define_tolerance: Define tolerance values for ABC model in mcfly

In GabrielNakamura/mcfly: Simulation framework to estimate the influence of niche adaptation rate and dispersal limitation on species diversity distribution across environmental gradients

Define tolerance values for ABC model in mcfly

Description

Define tolerance values for ABC model in mcfly

Usage

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)
)

Arguments

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 renyi. Default is 1
niche.breadth	Numeric value indicating the width of niche of species in the metacommunity, as accepted by metasim. Default is 10
m	Numeric value indicating the immigration rate at each site, reported as Hubbel´s m. This is the same parameter accepted by metasim.
n.timestep	Numeric value indicating the number of timesteps used in the simulation of metacommunities, this is the same argument used in metasim. Default is 50, it is not recommended the use of lower values.
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 metasim. Default is "doc".
output.dir.path	Character indicating the name of directory to save simulations results and metadata used in metasim. Default is "einstein".
probs	Numeric indicating the quantiles to be used in tolerance distribution values. Default is c(0.8,0.9,0.95,0.99)

Value

A list containing the following objects:

Posterior	A numerical vector with posterior distribution
Tolerance	A numerical vector with tolerance values

GabrielNakamura/mcfly documentation built on July 27, 2023, 12:45 p.m.