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317 results for “R code”
Nest shading experiment R code and data
<p>Data and R code associated with a study conducted by the University of Exeter and Ascension Island Government titled "Efficacy of artificial nest shading as a climate change adaptation measure for marine turtles at Ascension Island.</p>
Raw data and R code for: Negative effects of urbanisation on diurnal and nocturnal pollen-transport networks
<p>Pollinating insects are declining due to habitat loss and climate change, and cities with limited habitat and floral resources may be particularly vulnerable. The effects of urban landscapes on pollination networks remain poorly understood, and comparative studies of taxa with divergent niches are lacking. Here, for the first time, we simultaneously compare nocturnal moth and diurnal bee pollen-transport networks using DNA metabarcoding and ask how pollination networks are affected by increasing urbanisation. Bees and moths exhibited substantial divergence in the communities of plants they interact with. Increasing urbanisation had comparable negative effects on pollen-transport networks of both taxa, with significant declines in pollen species richness. We show that moths are an important, but overlooked, component of urban pollen-transport networks for wild flowering plants, horticultural crops, and trees. Our findings highlight the need to include both bee and non-bee taxa when assessing the status of critical plant-insect interactions in urbanised landscapes.</p>
Context-dependent evolution of high trophic position drives functional disparity in subterranean crustaceans: data and R code
<p>The dataset contains morphological data, phylogenetic tree, and R code used in the analyses presented in the paper titled "Context-dependent evolution of high trophic position drives functional disparity in subterranean crustaceans". </p> <p>Niphargus_morpho_data.xlsx: morphological data for import in R<br> Niphargus_tree.nex: consensus phylogenetic tree for import in R<br> Rcode.Rmd: the R script in R markdown format to reproduce the analyses<br> Rcode.html: the R script in html format <br> Reproducibility_report.doc: Functional diversity protocol checklist created with stepFD (https://facuxpalacio.shinyapps.io/stepFD/)</p>
Data and R-code to reproduce analyses in: A Picture is Worth a Thousand Dollars: A photographic approach to studying color in anoles
<p>Data archive for MS: </p> <p><strong>A Picture is Worth a Thousand Dollars: A photographic approach to studying color in anoles</strong></p> <p>by Jacobs J, Salazar, J, and Winchell K.</p> <p>Archive includes 5 files:</p> <p>1. archived R markdown script (archiveddewlap_final.Rmd) with all analyses from the manuscript executable with the additional archived files (#3-5 below)</p> <p>2. pdf version of R markdown script with code and output (archiveddewlap_final.pdf)</p> <p>3. csv of dewlap color data from photographs (dewlap_archivedata_v1.csv)</p> <p>4. csv of metadata of population identity, SVL, and mass for all lizards (speciesbypopulation.csv)</p> <p>5. compressed file containing three folders: Bahamas specs, DR specs, and Jamaica specs, which include all spectral files for all lizards in the analysis (specs.zip)</p>
Data and R code for "Negative effects of wind on plant hydraulics at the global scale"
<p>To minimize ontogenetic and methodological variation, we only included trait data that met the following criteria: (a) plants were grown in natural ecosystems, excluding greenhouse and common garden experiments; (b) measurements were made on adult plants and not on seedlings; (c) hydraulic traits were measured on terminal stem or branch segments in the sapwood at the crown; and (d) trait data were calculated as the mean value for each species at the same site when data were from multiple sources.</p> <p>Climate data were obtained either from the original reports or from WorldClim version 2 (http://worldclim.org/version2) if the original data were not available. The following variables were extracted from WorldClim: mean annual wind speed, mean annual precipitation, mean annual temperature, precipitation seasonality, temperature seasonality, precipitation of driest month, and minimum temperature of coldest month. The VPD data was extracted from the TerraClimate dataset (http://www.climatologylab.org/terraclimate.html). Annual PET (potential evapotranspiration) data were extracted from the CGIAR-CSI consortium (http://www.cgiar-csi.org/data). The moisture index (MI) is the ratio of precipitation to PET.</p> <p>Simple linear regression was used to examine the relationships between two variables, utilizing the 'lm' function in R software. Partial regression analysis was conducted using the R package VISREG to investigate the relationships between wind speed and plant hydraulics while controlling for other variables. This analysis helped to illustrate the independent effect of wind on plant hydraulics. The Random Forest machine-learning algorithm (implemented using the R package randomForest) was utilized to assess the relative importance of environmental variables for each plant hydraulic trait. The Mean Decrease in Gini was calculated as the average of a variable's total decrease in node impurity, taking into account the proportion of samples that reach that node in each individual decision tree in the random forest. This provides a measure of a variable's importance in estimating the value of the target variable across all of the trees in the forest. A higher Mean Decrease in Gini value indicates greater importance of the variable. Multiple regression analyses were performed to develop predictive equations for plant hydraulic traits using environmental variables. To test for hydraulic traits-wind speed slope directions and differences among species groups in different climatic regions, we used standardized major axis (SMA) analyses. The R package SMATR was employed for these analyses. We considered <em>p </em>< 0.05 as the threshold for statistical significance in all models.</p>
Bayesian phylodynamic and phylogeographic analyses of invasive, hypervirulent Streptococcus agalactiae sequence type 283 dataset and R code
<p>Supplementary dataset S1, R code, and subsampled trees</p>
Raw data and R code for: Negative effects of urbanisation on diurnal and nocturnal pollen-transport networks
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Serological dataset and R code for: Patterns and processes of pathogen exposure in gray wolves across North America
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Data and R Code for publication: Should dispersers be fast learners? Modelling the role of cognition in dispersal
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Manhattan, New York City, 2020 Traffic Time Series + R Code for Analysis
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Data and R code from: Fire-induced loss of the world’s most biodiverse forests in Latin America
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R code from: Diagnosing common sources of lack of fit to composition data in fisheries stock assessment models using One-Step-Ahead (OSA) residuals
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R code and data for running models in "Rapid Growth of the Swainson’s Hawk Population in California since 2005"
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Data and R code from: Rethinking global hotspots for threatened terrestrial vertebrates
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The role of boundary length and adjacent patch contrast in guppy mate choice: Dataset, Matlab and R codes
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R code, spatial and tabular data to fully reproduce STEPS simulations of population change for common brushtail possum, grassland melomys and northern brown bandicoot in northern Australia
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R code for identification and correction of Photosynthetically Active Radiation sensor drift
R code was created to model maximum solar radiation and photosynthetically active radiation (PAR) based on location, date, temperature, atmospheric pressure and humidity. Additional code compares actual data with the predicted peaks in the solar radiation curves and identifies places where there is significant deviation from the predicted maximum and adjusts the output data to make it so that monthly peaks (assuming at least one day in the month was clear!) correspond to the predicted maximum. PAR is calculated as 45% of the solar radiation.
Data and R code for Anthropogenic stressors impact fish sensory development and survival via thyroid disruption
<p>The zip document contains all the data and R code used in the manuscript "Anthropogenic stressors impact fish sensory development and survival via thyroid disruption".</p>
Evidence that male sea lamprey increase pheromone release after perceiving a competitor: raw data, R-code, R analyses
<p class="CxSpFirst">Sexual signals evolve via selective pressures arising from male-male competition and female choice, including those originating from unintended receivers that detect the signal. For example, males can acquire information from other males signaling to females and alter their own signal. Relative to visual and acoustic signals, less is known about how such communication networks influence chemical signaling among animals. In sea lamprey (<i>Petromyzon marinus</i>), chemical communication system is essential for reproduction, offering a useful system to study a pheromone communication network that includes signalers and both intended and unintended receivers. Male sea lamprey aggregate on spawning grounds where individuals build nests and signal to females using sex pheromones. We examined how exposure to a major component of the male pheromone, 3keto-petromyzonol sulfate (3kPZS), influenced male pheromone signaling, and whether females had a preference for males that altered their signal. Exposure to 3kPZS, at a concentration of 5x10<sup>-10 </sup>M, simulated the presence of other male(s) and led to increased 3kPZS release rates within 10 min, followed by a return to baseline levels within 30 min. Exposure also led to increases in hepatic synthesis and circulatory transport of pheromone components. In behavioral assays, females preferred the odor of males that had been exposed to 3kPZS; therefore, males likely benefit from upregulating 3kPZS release after detecting competition for mates. Here, we define how a specific pheromone component influences chemical signaling during intrasexual competition, and show a rare example of how changes in chemical signaling strategies resulting from male competition may influence mate choice.</p>
Quina retouch does not maintain edge angle over reduction - R code and data
<p>R code and data used in the paper "Quina retouch does not maintain edge angle over reduction" in <em>Lithic Technology</em>.</p>
ScienceDex guides
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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.