View source: R/define_tolerance.R

define_tolerance | R Documentation |

Define tolerance values for ABC model in mcfly

define_tolerance( comm, phylo, envir, xy.coords, occurrence, entropy.order, niche.breadth = 10, m = 0.5, n.timestep = 50, OU.alpha = c("uniform", "half-life"), max.sample.size.prior = 100 * parallel, sample.size.posterior = 20 * parallel, parallel = NULL, scenario.ID = "doc", output.dir.path = "einstein", probs = c(0.8, 0.9, 0.95, 0.99) )

`comm` |
Matrix containing occurrences or abundances of species in sites. Species in columns and sites in rows. |

`phylo` |
Newick object containing the phylogenetic relationship among species. |

`envir` |
A one column matrix containing environmental variable for each community |

`xy.coords` |
A two column matrix containing the coordinates of each community |

`occurrence` |
Logical argument (TRUE or FALSE) indicating if community matrix must be transformed to presence/absence |

`entropy.order` |
Numeric value indicating the scale of Rényi diversity, as accepted by |

`niche.breadth` |
Numeric value indicating the width of niche of species in the metacommunity, as accepted by |

`m` |
Numeric value indicating the immigration rate at each site, reported as Hubbel´s m. This is the same parameter accepted by |

`n.timestep` |
Numeric value indicating the number of timesteps used in the simulation of metacommunities,
this is the same argument used in |

`OU.alpha` |
Character indicating the type of prior that will be used in ABC model. The options were "uniform" for a uniform sample of alpha values and "half-life" for a prior of alpha values represented as being half-life values, calculated as being log(). |

`max.sample.size.prior` |
Numeric indicating the maximum number of sampling in prior distribution. Default is 100 times the number of parallel process. |

`sample.size.posterior` |
Numeric value that defines the minimum size of the posterior distribution. Default is 240. |

`parallel` |
Numerical value indicating the numbers of cores that must be used in the parallel computation. Default is NULL, indicating that the calculations of ABC model will not be parallelized. |

`scenario.ID` |
Character indicating the name of the simulation scenario. The same as used in |

`output.dir.path` |
Character indicating the name of directory to save simulations results and metadata used in |

`probs` |
Numeric indicating the quantiles to be used in tolerance distribution values. Default is c(0.8,0.9,0.95,0.99) |

A list containing the following objects:

`Posterior` |
A numerical vector with posterior distribution |

`Tolerance` |
A numerical vector with tolerance values |

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