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317 results for “R code”
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
Darwin's naturalization conundrum can be explained by spatial scale: R replication code
<p>1) Code for extracting climatic data:<br> 1_extract_env.R<br> 2_extract_env_county.R<br> 3_relatePlotCounty.R</p> <p>2) Code for generating composite phylogenies:<br> 1_making_sunplin_trees.R</p> <p>3) Code for relatedness analyses:<br> DNH_calculations_PHY_obs.cluster.R<br> DNH_calculations_PHY_random.cluster.R<br> DNH_calculations_TAX.cluster_obs.R<br> DNH_calculations_TAX.cluster_random.R</p> <p> </p> <p> </p>
R code and radiocarbon dates to reproduce figures and results of our paper "Population dynamics ..."
<p>R Codes and dataset to reproduce figures and results of the paper <strong><em>Population dynamics during the Neolithic transition and the onset of megalithism in Portugal according to summed probability distribution of radiocarbon determinations</em>. </strong></p>
Dataset, Survey, and R Notebooks for "Does Surprisal Predict Code Comprehension Difficulty?"
<p>(Version 1.1 Update)</p> <p>- Removed anonymization after reviewing period ended and paper was accepted at Cogsci 2020.</p> <p>- Added Qualtrics Survey in exported form</p> <p>Dataset and R analysis scripts for the paper "Does Surprisal Predict Code Comprehension Difficulty?". For more details, see "ComprehensionREADME.md" in the included zip file.</p>
R code and data to reproduce figures from the "Multivariate autoregressive modelling and conditional simulation for temporal uncertainty analysis of an urban water system in Luxembourg" paper
<p>This repository contains the R code and data to reproduce figures from the "Multivariate autoregressive modelling and conditional simulation for temporal uncertainty analysis of an urban water system in Luxembourg" paper.</p>
Data and R code for the revised manuscript "Downscaling digital soil maps using electromagnetic induction and aerial imagery"
<p>Data and R code for the revised manuscript "Downscaling digital soil maps using electromagnetic induction and aerial imagery". This is the code for the revised version of the manuscript, after adressing comments from reviewers. The data and code for the preprint, before submission to peer review (Møller et al., 2020), is available at <a href="https://doi.org/10.5281/zenodo.3699130">https://doi.org/10.5281/zenodo.3699130</a>.</p> <p>The R code was written for R version 3.6.3.</p> <p>References<br> Møller, A.B., Koganti, T., Beucher, A., Iversen, B.V. and Greve, M.H., 2020. Downscaling digital soil maps using electromagnetic induction and aerial imagery. EarthArXiv. <a href="http://dx.doi.org/10.31223/osf.io/a7xz6">http://dx.doi.org/10.31223/osf.io/a7xz6</a>. [preprint]</p>
Data and R code from: Pollination interactions reveal direct costs and indirect benefits of plant–plant facilitation for ecosystem engineers
Ecosystem engineers substantially modify the environment via their impact on abiotic conditions and the biota, resulting in facilitation of associated species that would not otherwise grow. Yet, reciprocal effects are poorly understood as studies of plant–plant interactions usually estimate only benefits for associated species while hardly considering how another trophic level may mediate direct and indirect effects for ecosystem engineers. We run a field experiment with ecosystem engineers blooming either alone or with associated plants to decompose net effects and to test the hypothesis that pollinator-mediated interactions provide benefits which balance costs of facilitation by ecosystem engineers. We found that net costs of facilitation are accompanied by pollinator-mediated benefits. Despite ecosystem engineers producing less flowers per plant, they were visited by more and more diverse pollinators per flower when blooming with associated plants than when blooming alone. However, fruit set was unaffected by the presence of associated plants and seed production per plant was higher when ecosystem engineers bloomed alone. Our findings suggest that besides experiencing direct costs, ecosystem engineers can also benefit from facilitating other species via increasing their own visibility to pollinators. This study illuminates how the outcome of direct plant–plant interactions might be mediated by indirect interactions including third players.
Supplementary files for Silva et al. 2020 "Reptiles on the wrong track?": R Code, data and figures
<p>Datasets, R code and figures pertaining to the manuscript: Silva, I., Crane, M., Marshall, B.M., & Strine, C.T. (2020).<em> </em> <em>Reptiles on the wrong track? Moving beyond traditional estimators with dynamic Brownian Bridge Movement Models.</em> Movement Ecology 8, 43 DOI: 10.1186/s40462-020-00229-3</p> <p>Article available at: <a href="https://movementecologyjournal.biomedcentral.com/articles/10.1186/s40462-020-00229-3">https://movementecologyjournal.biomedcentral.com/articles/10.1186/s40462-020-00229-3</a></p>
Supplementary files for Crane et al., "On a wing and a prayer": R Code, data and figures
<p>Datasets, R code and figures pertaining to the manuscript: Crane M, Silva I, Grainger MJ, & Gale GA.<em> On a wing and a prayer: limitations and gaps in global bat wing morphology trait data</em></p>
Replication R code and data for "Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes"
<p>This repository holds various files and R code used in the publication of the manuscript entitled "Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes".</p> <p>Data files include: The 3D landmark coordinates of each individual specimen (Fox_data_Morphologika.txt), the linear measurement data associated with those foxes (fox_linear_volume_data.csv), and replication data measurements. </p> <p>The following files include the R code used to perform the analyses contained within the paper:</p> <p>1_Procrustes_analysis - details the Geometric morphometrics analyses performed</p> <p>2_linear_models - details the model specification for the GLS models employed in the paper</p> <p>3_graph_code - contains R script for the creation of the graphs displayed in the paper</p> <p>4_repeatability_script - contains R code that details the statistical calculations made with the repeatability measurements indicated above. </p> <p> </p> <p> </p> <p> </p>
Really a nontraded commodity? A look at the international potato trade network (dataset and R code)
<p>This archive contains code and data for a social network analysis of international potato trade that was published at https://perspectivesandforesight.wordpress.com/2012/11/08/really-a-nontraded-commodity-a-look-at-the-international-potato-trade-network/ on 08 November, 2012.</p> <p>It can serve as a reference for understanding the analysis, and as a basis for replication of the results as well as for carrying out more detailed analyses of international potato trade.</p> <p>The following information and data is included:</p> <p>- The R code used for the social network analysis of international potato trade.</p> <p>- Data files with bilateral matrices of global trade in fresh, frozen and seed potatoes.</p> <p>- Data files with supplementary data used for the analysis.</p> <p>- A copy of the original blog post that was written using the data and code provided herewith.</p>
Anthropoid morphometric and phylogenetic data, with R replication code.
<p>This repository contains four files: 1) a NEXUS phylogeny of 100 anthropoid primates; 2) a CSV text file of anthropoid primate lower molar areas, body mass, and primary dietary category; 3) a CSV text file of modern human lower molar area proportions; and, 4) an R script containing replication code for fitting Bayesian phylogenetic generalized linear mixed models to the morphometric data. These files are associated with the paper "The Evolution of Anthropoid Molar Proportions" in BMC Evolutionary Biology (2016).</p>
Relative width and height of handwritten letters. R code.
<p>Heigths and widths of handwritten letters of 21 writers. 500 letters of each writer.</p> <p>R code for data analysis. The codes are in beta phase, the codes have no help or explanations. Units mm/100.</p>
Individual-based simulation model of annual movement paths for the Darwin's frog (R code and data)
<p>Desprition of the R code</p> <p>I constructed an individual-based simulation model that describes the movement path of an individual<em> Rhinoderma darwinii</em> through 3-month displacement steps. This model was primarily developed to evaluate the age-specific movement behaviour of Darwin's frogs, however, I also used it to provide better estimates (i.e. alleviating for movement censoring) of age-specific annual displacements in the species. I developed several variations of this model through a combination of different random walk sub-models for juveniles and adults: uncorrelated non-stationary random walks (NRW), correlated non-stationary random walks (CRW), and stationary random walks (SRW). The NRW and CRW were modelled as a first-order Markovian process where the location of an individual <em>i</em> in time<em> t</em> depends on its spatial location in <em>t </em>- 1. The NRW is unbiased, i.e., there is no preferred direction in each movement step. In contrast, the CRW includes persistence in the directionality of movement, so there is a correlation between successive step orientations. Finally, the SRW assumes that individuals have an activity centre to which all their spatial locations are related.</p> <p>Related data are provided (y.txt, x.txt and age.txt)</p>
Data sets and R codes for "It's about her: male within-season movements are related to mate searching in a songbird"
<p><strong>Abstract</strong></p><p>In species with resource-defense mating systems (such as most temperate-breeding songbirds), male dispersal is often considered to be limited in both frequency and spatial extent. When dispersal occurs within a breeding season, the favored explanation is ecological resource tracking. In contrast, movements of male birds associated with temporary emigration, such as polyterritoriality (i.e., defense of an additional location after attracting a female in the initial territory), are usually attributed to mate searching. We suggest that male dispersal and polyterritoriality are functionally related, and that mate searching may be a unifying hypothesis for predicting the within-season movements of male songbirds. Here, we test three key predictions derived from this hypothesis in Wood Warblers <i>Phylloscopus sibilatrix</i>. We collected data on the spatial behavior of 107 males between 2017 and 2019, and related male movements to a new territory (both in a dispersal and polyterritorial context) to mating potential in the current territory. Most males dispersed from their territories within days or weeks after failing to attract a female, despite occupying territories in apparently suitable habitat. Probability of polyterritoriality by paired males increased after the peak fertile period of their mate. Males never dispersed following nest predation if the female remained to renest. Thus, our data are consistent with the hypothesis that both movement types are functionally related to mate searching.</p>
Raw absorbance data and R codes for analysing enzymatic activities
<p>Raw absorbance data and sample metadata for study by Prokkola et al. (submitted 2023). See README.</p><p>Statistical analysis of data available in another repository https://doi.org/10.5281/zenodo.8014314.</p><p> </p>
Data and R code from: Fin whale song evolution in the North Atlantic
<p>Animal songs can change within and between populations as the result of different evolutionary processes. When these processes include cultural transmission, the social learning of information or behaviours from conspecifics, songs can undergo rapid evolutions because cultural novelties can emerge more frequently than genetic mutations. Understanding these song variations over large temporal and spatial scales can provide insights into the patterns, drivers and limits of song evolution that can ultimately inform on the species' capacity to adapt to rapidly changing acoustic environments.</p> <p>In this study, we analysed changes in fin whale (<em>Balaenoptera physalus</em>) songs recorded over two decades (1999–2020) across the central and eastern North Atlantic Ocean. We document a rapid replacement of song INIs (inter-note intervals) over just four singing seasons (2000/2001–2004/2005) in the southeast location of the Oceanic Northeast Atlantic (ONA) region, that co-occurred with hybrid songs (with both INIs). During the transition in song INIs (2002/2003) we show a clear geographic gradient in the occurrence of different song INIs in the whole ONA region. We also found gradual changes in song INIs (Figure 3A) and 20-Hz note (Figure 3B) and HF note (Figure 3C) peak frequencies over more than a decade with fin whales adopting song changes. These results provide evidence of vocal learning in fin whales and reveal patterns of song evolution that raise questions on the limits of song variation in this species.</p>
Code and example images from: recolorize: An R package for flexible color segmentation of biological images
<p>Color pattern variation provides biological information in fields ranging from disease ecology to speciation dynamics. Comparing color pattern geometries across images requires color segmentation, where pixels in an image are assigned to one of a set of color classes shared by all images. Manual methods for color segmentation are slow and subjective, while automated methods can struggle with high technical variation in aggregate image sets. We present recolorize, an R package toolbox for human-subjective color segmentation with functions for batch-processing low-variation image sets and additional tools for handling images from diverse (high variation) sources. The package also includes export options for a variety of formats and color analysis packages. This paper illustrates recolorize for three example datasets, including high variation, batch processing, and combining with reflectance spectra, and demonstrates the downstream use of methods that rely on this output.</p>
Data and R code used in: Plant geographic distribution influences chemical defenses in native and introduced Plantago lanceolata populations
<p>Plants growing outside their native range may be confronted by new regimes of herbivory, but how this affects plant chemical defense profiles has rarely been studied. Using <em>Plantago lanceolata</em> as a model species, we investigated whether introduced populations show significant differences from native populations in several growth and chemical defense traits. <em>Plantago lanceolata </em>(ribwort plantain) is an herbaceous plant species native to Europe and Western Asia that has been introduced to numerous countries worldwide. We sampled seeds from nine native and ten introduced populations that covered a broad geographic and environmental range and performed a common garden experiment in a greenhouse, in which we infested half of the plants in each population with caterpillars of the generalist herbivore <em>Spodoptera littoralis</em>. We then measured size-related and resource-allocation traits as well as the levels of constitutive and induced chemical defense compounds in roots and shoots of <em>P. lanceolata</em>. When we considered the environmental characteristics of the site of origin, our results revealed that populations from introduced ranges were characterized by an increase of chemical defense compounds without compromising plant biomass. The concentrations of iridoid glycosides and verbascoside, the major anti-herbivore defense compounds of <em>P. lanceolata</em>,<em> </em>were higher in introduced populations than in native populations. In addition, introduced populations exhibited greater rates of herbivore-induced volatile organic compound emission and diversity, and similar chemical diversity based on untargeted analyses of leaf methanol extracts. In general, the geographic origin of the populations had a significant influence on morphological and chemical plant traits, suggesting that <em>P. lanceolata</em> populations are not only adapted to different environments in their native range but also in their introduced range.</p>
Overcoming confusion and stigma in habitat fragmentation research - supplementary data and R code
<p>Data and code necessary to produce results and figures for the manuscript:</p> <p>Riva, Koper and Fahrig (2024). "Overcoming confusion and stigma in habitat fragmentation research". Biol Rev. Accepted conditional on minor revisions. </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.