Description Usage Arguments Value Author(s)

View source: R/cluster_ssh_functions.R

Returns a matrix containing all possible permutations of parameters input by the user. Each line of the matrix can then be used to initialize an experiment.

1 2 3 4 5 6 | ```
experiment_setup(time = c(2, 3, 6), M = 1000, lac = c(7.48223 *
10^-6, 2.24467e-05, 7.48223e-05), mu = c(1), K = c(100/13500,
30/13500, 10/13500), gam = c(0.001), laa = c(1),
island_ontogeny = "beta", replicates = 1000, mu_min = 0.1,
mu_max = mu_min + mu_min * 0.1, Amax = c(13500), Apeak = c(0.1),
Asharpness = c(1), Atotalage = c(9), divdepmodel = 1)
``` |

`time` |
Numeric vector containing length of the simulation in time units. For example, if an island is know to be 4 million years old, setting time = 4 will simulate entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island. |

`M` |
Numeric vector containing the size of the mainland pool, i.e the number of species that can potentially colonize the island |

`lac` |
Numeric vector containing the cladogenesis rate (lambda^c) |

`mu` |
Numeric vector containing the extinction rate. Used only on non ontogeny scenarios. |

`K` |
Numeric vector containing the carrying capacity (clade level).
Set |

`gam` |
Numeric vector containing the immigration rate (gamma) |

`laa` |
Numeric vector containing the anagenesis rate (lambda^a) |

`island_ontogeny` |
Vector of strings or |

`replicates` |
Numeric vector specifying how many replicates should be run for each experiment |

`mu_min` |
Numeric vector containing the minimum extinction when area is at peak, used only on ontogeny scenarios |

`mu_max` |
Numeric vector containing the extinction rate when current area is 0.10 of maximum area, used only on ontogeny scenarios |

`Amax` |
Numeric vector containing the maximum area, used only on ontogeny scenarios |

`Apeak` |
Numeric vector containing the value from 0 to 1 indicating where in the island's history the peak area is achieved, used only on ontogeny scenarios |

`Asharpness` |
Numeric vector containing the sharpness of peak, used only on ontogeny scenarios |

`Atotalage` |
Numeric vector containing the total island age, used only on ontogeny scenarios |

`divdepmodel` |
Numeric vector specifying the type of diversity
dependence. |

Matrix with all possible combinations of experiment setups

Giovanni Laudanno, Pedro Neves

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