Find research datasets worth reusing

opencc-by-4.0Aug 2022View details →

Simulated data from abmAnimalMovement: An R package for simulating animal movement using an agent-based model

Contained here are the data simulated as part of the manuscript: "abmAnimalMovement: An R package for simulating animal movement using an agent-based model" that can be found at: https://github.com/BenMMarshall/abmAnimalMovement (and archived at: https://doi.org/10.5281/zenodo.6951937). - BADGER_locations.csv: A csv file that contains the realised locations of the example badger simulation, where each row is equal to a timestep. Columns include: timestep, the timestep as an integer; x, the x coordinate of the animal; y, the y coordinate of the animal; sl, the step length between locations used during the simulation; sl_rescale the rescale factor required to return step lengths back to the input scale; ta, turning angle between locations in degrees; behave, the behavioural mode the animal was in at a given timestep; chosen, the location chosen out of the number of options available; destination_x and destination_y the point the animal was attracted to at that time (note exploratory behaviour is not subject attraction). - BADGER_options.csv: A csv file that contains the options available to the example badger simulation over the entire simulation duration, where each row is equal to an option repeated for each timestep. Columns include: timestep, the timestep as an integer; oall_x, and oall_y show the x and y coordinates of all the options available to an animal at a timestep; oall_steplengths are the step lengths from the current location compared to all the options. - completelist.RDS: This RDS file contains a list object of length three, where the full simulation outputs from each three examples are stored. Each species slot contains the “locations” dataframe (see description of locations.csv), the "options" dataframe (see description of options.csv), and a nested list containing all the "inputs" used to generate the simulated results (split into subsections: inputs_basic that contains inputs linked to simulation duration and intensity, inputs_destination that contains inputs linked to destination and attraction aspects, inputs_movement that contains inputs linked to movement capacity and behavioural switching, inputs_cycle that contains inputs linked to activity cycling, inputs_layerSeed that contains the environmental matrices and seed). A fourth object is returned called "others" that captures all other outputs, mainly used internally for debugging and checking. - KINGCOBRA_locations.csv: A csv file that contains the realised locations of the example king cobra simulation, where each row is equal to a timestep. The file structure follows the same as the BADGER_options.csv file. KINGCOBRA_options.csv: A csv file that contains the options available to the example king cobra simulation over the entire simulation duration, where each row is equal to an option repeated for each timestep. The file structure follows the same as the BADGER_options.csv file. - VULTURE_locations.csv: A csv file that contains the realised locations of the example vulture simulation, where each row is equal to a timestep. The file structure follows the same as the BADGER_locations.csv file. VULTURE_options.csv: A csv file that contains the options available to the example vulture simulation over the entire simulation duration, where each row is equal to an option repeated for each timestep. The file structure follows the same as the BADGER_locations.csv file. - eg_landscapedata_completelist.RDS: This RDS file contains the landscape matrices required for recreating the simulated outputs described in the manuscript named above. It is a list of three objects ("shelter", "forage", "movement"), each a numeric matrix of equal size, with values describing the quality of each landscape characteristic. - argument_table.csv: Descriptive table of the simulation inputs used in the walk-through manuscript.

opencc-by-4.0Nov 2018View details →

R code and data for "Flake selection and scraper retouch probability: an alternative model for explaining Middle Paleolithic assemblage retouch variability"

R code and data used for "Flake selection and scraper retouch probability: an alternative model for explaining Middle Paleolithic assemblage retouch variability" (Archaeological and Anthropological Sciences, Volume 10, Issue 7, pp 1791–1806)

opencc-by-4.0Nov 2022View details →

Supporting Data -- Evaluating Mask R-CNN Models to Extract Terracing across Oceanic High Islands: an example from Sāmoa.

This dataset provides supplemental information for the manuscript, "Diverse terracing practices revealed by automated lidar analysis across the Sāmoan islands", submitted to Archaeological Prospection. The dataset contains a trained Mask R-CNN deep learning model designed for detecting archaeological terracing features on the islands of American Samoa, associated training data, and the raw and cleaned output of detected terraces.

opencc-by-4.0Nov 2022View details →

Harmfull algae bloom monitoring program dataset; ERDDAP, ERA5 and ONI datasets; and R script for multicriteria analisys in Santa Catarina coastal zone, Brazil.

Project Harmful Algae Bloom (HAB) Monitoring Network in Santa Catarina, Brazil - Database and R script with data analysis. This project was funded by the Foundation for Research Support of the State of Santa Catarina – FAPESC and generated a database combining a HAB monitoring dataset with oceanographic (from ERDDAP) and climatic (from ERA5 and ONI) data which was submitted to multicriteria analysis using R. The HAB monitoring dataset was obtained from Cidasc/SC State Government (http://www.cidasc.sc.gov.br/defesasanitariaanimal/monitoramento-de-algas-nocivas/) and contains results of phytoplankton counts in water samples and toxin levels in shellfish samples obtained from 39 points located in shellfish farms distributed along the SC coastline. Oceanographic data were obtained from the ERDDAP/NOAA website (https://coastwatch.pfeg.noaa.gov/erddap/index.html), including the variables mean chlorophyll concentration (mg.m-3) and mean sea surface temperature (ºC); Climate data were obtained from Copernicus/ERA5 (https://cds.climate.copernicus.eu/) including the variables mean air temperature (ºC), mean pressure (Pasc.), mean cloud cover (%), mean precipitation (kg.m-2), radiation (Einsteins.m-2.day-1), mean U wind (m.s-1), and mean V wind (m.s-1).; Oceanic Niño Index (ONI) data were obtained from the NOAA website (https://origin.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/ONI_v5.php); The R script involves a pre-processing routine aimed at summarizing and integrating all datasets and the subsequent data analyses carried out to evidence temporal patterns related to different type of algal blooms. Detailed methods will be provided in a scientific article.

opencc-by-4.0Jan 2023View details →

Spectral data associated to the publication: "Near-infrared reflectance spectroscopy of sublimating salty ice analogues. Implications for icy moons" by R. Cerubini et al. (Planetary and Space Science 211, 2022)

This is the complete set of experimental NIR reflectance data collected by R. Cerubini and co-authors for the article "Near-infrared reflectance spectroscopy of sublimating salty ice analogues. Implications for icy moons" published in Planetary and Space Science 211 (2022). doi: https://doi.org/10.1016/j.pss.2021.105391. The article itself is published in open-access and provides the methodology for the spectral aquisitions, discussion of the errors and uncertainties, analysis of the spectra and implications for the composition of Solar System surfaces. The data are contained in ASCII files (columns separated by comma). The first column is the wavelength (in micrometers) and the other columns contain the reflectance data (in unit of reflectance factor). The different compositions are indicated in the filenames and correspond directly to the figures in the published paper.

opencc-by-4.0Oct 2021View details →

Refined Cropland Data Layer (R-CDL)

A decision tree algorithm was employed to refine Cropland Data Layer (CDL) using spatial and temporal information. The Refined Cropland Data Layer (R-CDL) could be used as an alternative to researchers as it provides more accurate cropland information. Annual RCDL maps were produced for the contiguous United States from the year 2017 to 2021. To explore the data online and access the web-based services, please visit the project homepage: https://cloud.csiss.gmu.edu/icrop/ To read our full paper on RCDL, please visit: https://www.nature.com/articles/s41597-022-01169-w Cite this article: Lin, L., Di, L., Zhang, C. et al. Validation and refinement of cropland data layer using a spatial-temporal decision tree algorithm. Sci Data 9, 63 (2022). https://doi.org/10.1038/s41597-022-01169-w Note: 2020 RCDL was reproduced with the Re-released CDL on February 1, 2022. More information could be found at: https://www.nass.usda.gov/Research_and_Science/Cropland/SARS1a.php 2021 RCDL was released with the official release of 2021 CDL on February 14, 2022 2022 RCDL was released on March 24, 2022

opencc-by-4.0Apr 2023View details →

The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex - Minimal Dataset

Minimal Dataset for "The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex", published at <a href="https://www.nature.com/nsmb/">NSMB</a>.

opencc-by-4.0May 2023View details →

Data and R scripts for KCC plots in Douville and Willett (2023)

CMIP6 data (historical and scenario SSP5-8.5, run 1 only), observation and R scripts to plot Fig.1 and Fig.2 of Douville and Willett (Sc. Adv., 2023)

opencc-by-4.0Jan 2023View details →

Open-population models for estimating roadkill rates - Data and R Code

Roadkill carcass capture-recapture data, capture histories for four and eight-occasion designs, and R code (with JAGS code) for roadkill rates estimation.

opencc-by-sa-4.0Dec 2022View details →

Data dan R Markdown Notebook untuk "PENONJOLAN PERAN SEMANTIS DAN KONSTRUKSI GRAMATIKAL PASANGAN VERBA -I DAN -KAN: KAJIAN GRAMATIKA KONSTRUKSIONAL BERBASIS KORPUS ATAS MENAWARI/MENAWARKAN"

Repositori <a href="https://r4ds.had.co.nz/workflow-projects.html">RStudio Project</a> yang mengandung data dan kode pemrograman R untuk analisis data dan penulisan makalah berjudul "Penonjolan Peran Semantis dan Konstruksi Gramatikal Pasangan Verba -i dan -kan: Kajian Gramatika Konstruksional Berbasis Korpus atas Menawari/Menawarkan". Makalah ini diterbitkan pada jurnal <a href="https://ojs.linguistik-indonesia.org/index.php/linguistik_indonesia/index">Linguistik Indonesia</a> di bulan Agustus, 2023. <ol> <li> Kode pemrograman R dan narasi teks makalah terintegrasi dalam berkas <a href="https://rmarkdown.rstudio.com">R Markdown</a> Notebook dengan nama <a href="https://github.com/gederajeg/profiled-participant-roles/blob/main/manuskrip-2.Rmd"><code>manuskrip-2.Rmd</code></a>. </li> <li> Data konkordansi terdapat pada berkas <a href="https://github.com/gederajeg/profiled-participant-roles/blob/main/menawari.txt"><code>menawari.txt</code></a> dan <a href="https://github.com/gederajeg/profiled-participant-roles/blob/main/menawarkan.txt"><code>menawarkan.txt</code></a>. </li> <li> Luaran visualisasi tersimpan pada direktori <a href="https://github.com/gederajeg/profiled-participant-roles/tree/main/plots"><code>plot</code></a>. </li> </ol>

opencc-by-4.0Sep 2023View details →

Marker parameter files for the cfTools R package

This Zenodo repository contains the data for the cfTools R package. It includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the shape parameters of beta distribution characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function.

openCC0Jan 2022View details →

Data and R code for “Individual-level variation in reproductive effort in chestnut oak (Quercus montana Willd.) and black oak (Q. velutina Lam.)”, Forest Ecology and Management, 2022

Masting is a population-level reproductive strategy, where individuals synchronize large but intermittent seed production. Despite the high degree of synchrony at the population level, there can be considerable variation in reproduction among individuals (intraspecific variation). Here, we use 18 years of acorn production data from individual chestnut oak and black oak from control and thinned stands, to understand what factors influence individual differences in reproductive effort and variability. We included a variety of tree-level measurements, environmental characteristics, and measurements from tree cores to determine if certain characteristics were associated variations in reproduction. We considered both mean annual acorn production per m2 crown and interannual variation in acorn production (CV) as response variables. We also classified individuals as super producers (i.e., those that consistently produce more acorns than others), good, fair and poor producers (i.e., those that consistently produce less or have a higher number of failure years). In chestnut oak, 14% of the individuals were classified as super producers and contributed 34% of the total acorns, while poor producers made up 35% of the trees and contributed only 16% to total acorn production. In black oak, super producers (14% of the individuals) contributed 31% of total acorns and poor producers (24% of the individuals) contributed only 9% of the acorns. Diameter at breast height (DBH) was the most consistent variable for explaining intraspecific variation in reproductive effort and variability (i.e., larger individuals had higher mean acorn production for both chestnut oak and black oak, and lower CV for black oak). Other variables that influenced reproduction and variation included elevation and clay content for chestnut oak, and slope for black oak. We found no significant effect from the thinning treatment on acorn production. Our results illustrate how tree-level and environmental characte

Relyea, R. A. 2002. Local population differences in phenotypic plasticity: Predator-induced changes in wood frog tadpoles. Ecological Monographs 72:77-93

Taxa that are divided into separate populations with low levels of interpopulation dispersal have the potential to evolve genetically based differences in their phenotypes and the plasticity of those phenotypes. These differences can be due to random processes, including genetic drift and founder effects, or they can be the result of different selection pressures among populations. I investigated population-level differences in predator- induced phenotypic plasticity in eight populations of larval wood frogs (Rana sylvatica) over a small geographic scale (interpopulation distances of 0.3–8 km). Using a common-garden experiment containing predator and no-predator environments, I found population differences in behavior, morphology, and life history. These responses exhibited a habitat-related pattern: the four populations from closed-canopy ponds did not differ from each other in any of their phenotypes whereas the four populations from opencanopy ponds did differ from each other in these traits. This phenotypic pattern matches the pattern of competitors and predators found in these two types of ponds. Based on two years of pond surveys, the four closed-canopy ponds contained very similar competitor and predator assemblages while the assemblages of the four open-canopy ponds were more diverse and highly variable among open-canopy ponds. When combined with past studies, which demonstrate that predators and competitors select for alternative behavioral and morphological traits, these patterns suggest that the population differences may have arisen via natural selection and not via random mutation or drift. In a second experiment, I cross-transplanted two of the populations into each other’s ponds to determine if the populations were locally adapted to the conditions of their native pond (using low and high competition crossed with the presence or absence of a lethal predator). The populations continued to exhibit phenotypic differences, and one of the two populations t

Relyea, R. A., and K. L. Yurewicz. 2002. Predicting community outcomes from pairwise interactions: Integrating density- and trait-mediated effects. Oecologia 131:569-579.

Understanding how species interactions shape the structure of ecological communities based on pairwise comparisons has been a difficult undertaking for ecologists because effects in reassembled communities can be different than simple density-mediated interactions would suggest. Part of this complexity occurs because many species change their behavior and morphology with different predators and competitors and, thus, change their per-capita interaction rates (i.e. trait-mediated interactions). Our objective was to use a simple experimental community of two predators (larval dragonflies, Anax longipes, and larval salamanders, Ambystoma tigrinum), two prey (larval green frogs, Rana clamitans, and larval bullfrogs, R. catesbeiana), and a shared prey resource to determine whether we can predict interactions in a reassembled community by combining our knowledge of density- and trait-mediated interactions,. We combined pairwise laboratory experiments on predation rates and predator-induced behaviors with a mesocosm experiment to examine density- and trait-mediated effects. We used a factorial combination of no predators, caged Anax (to induce anti-predator traits without changing prey density), and lethal Anax crossed with no predators, caged Ambystoma, and lethal Ambystoma. The species interactions in the reassembled community were qualitatively predictable based on the pairwise experiments. Lethal Anax preyed upon Ambystoma and green frogs while lethal Ambystoma only preyed upon green frogs. Anax also reduced the activity of the green frogs; this caused a decrease in salamander predation on green frogs, a decrease in green frog acquisition of resources, and an increase in bullfrog acquisition of resources. Ambystoma had no effect on green frog activity, no effect on resource acquisition by green frogs, and no effect on resource acquisition by bullfrogs. These results suggest that we can better understand how species interact in natural communities if we have a more deta

Relyea, R. A., and N. Mills. 2001. Predator-induced stress makes the pesticide carbaryl more deadly to grey treefrog tadpoles (Hyla versicolor). PNAS 98:2491-2496.

Global declines in amphibians likely have multiple causes, including widespread pesticide use. Our knowledge of pesticide effects on amphibians is largely limited to short-term (4-d) toxicity tests conducted under highly artificial conditions to determine lethal concentrations (LC50). We found that if we used slightly longer exposure times (10–16 d), low concentrations of the pesticide carbaryl (3–4% of LC504-d) killed 10–60% of gray treefrog (Hyla versicolor) tadpoles. If predatory cues also were present, the pesticide became 2–4 times more lethal, killing 60–98% of tadpoles. Thus, under more realistic conditions of increased exposure times and predatory stress, current application rates for carbaryl can potentially devastate gray treefrog populations. Further, because predator-induced stress is ubiquitous in animals and carbaryl’s mode of action is common to many pesticides, these negative impacts may be widespread in nature.

Relyea, R. A. 2001. The lasting effects of adaptive plasticity: Predator-induced tadpoles become long-legged frogs. Ecology 82:1947-1955.

Changes in environmental conditions often alter the traits of individuals; however, we have a poor understanding of how changes in phenotypically plastic traits early in development may affect traits later in life. Such effects are of particular interest in organisms with complex life cycles in which early and late life stages can have drastically different morphologies and occupy different habitats. In this study, I examined how differences in the mass, morphology, and larval period of wood frog tadpoles (Rana sylvatica) subsequently affected the mass and morphology of metamorphic frogs. I found three major patterns: (1) larval mass and larval period were positively related to metamorphic mass; (2) larval period was positively related to metamorph hindlimb and forelimb length and negatively related to metamorph body width; and (3) larval body length was positively related to metamorph forelimb size. I then used these correlations to interpret the connection between the traits of predator-induced tadpoles and the subsequent traits of metamorphic frogs. Tadpoles reared with caged predators (aeshnid dragonflies) developed relatively deeper tail fins and had shorter bodies, lower mass, and longer developmental times than tadpoles reared without predators. Metamorphs emerging from larval predator environments exhibited no differences in mass but developed relatively large hindlimbs and forelimbs and narrower bodies than metamorphs emerging from predator-free larval environments. These differences arose primarily due to predator-induced changes in larval development time and not due to the predator-induced changes in larval morphology. By focusing on a large number of traits and a wide range of trait values, one can readily generate predictions about how a variety of environments, which alter traits early in development, can subsequently alter traits later in development.

Cothran, R. D., F. Radarian, and R. A. Relyea. 2011. Altering aquatic food webs with a global insecticide: Arthropod-amphibian links in mesocosms that simulate wetland communities. Journal of the North American Benthological Society 30:893-912.

Pesticides play a critical role in maximizing yields of economically important crops and minimizing the human health threats of disease-carrying pests, but they often have collateral effects on nontarget species. We used a mesocosm study to address how the most commonly used insecticide in the USA, malathion, applied at low, ecologically relevant concentrations (20 and 110 mg/L) affects species interactions in aquatic communities. Unlike many community ecotoxicology studies, our study assessed how malathion affects both consumptive and nonconsumptive effects of predators. We also considered how the vertical distribution of predator cues and malathion (caused by potential stratification) affects species interactions. We found no evidence for vertical stratification of malathion, a result suggesting that exposure to the pesticide was uniform throughout the water column. Malathion was lethal to some primary consumers (cladocerans) at both concentrations and to top predators (dragonflies) at the highest concentration (110 mg/L). These lethal effects initiated density-mediated indirect effects in both cases. Malathion also may have decreased dragonfly foraging efficiency, resulting in increased tadpole survival (trait-mediated indirect effect), which decreased the resources used by tadpoles (periphyton). Collectively, our results show that malathion alters species interactions. However, we suggest that the degree to which pesticides affect aquatic communities will depend strongly on the species composition of communities. Therefore, the community-level consequences of pesticide exposure are likely to vary across the ecological landscape.

Relyea, R. A. 2001. Morphological and behavioral plasticity of larval anurans in response to different predators. Ecology 82:523-540.

Many organisms can adjust to a changing environment by developing alternative phenotypes that improve their fitness. Our understanding of phenotypic plasticity is largely based upon observations from single species responding to two different environments and measuring a single plastic trait. In this study, I examine predator-induced phenotypic plasticity in tadpoles by observing how six species of larval anurans respond to five different predator environments in 11 different traits (seven morphological traits, two behavioral traits, growth, and development). The results demonstrate that behavioral and morphological plasticity may be ubiquitous in larval anurans. The six prey species exhibited different responses to the same predator species, and each prey exhibited different responses to different predator species. This suggests that responses to a particular predator may not serve as general defense against all predators; rather, prey express predator-specific suites of responses. I also compared relative differences in plasticity among species and among traits. In contrast to earlier findings using only two predator environments, I found that different anurans possess similar degrees of plasticity for most of their traits when reared in a large number of environments. In addition, behavioral traits were always more plastic than morphological traits. Finally, I examined trait integration to address whether there were apparent trade-offs among traits and limits imposed by the abiotic environment. Trait integration, or the degree of correlated responses among traits across predator environments within a prey species, was very low. This further suggests that the suites of responses are predator specific and may be under independent directions of selection in different predator environments. Trait correlations across prey species indicated that there is an apparent trade-off between tail fin depth and body size. This relationship is supported by selection studies with

Relyea, R. A. 2001. The relationship between predation risk and anti-predator responses in larval anurans. Ecology 82:541-554.

Organisms that produce alternative, nondiscrete phenotypes in response to environmental conditions are expected to alter their phenotypes in relation to the degree of environmental change. This idea has been applied to the evolution of antipredator responses by prey, in which it has been hypothesized that prey should respond more strongly to predators that pose greater mortality risk. In a companion paper, I quantified predatorinduced behavioral and morphological responses in six species of larval anurans across five different predator environments and found that these responses were prey- and predatorspecific. In the present study, I addressed whether the responses were related to the level of predation risk posed by each of the predators. Within each prey species, I found that different predators posed different levels of predation risk; within each predator species, different prey species experienced different levels of risk. The differences in predation risk could be understood mechanistically after I quantified differences among predators in their ability to capture, handle, and consume prey and differences among prey in behavior and morphology. Using multivariate analyses, I found that predation risk had no significant effect on how a given prey responds to predators, although there were significant univariate behavioral effects; higher predation risk was related to greater decreases in activity and greater spatial avoidance. I also examined the relationship between risk and response across the six prey species within a predator treatment and found that higher predation risk across species leads to greater decreases in activity in the presence of Umbra and greater increases in tail depth in the presence of Anax. Thus, while previous studies have found relationships between predation risk and prey response when focusing on relatively few species, few predators, and a single trait, this more powerful test using 30 predator–prey combinations and nine traits sugge

Relyea, R. A. 2000. Trait-mediated indirect effects in larval anurans: Reversing competition with the threat of predation. Ecology 81:2278-2289.

Ecologists recently have been focusing on the role that trait-mediated indirect effects can have on community structure and composition. To date, this work has primarily focused on the effects of predator-induced behavioral plasticity on communities. However, predator-induced morphological plasticity, which has been documented in many taxa, might also lead to trait-mediated indirect effects. Here, I examined how predators altered the behavior and morphology of larval wood frogs (Rana sylvatica) and leopard frogs (R. pipiens) and how these phenotypic changes altered the outcome of competition between the two species. Competition in the absence of caged predators was asymmetric; when reared separately, leopard frogs grew more than wood frogs, but when competing (without predators), wood frogs grew faster than leopard frogs. The presence of caged predators reversed the outcome of competition between the two anuran prey. In the presence of larval dragonflies (Anax spp.) or caged mudminnows (Umbra limi), leopard frogs grew faster than wood frogs while total tadpole biomass production remained unchanged. Thus, there was a predator-mediated indirect effect. Because predators alter both the behavior and morphology of larval anurans and both of these traits are known to affect resource consumption and growth, both are potential mechanisms to explain the change in competitive outcome. Changes in behavior were not related to changes in growth, but changes in morphology (specifically mouth width and tail length) were related to changes in growth. When competitors were added (without predators), wood frogs increased their mouth width by 10% and their tail length by 3%, while leopard frogs increased their mouth width by 5% and did not change their tail length. The greater increase in mouth width for wood frogs should increase their forage intake, since tadpoles feed by scraping periphyton; the importance of a 3% longer tail in competitive ability is unknown. The presence of the p