| ecolottery-package {ecolottery} | R Documentation |
Coalescent-Based Simulation of Ecological Communities
Description
Coalescent-Based Simulation of Ecological Communities as proposed by Munoz et al. (2017) <doi:10.13140/RG.2.2.31737.26728>. The package includes a tool for estimating parameters of community assembly by using Approximate Bayesian Computation.
Details
The DESCRIPTION file:
| Package: | ecolottery |
| Type: | Package |
| Title: | Coalescent-Based Simulation of Ecological Communities |
| Version: | 1.0.0 |
| Authors@R: | c(person("François", "Munoz", role = c("aut", "cre"), email = "francois.munoz@hotmail.fr"), person("Matthias", "Grenié", role = "aut"), person("Pierre", "Denelle", role = "aut"), person("Adrien", "Taudière", role = "ctb"), person("Fabien", "Laroche", role = "ctb"), person("Caroline", "Tucker", role = "ctb"), person("Cyrille", "Violle", role = "ctb")) |
| URL: | https://github.com/frmunoz/ecolottery |
| BugReports: | https://github.com/frmunoz/ecolottery/issues |
| Depends: | R (>= 3.0.2) |
| Imports: | abc, stats, graphics, ggplot2, grDevices, parallel |
| Suggests: | ape, changepoint, knitr, picante, rmarkdown, testthat, untb, vegan |
| Description: | Coalescent-Based Simulation of Ecological Communities as proposed by Munoz et al. (2017) <doi:10.13140/RG.2.2.31737.26728>. The package includes a tool for estimating parameters of community assembly by using Approximate Bayesian Computation. |
| License: | GPL (>= 2) |
| Encoding: | UTF-8 |
| VignetteBuilder: | knitr |
| RoxygenNote: | 6.0.1 |
| Author: | François Munoz [aut, cre], Matthias Grenié [aut], Pierre Denelle [aut], Adrien Taudière [ctb], Fabien Laroche [ctb], Caroline Tucker [ctb], Cyrille Violle [ctb] |
| Maintainer: | NA |
Index of help topics:
abund Compute absolute and relative abundances in the
local community and the reference pool
coalesc Coalescent-based simulation of ecological
communities undergoing both neutral and
niche-base dynamics
coalesc_abc Estimation of neutral and non-neutral
parameters of community assembly using
Approximate Bayesian Computation (ABC)
ecolottery-package Coalescent-Based Simulation of Ecological
Communities
forward Simulation of neutral and niche-based community
dynamics forward in time
plot_comm Regional vs. Local trait distributions of
abundances
tcor Generates Correlated Traits
Two basic functions: coalesc for coalescent-based simulation, and forward for forward-in-time simulation
Author(s)
NA
Maintainer: NA
References
Hurtt, G. C. and S. W. Pacala (1995). "The consequences of recruitment limitation: reconciling chance, history and competitive differences between plants." Journal of Theoretical Biology 176(1): 1-12.
Hubbell, S. P. (2001). "The Unified Neutral Theory of Biodiversity". Princeton University Press.
Gravel, D., C. D. Canham, M. Beaudet and C. Messier (2006). "Reconciling niche and neutrality: the continuum hypothesis." Ecology Letters 9(4): 399-409.
Munoz, F., P. Couteron, B. R. Ramesh and R. S. Etienne (2007). "Estimating parameters of neutral communities: from one Single Large to Several Small samples." Ecology 88(10): 2482-2488.
Munoz, F., B. R. Ramesh and P. Couteron (2014). "How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions?" Ecology 95(8): 2179-2191.
Examples
## Coalescent-based simulation of stabilizing habitat filtering around
## t = 0.5
J <- 100; theta <- 50; m <- 0.5;
comm <- coalesc(J, m, theta, filt = function(x) 0.5 - abs(0.5 - x))
plot_comm(comm)
## Forward-in-time simulation of stabilizing habitat filtering around
## t = 0.5, over 100 time steps
# A regional pool including 100 species each including 10 individuals
pool <- sort(rep(as.character(1:100), 10))
# Initial community composed of 10 species each including 10 individuals,
# with trait information for niche-based dynamics
initial <- data.frame(sp = sort(rep(as.character(1:10), 10)),
trait = runif(100))
final <- forward(initial = initial, prob = 0.5, gens = 100, pool = pool,
filt = function(x) 0.5 - abs(0.5 - x))
plot_comm(final)