Showing 29 of total 29 results (show query)
quicklizard99
cheddar:Analysis and Visualisation of Ecological Communities
Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.
Maintained by Lawrence Hudson. Last updated 8 months ago.
31.8 match 15 stars 6.86 score 195 scripts
sborstein
dietr:Diet Estimated Trophic Levels
Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
Maintained by Samuel R. Borstein. Last updated 2 months ago.
25.8 match 5 stars 5.41 score 13 scripts
benjaminhlina
trps:Bayesian Trophic Position Models using 'stan'
Bayesian trophic position models using 'stan' by leveraging 'brms' for stable isotope data. Trophic position models are derived by using equations from Post (2002) <doi:10.1890/0012-9658(2002)083[0703:USITET]2.0.CO;2>, Vander Zanden and Vadeboncoeur (2002) <doi:10.1890/0012-9658(2002)083[2152:FAIOBA]2.0.CO;2>, and Heuvel et al. (2024) <doi:10.1139/cjfas-2024-0028>.
Maintained by Benjamin L. Hlina. Last updated 10 days ago.
26.8 match 3.54 score 4 scripts
giopogg
webSDM:Including Known Interactions in Species Distribution Models
A collection of tools to fit and work with trophic Species Distribution Models. Trophic Species Distribution Models combine knowledge of trophic interactions with Bayesian structural equation models that model each species as a function of its prey (or predators) and environmental conditions. It exploits the topological ordering of the known trophic interaction network to predict species distribution in space and/or time, where the prey (or predator) distribution is unavailable. The method implemented by the package is described in Poggiato, Andréoletti, Pollock and Thuiller (2022) <doi:10.22541/au.166853394.45823739/v1>.
Maintained by Giovanni Poggiato. Last updated 9 months ago.
14.1 match 17 stars 5.71 score 9 scripts
cran
trps:Bayesian Trophic Position Models using 'stan'
Bayesian trophic position models using 'stan' by leveraging 'brms' for stable isotope data. Trophic position models are derived by using equations from Post (2002) <doi:10.1890/0012-9658(2002)083[0703:USITET]2.0.CO;2>, Vander Zanden and Vadeboncoeur (2002) <doi:10.1890/0012-9658(2002)083[2152:FAIOBA]2.0.CO;2>, and Heuvel et al. (2024) <doi:10.1139/cjfas-2024-0028>.
Maintained by Benjamin L. Hlina. Last updated 11 days ago.
26.8 match 2.70 score
marcohlmann
metanetwork:Handling and Representing Trophic Networks in Space and Time
A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks. The package also implements network diversity indices at different aggregation levels and connectance computation.
Maintained by Marc Ohlmann. Last updated 2 years ago.
14.0 match 2 stars 3.89 score 77 scripts
polehalieutique
EcoTroph:An implementation of the EcoTroph Ecosystem modelling approach
An approach and software for modelling marine and freshwater ecosystems. It is articulated entirely around trophic levels. EcoTroph's key displays are bivariate plots, with trophic levels as the abscissa, and biomass flows or related quantities as ordinates. Thus, trophic ecosystem functioning can be modelled as a continuous flow of biomass surging up the food web, from lower to higher trophic levels, due to predation and ontogenic processes. Such an approach, wherein species as such disappear, may be viewed as the ultimate stage in the use of the trophic level metric for ecosystem modelling, providing a simplified but potentially useful caricature of ecosystem functioning and impacts of fishing. This version contains catch trophic spectrum analysis (CTSA) function and corrected versions of the mf.diagnosis and create.ETmain functions.
Maintained by Jerome Guitton. Last updated 2 years ago.
18.5 match 1 stars 2.93 score 17 scripts
poissonconsulting
wqbench:Calculate Aquatic Life Benchmarks
Download recent versions of the US EPA ECOTOX database. Clean, standardize and classify data so values are comparable. Use a SSD or deterministic method to determine the critical toxicity value and assessment factors to compute the aquatic life water quality benchmark for a compound.
Maintained by Angeline Tillmanns. Last updated 2 months ago.
8.7 match 4.86 score 5 scripts 1 dependents
biometry
bipartite:Visualising Bipartite Networks and Calculating Some (Ecological) Indices
Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
Maintained by Carsten F. Dormann. Last updated 22 days ago.
3.3 match 37 stars 10.93 score 592 scripts 15 dependents
james-thorson-noaa
dsem:Fit Dynamic Structural Equation Models
Applies dynamic structural equation models to time-series data with generic and simplified specification for simultaneous and lagged effects. Methods are described in Thorson et al. (2024) "Dynamic structural equation models synthesize ecosystem dynamics constrained by ecological mechanisms."
Maintained by James Thorson. Last updated 21 days ago.
5.0 match 11 stars 6.90 score 24 scripts
robertwbuchkowski
soilfoodwebs:Soil Food Web Analysis
Analyzing soil food webs or any food web measured at equilibrium. The package calculates carbon and nitrogen fluxes and stability properties using methods described by Hunt et al. (1987) <doi:10.1007/BF00260580>, de Ruiter et al. (1995) <doi:10.1126/science.269.5228.1257>, Holtkamp et al. (2011) <doi:10.1016/j.soilbio.2010.10.004>, and Buchkowski and Lindo (2021) <doi:10.1111/1365-2435.13706>. The package can also manipulate the structure of the food web as well as simulate food webs away from equilibrium and run decomposition experiments.
Maintained by Robert Buchkowski. Last updated 11 months ago.
7.3 match 5 stars 4.40 score 4 scripts
andrewljackson
SIBER:Stable Isotope Bayesian Ellipses in R
Fits bi-variate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.
Maintained by Andrew Jackson. Last updated 10 months ago.
community-ecologyecologyniche-modellingstable-isotopesjagscpp
3.4 match 37 stars 9.15 score 187 scripts 1 dependents
karlines
NetIndices:Estimating Network Indices, Including Trophic Structure of Foodwebs in R
Given a network (e.g. a food web), estimates several network indices. These include: Ascendency network indices, Direct and indirect dependencies, Effective measures, Environ network indices, General network indices, Pathway analysis, Network uncertainty indices and constraint efficiencies and the trophic level and omnivory indices of food webs.
Maintained by Karline Soetaert. Last updated 3 years ago.
6.9 match 3.91 score 134 scripts 2 dependents
derek-corcoran-barrios
NetworkExtinction:Extinction Simulation in Ecological Networks
Simulates the extinction of species in ecological networks and it analyzes its cascading effects, described in Dunne et al. (2002) <doi:10.1073/pnas.192407699>.
Maintained by Derek Corcoran. Last updated 5 months ago.
4.0 match 5 stars 5.15 score 19 scripts
europeanifcbgroup
iRfcb:Tools for Managing Imaging FlowCytobot (IFCB) Data
A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.
Maintained by Anders Torstensson. Last updated 4 days ago.
data-exportimaging-flow-cytometryimaging-flowcytobotoceanographyplanktonquality-control
3.0 match 1 stars 5.76 score
pyhernvann
EcoDiet:Estimating a Diet Matrix from Biotracer and Stomach Content Data
Biotracers and stomach content analyses are combined in a Bayesian hierarchical model to estimate a probabilistic topology matrix (all trophic link probabilities) and a diet matrix (all diet proportions). The package relies on the JAGS software and the 'jagsUI' package to run a Markov chain Monte Carlo approximation of the different variables.
Maintained by Pierre-Yves Hernvann. Last updated 1 years ago.
3.1 match 4 stars 5.33 score 12 scriptsbenjaminhlina
nichetools:Complementary Package to 'nicheROVER' and 'SIBER'
Provides functions complementary to packages 'nicheROVER' and 'SIBER' allowing the user to extract Bayesian estimates from data objects created by the packages 'nicheROVER' and 'SIBER'. Please see the following publications for detailed methods on 'nicheROVER' and 'SIBER' Hansen et al. (2015) <doi:10.1890/14-0235.1>, Jackson et al. (2011) <do i:10.1111/j.1365-2656.2011.01806.x>, and Layman et al. (2007) <doi:10.1890/0012-9658(2007)88[42:CSIRPF]2.0.CO;2>, respectfully.
Maintained by Benjamin L. Hlina. Last updated 11 days ago.
2.6 match 2 stars 6.39 score 17 scripts
brianstock
MixSIAR:Bayesian Mixing Models in R
Creates and runs Bayesian mixing models to analyze biological tracer data (i.e. stable isotopes, fatty acids), which estimate the proportions of source (prey) contributions to a mixture (consumer). 'MixSIAR' is not one model, but a framework that allows a user to create a mixing model based on their data structure and research questions, via options for fixed/ random effects, source data types, priors, and error terms. 'MixSIAR' incorporates several years of advances since 'MixSIR' and 'SIAR'.
Maintained by Brian Stock. Last updated 4 years ago.
1.8 match 98 stars 9.27 score 122 scriptscran
ATNr:Run Allometric Trophic Networks Models
Implements the differential equations associated to different versions of Allometric Trophic Models (ATN) to estimate the temporal dynamics of species biomasses in food webs. It offers several features to generate synthetic food webs and to parametrise models as well as a wrapper to the ODE solver deSolve.
Maintained by Benoit Gauzens. Last updated 2 years ago.
5.4 match 3.00 scorecran
benthos:Marine Benthic Ecosystem Analysis
Preprocessing tools and biodiversity measures (species abundance, species richness, population heterogeneity and sensitivity) for analysing marine benthic data. See Van Loon et al. (2015) <doi:10.1016/j.seares.2015.05.002> for an application of these tools.
Maintained by Dennis Walvoort. Last updated 3 years ago.
6.8 match 2.00 scorejames-thorson-noaa
ecostate:State-Space Mass-Balance Model for Marine Ecosystems
Fits a state-space mass-balance model for marine ecosystems, which implements dynamics derived from `Ecopath with Ecosim` (`EwE`) <https://ecopath.org/> while fiting to time-series of fishery catch, biomass indices, age-composition samples, and weight-at-age data. `Ecostate` fits biological parameters (e.g., equilibrium mass) and measurement parameters (e.g., catchability coefficients) jointly with residual variation in process errors, and can include Bayesian priors for parameters.
Maintained by James T. Thorson. Last updated 21 days ago.
1.8 match 13 stars 5.99 score 6 scripts
le-huynh
lehuynh:Le-Huynh Truc-Ly's R Code and Templates
Miscellaneous R functions (for graphics, data import, data transformation, and general utilities) and templates (for exploratory analysis, Bayesian modeling, and crafting scientific manuscripts).
Maintained by Truc-Ly Le-Huynh. Last updated 10 months ago.
1.8 match 3 stars 3.88 score 4 scripts
mrheath
StrathE2E2:End-to-End Marine Food Web Model
A dynamic model of the big-picture, whole ecosystem effects of hydrodynamics, temperature, nutrients, and fishing on continental shelf marine food webs. The package is described in: Heath, M.R., Speirs, D.C., Thurlbeck, I. and Wilson, R.J. (2020) <doi:10.1111/2041-210X.13510> StrathE2E2: An R package for modelling the dynamics of marine food webs and fisheries. 8pp.
Maintained by Michael Heath. Last updated 4 years ago.
1.6 match 3.10 score 25 scripts
juanmac17
metrix:Water Quality Metrics Calculator
Calculate different metrics based on aquatic macroinvertebrate density data (individuals per square meter) to assess water quality (Prat N et al. 2009).
Maintained by Juan Manuel Cabrera. Last updated 2 years ago.
2.3 match 1.00 score 1 scripts
vmielecnrs
econetwork:Analyzing Ecological Networks
A collection of advanced tools, methods and models specifically designed for analyzing different types of ecological networks - especially antagonistic (food webs, host-parasite), mutualistic (plant-pollinator, plant-fungus, etc) and competitive networks, as well as their variability in time and space. Statistical models are developed to describe and understand the mechanisms that determine species interactions, and to decipher the organization of these ecological networks (Ohlmann et al. (2019) <doi:10.1111/ele.13221>, Gonzalez et al. (2020) <doi:10.1101/2020.04.02.021691>, Miele et al. (2021) <doi:10.48550/arXiv.2103.10433>, Botella et al (2021) <doi:10.1111/2041-210X.13738>).
Maintained by Vincent Miele. Last updated 2 years ago.
1.8 match 1.04 score 11 scriptscran
fluxweb:Estimate Energy Fluxes in Food Webs
Compute energy fluxes in trophic networks, from resources to their consumers, and can be applied to systems ranging from simple two-species interactions to highly complex food webs. It implements the approach described in Gauzens et al. (2017) <doi:10.1101/229450> to calculate energy fluxes, which are also used to calculate equilibrium stability.
Maintained by Benoit Gauzens. Last updated 7 years ago.
0.5 match 1 stars 2.00 score