An official website of the United States government
Abstract Accurate quantification of soil carbon fluxes is essential to reduce uncertainty in estimates of the terrestrial carbon sink. However, these fluxes vary over time and across ecosystem types and so, it can be difficult to estimate them accurately across large scales. The flux‐gradient method estimates soil carbon fluxes using co‐located measurements of soil CO2concentration, soil temperature, soil moisture and other soil properties. The National Ecological Observatory Network (NEON) provides such data across 20 ecoclimatic domains spanning the continental U.S., Puerto Rico, Alaska and Hawai‘i.We present an R software package (neonSoilFlux) that acquires soil environmental data to compute half‐hourly soil carbon fluxes for each soil replicate plot at a given terrestrial NEON site. To assess the computed fluxes, we visited six focal NEON sites and measured soil carbon fluxes using a closed‐dynamic chamber approach.Outputs from theneonSoilFluxshowed agreement with measured fluxes (R2between measured andneonSoilFluxoutputs ranging from 0.12 to 0.77 depending on calculation method used); measured outputs generally fell within the range of calculated uncertainties from the gradient method. Calculated fluxes fromneonSoilFluxaggregated to the daily scale exhibited expected site‐specific seasonal patterns.While the flux‐gradient method is broadly effective, its accuracy is highly sensitive to site‐specific inputs, including the extent to which gap‐filing techniques are used to interpolate missing sensor data and to estimates of soil diffusivity and moisture content. Future refinement and validation ofneonSoilFluxoutputs can contribute to existing databases of soil carbon flux measurements, providing near real‐time estimates of a critical component of the terrestrial carbon cycle.
more »
« less
popler: An r package for extraction and synthesis of population time series from the long‐term ecological research (LTER) network
Abstract Population dynamics play a central role in the historical and current development of fundamental and applied ecological science. The nascent culture of open data promises to increase the value of population dynamics studies to the field of ecology. However, synthesis of population data is constrained by the difficulty in identifying relevant datasets, by the heterogeneity of available data and by access to raw (as opposed to aggregated or derived) observations.To obviate these issues, we built a relational database,popler, and itsRclient, the library popler.popleraccommodates the vast majority of population data under a common structure, and without the need for aggregating raw observations. The popler R library is designed for users unfamiliar with the structure of the database and with the SQL language. ThisRlibrary allows users to identify, download, explore and cite datasets salient to their needs.We implemented popler as a PostgreSQL instance, where we stored population data originated by the United States Long Term Ecological Research (LTER) Network. Our focus on the US LTER data aims to leverage the potential of this vast open data resource. The database currently contains 305 datasets from 25 LTER sites.popleris designed to accommodate automatic updates of existing datasets, and to accommodate additional datasets from LTER as well as non‐LTER studies.The combination of the online database and theRlibrary popler is a resource for data synthesis efforts in population ecology. The common structure ofpoplersimplifies comparative analyses, and the availability of raw data confers flexibility in data analysis. The popler R library maximizes these opportunities by providing a user‐friendly interface to the online database.
more »
« less
- Award ID(s):
- 1655499
- PAR ID:
- 10457227
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Methods in Ecology and Evolution
- Volume:
- 11
- Issue:
- 2
- ISSN:
- 2041-210X
- Page Range / eLocation ID:
- p. 258-264
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Shape characterizers are metrics that quantify aspects of the overall geometry of a three‐dimensional (3D) digital surface. When computed for biological objects, the values of a shape characterizer are largely independent of homology interpretations and often contain a strong ecological and functional signal. Thus, shape characterizers are useful for understanding evolutionary processes. Dirichlet normal energy (DNE) is a widely used shape characterizer in morphological studies.Recent studies found that DNE is sensitive to various procedures for preparing 3D mesh from raw scan data, raising concerns regarding comparability and objectivity when utilizing DNE in morphological research. We providearobustlyimplementedalgorithm for computing the Dirichlet energy of the normal (ariaDNE) on 3D meshes.We show through simulation that the effects of preparation‐related mesh surface attributes, such as triangle count, mesh representation, noise, smoothing and boundary triangles, are much more limited on ariaDNE than DNE. Furthermore, ariaDNE retains the potential of DNE for biological studies, illustrated by its effectiveness in differentiating species by dietary preferences.Use of ariaDNE can dramatically enhance the assessment of the ecological aspects of morphological variation by its stability under different 3D model acquisition methods and preparation procedure. Towards this goal, we provide scripts for computing ariaDNE and ariaDNE values for specimens used in previously published DNE analyses.more » « less
-
For everything there is a season: Analysing periodic mortality patterns with the cyclomort r packageAbstract Many important demographic processes are seasonal, including survival. For many species, mortality risk is significantly higher at certain times of the year than at others, whether because resources are scarce, susceptibility to predators or disease is high, or both. Despite the importance of survival modelling in wildlife sciences, no tools are available to estimate the peak, duration and relative importance of these ‘seasons of mortality’.We presentcyclomort, anrpackage that estimates the timing, duration and intensity of any number of mortality seasons with reliable confidence intervals. The package includes a model selection approach to determine the number of mortality seasons and to test whether seasons of mortality vary across discrete grouping factors.We illustrate the periodic hazard function model and workflow of cyclomort with simulated data. We then estimate mortality seasons of two caribouRangifer taranduspopulations that have strikingly different mortality patterns, including different numbers and timing of mortality peaks, and a marked change in one population over time.Thecyclomortpackage was developed to estimate mortality seasons for wildlife, but the package can model any time‐to‐event processes with a periodic component.more » « less
-
Abstract Collective motion, that is the coordinated spatial and temporal organisation of individuals, is a core element in the study of collective animal behaviour. The self‐organised properties of how a group moves influence its various behavioural and ecological processes, such as predator–prey dynamics, social foraging and migration. However, little is known about the inter‐ and intra‐specific variation in collective motion. Despite the significant advancement in high‐resolution tracking of multiple individuals within groups, providing collective motion data for animals in the laboratory and the field, a framework to perform quantitative comparisons across species and contexts is lacking.Here, we present theswaRmversepackage. Building on two existing R packages,trackdfandswaRm,swaRmverseenables the identification and analysis of collective motion ‘events’, as presented in Papadopoulou et al. (2023), creating a unit of comparison across datasets. We describe the package's structure and showcase its functionality using existing datasets from several species and simulated trajectories from an agent‐based model.From positional time‐series data for multiple individuals (x‐y‐t‐id),swaRmverseidentifies events of collective motion based on the distribution of polarisation and group speed. For each event, a suite of validated biologically meaningful metrics are calculated, and events are placed into a ‘swarm space’ through dimensional reduction techniques.Our package provides the first automated pipeline enabling the analysis of data on collective behaviour. The package allows the calculation and use of complex metrics for users without a strong quantitative background and will promote communication and data‐sharing across disciplines, standardising the quantification of collective motion across species and promoting comparative investigations.more » « less
-
Fast mvSLOUCH : Multivariate Ornstein–Uhlenbeck‐based models of trait evolution on large phylogeniesAbstract ThePCMBase Rpackage is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models.Taking advantage of it, we redesigned theRpackagemvSLOUCH.Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein–Uhlenbeck processes.The results of our analysis demonstrate the ability of the modelling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms.more » « less
