Showing 19 of total 19 results (show query)
radicalcommecol
cxr:A Toolbox for Modelling Species Coexistence in R
Recent developments in modern coexistence theory have advanced our understanding on how species are able to persist and co-occur with other species at varying abundances. However, applying this mathematical framework to empirical data is still challenging, precluding a larger adoption of the theoretical tools developed by empiricists. This package provides a complete toolbox for modelling interaction effects between species, and calculate fitness and niche differences. The functions are flexible, may accept covariates, and different fitting algorithms can be used. A full description of the underlying methods is available in García-Callejas, D., Godoy, O., and Bartomeus, I. (2020) <doi:10.1111/2041-210X.13443>. Furthermore, the package provides a series of functions to calculate dynamics for stage-structured populations across sites.
Maintained by David Garcia-Callejas. Last updated 1 months ago.
36.7 match 10 stars 6.51 score 27 scripts
hankstevens
primer:Functions and Data for the Book, a Primer of Ecology with R
Functions are primarily functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices; data are for examples.
Maintained by Hank Stevens. Last updated 4 years ago.
25.2 match 14 stars 5.92 score 118 scripts
mjg211
phaseR:Phase Plane Analysis of One- And Two-Dimensional Autonomous ODE Systems
Performs a qualitative analysis of one- and two-dimensional autonomous ordinary differential equation systems, using phase plane methods. Programs are available to identify and classify equilibrium points, plot the direction field, and plot trajectories for multiple initial conditions. In the one-dimensional case, a program is also available to plot the phase portrait. Whilst in the two-dimensional case, programs are additionally available to plot nullclines and stable/unstable manifolds of saddle points. Many example systems are provided for the user. For further details can be found in Grayling (2014) <doi:10.32614/RJ-2014-023>.
Maintained by Michael J Grayling. Last updated 3 years ago.
biological-modelingdifferential-equationsdynamical-systemsecological-modellinglotka-volterramanifoldsmodeling-dynamic-systemsmorris-lecarperturbation-analysisphase-planesir-modelspecies-interactionsvan-der-pol
19.0 match 15 stars 6.63 score 94 scripts 1 dependents
darrenjw
smfsb:Stochastic Modelling for Systems Biology
Code and data for modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data associated with the second and third editions of the book Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC Press.
Maintained by Darren Wilkinson. Last updated 1 years ago.
40.5 match 2.94 score 88 scripts
tpetzoldt
simecol:Simulation of Ecological (and Other) Dynamic Systems
An object oriented framework to simulate ecological (and other) dynamic systems. It can be used for differential equations, individual-based (or agent-based) and other models as well. It supports structuring of simulation scenarios (to avoid copy and paste) and aims to improve readability and re-usability of code.
Maintained by Thomas Petzoldt. Last updated 7 months ago.
14.1 match 4.76 score 190 scripts
bioc
miaSim:Microbiome Data Simulation
Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.
Maintained by Yagmur Simsek. Last updated 5 months ago.
microbiomesoftwaresequencingdnaseqatacseqcoveragenetwork
7.1 match 21 stars 6.64 score 23 scripts
marshalllab
MGDrivE2:Mosquito Gene Drive Explorer 2
A simulation modeling framework which significantly extends capabilities from the 'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets. For more information about 'MGDrivE', see our publication: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13318>. Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations, epidemiological dynamics, time-varying parameters, and a continuous-time simulation framework with various sampling algorithms for both deterministic and stochastic interpretations. 'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we suggest installing that package initially.
Maintained by Sean L. Wu. Last updated 4 years ago.
5.8 match 6 stars 6.33 score 30 scripts
richardgeveritt
ggsmc:Visualising Output from Sequential Monte Carlo and Ensemble-Based Methods
Functions for plotting, and animating, the output of importance samplers, sequential Monte Carlo samplers (SMC) and ensemble-based methods. The package can be used to plot and animate histograms, densities, scatter plots and time series, and to plot the genealogy of an SMC or ensemble-based algorithm. These functions all rely on algorithm output to be supplied in tidy format. A function is provided to transform algorithm output from matrix format (one Monte Carlo point per row) to the tidy format required by the plotting and animating functions.
Maintained by Richard G Everitt. Last updated 2 months ago.
6.4 match 4.48 score 6 scripts
kenaho1
asbio:A Collection of Statistical Tools for Biologists
Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Maintained by Ken Aho. Last updated 2 months ago.
3.4 match 5 stars 7.32 score 310 scripts 3 dependents
mrc-ide
odin:ODE Generation and Integration
Generate systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL). The DSL uses R's syntax, but compiles to C in order to efficiently solve the system. A solver is not provided, but instead interfaces to the packages 'deSolve' and 'dde' are generated. With these, while solving the differential equations, no allocations are done and the calculations remain entirely in compiled code. Alternatively, a model can be transpiled to R for use in contexts where a C compiler is not present. After compilation, models can be inspected to return information about parameters and outputs, or intermediate values after calculations. 'odin' is not targeted at any particular domain and is suitable for any system that can be expressed primarily as mathematical expressions. Additional support is provided for working with delays (delay differential equations, DDE), using interpolated functions during interpolation, and for integrating quantities that represent arrays.
Maintained by Rich FitzJohn. Last updated 9 months ago.
2.5 match 106 stars 9.74 score 290 scripts 3 dependents
cran
capn:Capital Asset Pricing for Nature
Implements approximation methods for natural capital asset prices suggested by Fenichel and Abbott (2014) <doi:10.1086/676034> in Journal of the Associations of Environmental and Resource Economists (JAERE), Fenichel et al. (2016) <doi:10.1073/pnas.1513779113> in Proceedings of the National Academy of Sciences (PNAS), and Yun et al. (2017) in PNAS (accepted), and their extensions: creating Chebyshev polynomial nodes and grids, calculating basis of Chebyshev polynomials, approximation and their simulations for: V-approximation (single and multiple stocks, PNAS), P-approximation (single stock, PNAS), and Pdot-approximation (single stock, JAERE). Development of this package was generously supported by the Knobloch Family Foundation.
Maintained by Seong Do Yun. Last updated 8 years ago.
17.1 match 1.38 score 24 scripts
mlysy
msde:Bayesian Inference for Multivariate Stochastic Differential Equations
Implements an MCMC sampler for the posterior distribution of arbitrary time-homogeneous multivariate stochastic differential equation (SDE) models with possibly latent components. The package provides a simple entry point to integrate user-defined models directly with the sampler's C++ code, and parallelizes large portions of the calculations when compiled with 'OpenMP'.
Maintained by Martin Lysy. Last updated 3 years ago.
4.8 match 4.91 score 27 scripts
surmann
ODEsensitivity:Sensitivity Analysis of Ordinary Differential Equations
Performs sensitivity analysis in ordinary differential equation (ode) models. The package utilize the ode interface from 'deSolve' and connects it with the sensitivity analysis from 'sensitivity'. Additionally we add a method to run the sensitivity analysis on variables with class 'ODEnetwork'. A detailed plotting function provides outputs on the calculations. The method is described by Weber, Theers, Surmann, Ligges, and Weihs (2018) <doi:10.17877/DE290R-18874>.
Maintained by Dirk Surmann. Last updated 6 years ago.
2.5 match 6 stars 5.47 score 49 scripts
roliveros-ramos
ibm:Individual Based Models in R
Implementation of some (simple) Individual Based Models and methods to create new ones, particularly for population dynamics models (reproduction, mortality and movement). The basic operations for the simulations are implemented in Rcpp for speed.
Maintained by Ricardo Oliveros-Ramos. Last updated 1 years ago.
3.6 match 1 stars 3.61 score 27 scripts
kevinegan31
ARGOS:Automatic Regression for Governing Equations (ARGOS)
Comprehensive set of tools for performing system identification of both linear and nonlinear dynamical systems directly from data. The Automatic Regression for Governing Equations (ARGOS) simplifies the complex task of constructing mathematical models of dynamical systems from observed input and output data, supporting various types of systems, including those described by ordinary differential equations. It employs optimal numerical derivatives for enhanced accuracy and employs formal variable selection techniques to help identify the most relevant variables, thereby enabling the development of predictive models for system behavior analysis.
Maintained by Kevin Egan. Last updated 1 years ago.
4.0 match 2 stars 3.00 score 3 scripts
pabrod
waydown:Computation of Approximate Potentials for Weakly Non-Gradient Fields
Computation of approximate potentials for both gradient and non gradient fields. It is known from physics that only gradient fields, also known as conservative, have a well defined potential function. Here we present an algorithm, based on the classical Helmholtz decomposition, to obtain an approximate potential function for non gradient fields. More information in Rodríguez-Sánchez (2020) <doi:10.1371/journal.pcbi.1007788>.
Maintained by Pablo Rodríguez-Sánchez. Last updated 1 years ago.
2.4 match 3 stars 4.18 score 6 scripts
fbrun-acta
ZeBook:Working with Dynamic Models for Agriculture and Environment
R package accompanying the book Working with dynamic models for agriculture and environment, by Daniel Wallach (INRA), David Makowski (INRA), James W. Jones (U.of Florida), Francois Brun (ACTA). 3rd edition 2018-09-27.
Maintained by Francois Brun. Last updated 6 years ago.
3.3 match 4 stars 2.37 score 59 scriptscran
EcoVirtual:Simulation of Ecological Models
Computer simulations of classical ecological models as a learning resource.
Maintained by Alexandre Adalardo de Oliveira. Last updated 6 years ago.
3.8 match 1.48 score 1 dependents