execute_next_setup: Execute experimental setup
In Neves-P/utilSIE: Utility Functions for DAISIE

Description Usage Arguments Value Author(s)

Prepares and executes the one or a set of experiments to be run on the Peregrine HPC at the University of Groningen. # nolint

execute_next_setup(project_name = utilSIE::get_project_name(),
  account = utilSIE::get_available_accounts(), download_files = TRUE,
  partition = "gelifes", 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),
  divdepmodel = 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),
  complete_analysis = FALSE, branch = "@develop", force = FALSE)

`project_name`	String containing project name as returned by `get_project_name`.
`account`	String with p-number to be used for connecting with peregrine. Use as returned by `get_available_accounts`.
`download_files`	Boolean stating if files in cluster should be downloaded locally before new analysis is run. Default is `TRUE`. If downloaded, files are removed from peregrine.
`partition`	String with peregrine partition name that shuold be used. Defaults to `"gelifes"`. Can be `"regular"` or `"short"`.
`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 `K = Inf` for no diversity dependence.
`gam`	Numeric vector containing the immigration rate (gamma)
`laa`	Numeric vector containing the anagenesis rate (lambda^a)
`divdepmodel`	Numeric vector specifying the type of diversity dependence. `divdepmodel = "CS"` runs a model with clade-specific carrying capacity, where diversity-dependence operates only within single clades, i.e. only among species originating from the same mainland colonist. Option divdepmodel = 'IW' runs a model with island-wide carrying capacity, where diversity-dependence operates within and among clades.
`island_ontogeny`	Vector of strings or `NULL` indicating type of island ontogeny process. Can be `"beta"`. For no ontogeny `NULL` is used.
`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
`complete_analysis`	Boolean stating if a ML run from simulation output generated with current parameters should be started as soon as simulations are over.
`branch`	String with branch of github repository to be used for installation. Default is `"@develop"`.
`force`	Boolean stating if package should be force installed from github. See `install_github` for details.