interact with, and extract meat from, unfamiliar natural prey, and (ii) how their exploitation of such prey compared to their ability to overcome artificial foraging tasks containing familiar food rewards. Network-based diffusion analysis showed that otters learned to interact with unfamiliar natural prey by observing their group mates. However, once interacting with the prey, they learned to extract the meat mainly asocially. In addition, otters took longer to overcome the protective measures of unfamiliar natural prey than those of extractive food puzzles. Asian short-clawed otter populations are declining in the wild. Increasing our understanding of how they learn to overcome novel foraging challenges could help develop pre-release training procedures as part of reintroduction programmes for otter conservation.</p>
Data and R code for long-term study of fire and climate effects on water quality in Clear Lake, California
<p>Long-term relationships between water quality, fire and climate for Clear Lake, California. Although the watershed has historically experienced frequent fire, the 2018 Mendocino Complex, which was the largest wildfire complex in state history, burned approximately 40% of the watershed, sparking concerns about drinking water quality and lake ecosystem health. This analysis spans approximately 1968-2021.</p>
Maps and R code from: Marginality indices for biodiversity conservation in forest trees
<p>This dataset provides the raster map of marginality indices for eight European tree species as described in the article "Marginality indices for biodiversity conservation in forest tree". It also provided the R code to compute the marginality indices.</p> <p>The eight species are the following:</p> <ul> <li><em>Abies alba</em> Mill. (silver fir)</li> <li><em>Fagus sylvatica</em> L. (European beech)</li> <li><em>Picea abies</em> (L.) H.Karst. (Norway spruce) </li> <li><em>Pinus halepensis</em> Mill. (Aleppo pine)</li> <li><em>Pinus nigra</em> J.F.Arnold (black pine)</li> <li><em>Pinus pinaster</em> Aiton (maritime pine) </li> <li><em>Pinus pinea</em> L. (stone pine)</li> <li><em>Pinus sylvestris</em> L. (Scots pine)</li> </ul> <p>For each species, a 7z archive of a multi-layered image of the raster maps of the marginality indices is given. Each image has 12 layers:</p> <ul> <li>Layer 1: distribution map of the species</li> <li>Layer 2: map of the probability of being marginal according to the Maxent model using eight marginality indices and countries as predictors</li> <li>Layer 3: map of the environmental marginality index, defined as the z-transform of the suitability of each location as predicted by a species distribution model using climatic variables as predictors</li> <li>Layer 4: map of the segmented distribution according to morphological spatial pattern analysis</li> <li>Layer 5: map of the area index</li> <li>Layer 6: map of the gravity index</li> <li>Layer 7: map of the centroid index</li> <li>Layer 8: map of the edge index</li> <li>Layer 9: map of the isolation index</li> <li>Layer 10: map of the second nearest core index</li> <li>Layer 11: map of the north/south index</li> <li>Layer 12: map of the east/west index</li> </ul>
Onthophagus babirussa sexual size dimporphism and male sexual trait files and R codes
<p><span>Sexual size dimorphism (SSD) arises when natural selection and sexual selection act differently on males and females. Male-biased SSD is rare in insects and usually indicates strong selection pressure on a population or species. Patterns of SSD can also vary between populations of species that are exposed to different environmental conditions, such as differing resource availability and diversity. Here, we investigate intra-specific variation in SSD as well as relative investment in precopulatory (horn length) and postcopulatory traits (sperm length and testes weight) in a tropical rainforest dung beetle<em> Onthophagus babirussa </em>across Singapore and Peninsular Malaysia. Overall, three out of four populations displayed significant male-biased SSD and SSD was greater in populations with smaller overall body size. Average male body size was similar across all populations while female body size was significantly smaller in Singapore, suggesting that the pronounced SSD may also be due to stronger sexual selection on male body size in Singapore populations. All populations showed significant investment in horns as a weapon used in precopulatory competition, while postcopulatory traits showed no clear scaling relationship with body size, suggesting a higher priority on precopulatory sexual traits in the mating system of this species.</span></p>
Data and R code from: Spatiotemporal risk factors predict landscape-scale survivorship for a northern ungulate
<p>These data and computer code (written in R, https://www.r-project.org) were created to statistically evaluate a suite of spatiotemporal covariates that could potentially explain pronghorn (Antilocapra americana) mortality risk in the Northern Sagebrush Steppe (NSS) ecosystem (50.0757<sup>o</sup> N, −108.7526<sup>o</sup> W). Known-fate data were collected from 170 adult female pronghorn monitored with GPS collars from 2003-2011, which were used to construct a time-to-event (TTE) dataset with a daily timescale and an annual recurrent origin of 11 November. Seasonal risk periods (winter, spring, summer, autumn) were defined by median migration dates of collared pronghorn. We linked this TTE dataset with spatiotemporal covariates that were extracted and collated from pronghorn seasonal activity areas (estimated using 95% minimum convex polygons) to form a final dataset. Specifically, average fence and road densities (km/km2), average snow water equivalent (SWE; kg/m2), and maximum decadal normalized difference vegetation index (NDVI) were considered as predictors. We tested for these main effects of spatiotemporal risk covariates as well as the hypotheses that pronghorn mortality risk from roads or fences could be intensified during severe winter weather (i.e., interactions: SWE*road density and SWE*fence density). We also compare an analogous frequentist implementation to estimate model-averaged risk coefficients. Ultimately, the study aimed to develop the first broad-scale, spatially explicit map of predicted annual pronghorn survivorship based on anthropogenic features and environmental gradients to identify areas for conservation and habitat restoration efforts.</p> <p> </p>
Data and R computer code from: Summer elk calf survival in a partially migratory population
<p>These data and computer code (written in R, https://www.r-project.org) were created to statistically evaluate a suite of intrinsic and extrinsic risk factors related to calf elk and their mothers' body condition and age. Specifically, known-fate data were collected from 94 elk calves monitored from 2013-2016 in a partially migratory elk (<em>Cervus</em> <em>canadensis</em>) population in Alberta, Canada. Along with adult female data on pregnancy status, age, and body condition, we created a time-to-event dataset that allowed us to analyze calf mortality risk in a time-to-event approach. We also estimated pooled survivorship and cause-specific mortality, as well as stratifying these metrics by migration tactic (resident vs. eastern migrant). Cox proportional hazards models were used to evaluate calf mortality risk in terms of forage biomass (kg/ha), bear predation risk (from an RSF), and other factors that varied between migration tactics. We tested for differences in a number of maternal reproductive parameters (e.g., pregnancy status) and for calf explanatory variables between migrant and resident elk segments. We also use cumulative incidence functions to estimate cause-specific mortality in this multiple carnivore system. Ultimately, we hope that this work helps wildlife managers anticipate how elk calf survival and partial migration dynamics are affected by grizzly bear predation, and our study builds on a long-term partial migration study at the Ya Ha Tinda Ranch in Alberta, Canada. </p>
Occurrences and R code for: Dynamic distribution modeling of the Swamp Tigertail dragonfly Synthemis eustalacta (Odonata: Anisoptera: Synthemistidae) over a 20-year bushfire regime
<p>Intensity and severity of bushfires in Australia have increased over the past few decades due to climate change, threatening habitat loss for numerous species. Although the impact of bushfires on vertebrates is well-documented, the corresponding effects on insect taxa are rarely examined, although they are responsible for key ecosystem functions and services. Understanding the effects of bushfire seasons on insect distributions could elucidate long-term impacts and patterns of ecosystem recovery. Here, we investigated the effects of recent bushfires, land-cover change, and climatic variables on the distribution of a common and endemic dragonfly, the swamp tigertail (<em>Synthemis</em> <em>eustalacta</em> (Burmeister, 1839)), which inhabits forests that have recently undergone severe burning. We used a temporally dynamic species distribution modeling approach that incorporated 20 years of community-science data on dragonfly occurrence and predictors based on fire, land cover, and climate to make yearly predictions of suitability. We also compared this to an approach that combines multiple temporally static models that use annual data. We found that for both approaches, fire-specific variables had negligible importance for the models, while percent of tree and non-vegetative cover were the most important. We also found that the dynamic model outperformed the static ones when evaluated with cross-validation. Model predictions indicated temporal variation in area and spatial arrangement of suitable habitat but no patterns of habitat expansion, contraction, or shifting. These results highlight not only the efficacy of dynamic modeling to capture spatiotemporal variables, such as vegetation cover for an endemic insect species, but also provide a novel approach to mapping species distributions with sparse locality records.</p>
R code and associated data for: A review of riverine ecosystem service quantification: research gaps and recommendations
<p>This publication contains the R code and associated data used in the Journal of Applied Ecology publication entitled "A review of riverine ecosystem service quantification: research gaps and recommendations". </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.