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Print session and run info to console/log file

Source: R/print_metadata.R
print_metadata.Rd

Useful to call as at the start of normal job scripts to run on the cluster so that metadata is recorded in the log files.

Usage

print_metadata(data_name, model, array_index, seed, methode, optimmethod)

Arguments

data_name

String. Will be used for the name of the created output folder.

model

A string with model that should run. Models are as follows:

  • "cr_dd" Clade specific model - diversity dependent. All parameters free.

  • "cr_di" Clade specific model - diversity independent (K = Inf). All other parameters free.

  • "cr_dd_0laa" Clade specific model - diversity dependent and no anagenesis (laa fixed to zero). All other parameters free.

  • "cr_di_0laa" Clade specific model - diversity independent (K = Inf) and no anagenesis (laa fixed to zero). All other parameters free.

  • "cr_di_0lac" Clade specific model - diversity indendent (K = Inf) and no cladogenesis (lac fixed to zero). All other parameters free.

  • "cr_dd_0lac" Clade specific model - diversity dependent and no cladogenesis (lac fixed to zero). All other parameters free.

  • "rr_lac_di" Clade specific model - diversity independent (K = Inf) and relaxed cladogenesis. All other parameters free.

  • "rr_lac_dd" Clade specific model - diversity dependent and relaxed cladogenesis. All other parameters free.

  • "rr_mu_di" Clade specific model - diversity independent (K = Inf) and relaxed extinction. All other parameters free.

  • "rr_mu_dd" Clade specific model - diversity dependent and relaxed extinction. All other parameters free.

  • "rr_k" Clade specific model - diversity dependent and relaxed carrying capacity. All other parameters free.

  • "rr_gam_di" Clade specific model - diversity independent (K = Inf) and relaxed colonisation. All other parameters free.

  • "rr_gam_dd" Clade specific model - diversity dependent and relaxed colonisation. All other parameters free.

  • "rr_laa_di" Clade specific model - diversity independent (K = Inf) and relaxed anagenesis. All other parameters free.

  • "rr_laa_dd" Clade specific model - diversity dependent and relaxed anagenesis. All other parameters free.

  • "rr_mu_di_0lac" Clade specific model - diversity independent, relaxed extinction, and no cladogenesis (lac fixed to zero). All other parameters free.

  • "rr_mu_dd_0lac" Clade specific model - diversity dependent, relaxed extinction, and no cladogenesis (lac fixed to zero). All other parameters free.

  • "rr_k_0lac" Clade specific model - diversity dependent, relaxed carrying capacity, and no cladogenesis (lac fixed to zero). All other parameters free.

  • "rr_gam_di_0lac" Clade specific model - diversity independent, relaxed colonisation, and no cladogenesis (lac fixed to zero). All other parameters free.

  • "r_gam_dd_0lac" Clade specific model - diversity dependent, relaxed colonisation, and no cladogenesis (lac fixed to zero). All other parameters free.

  • "rr_laa_di_0lac" Clade specific model - diversity independent, relaxed anagenesis, and no cladogenesis (lac fixed to zero). All other parameters free.

  • "r_laa_dd_0lac" Clade specific model - diversity dependent, relaxed anagenesis, and no cladogenesis (lac fixed to zero). All other parameters free.

  • "rr_lac_di_0laa" Clade specific model - diversity independent, relaxed cladogenesis, and no anagenesis (laa fixed to zero)

  • "rr_lac_dd_0laa" Clade specific model - diversity dependent

  • "rr_mu_di_0laa" Clade specific model - diversity independent

  • "rr_mu_dd_0laa" Clade specific model - diversity dependent

  • "rr_k_0laa" Clade specific model - diversity dependent

  • "rr_gam_di_0laa" Clade specific model - diversity independent, relaxed colonisation, and no anagenesis (laa fixed to zero). All other parameters free

  • "rr_gam_dd_0laa" Clade specific model - diversity dependent, relaxed colonisation, and no anagenesis (laa fixed to zero). All other parameters free

array_index

A single numeric with the array index. It is used for naming the output file.

seed

Integer with value to be used as the seed for Mersenne-Twister. This value is determined by Sys.time() and array_index to ensure parallel jobs have different seeds. Only the last 6 digits of the Sys.time() (as an integer) are used.

methode

Method of the ODE-solver. Supported Boost ODEINT solvers (steppers) are: "odeint::runge_kutta_cash_karp54" "odeint::runge_kutta_fehlberg78" "odeint::runge_kutta_dopri5" "odeint::bulirsch_stoer" without odeint::-prefix, \link{deSolve}{ode}() method is assumed. The default method overall is "lsodes" for \link{DAISIE_ML_CS}() and "ode45" from \link[deSolve]{ode}() for \link{DAISIE_ML_IW}().

optimmethod

Method used in likelihood optimization. Default is subplex (see \link[subplex]{subplex}() for full details). Alternative is "simplex" which was the method in previous versions.

Value

Nothing. Prints session and run info used by DAISIE to console.

Note

Message is used to print function arguments. To retain formatting, a simple sessioninfo::session_info() is used for session info, which uses print. Hence, session_info() will go on stdout, while the remaining output of this function will go to stderr.

Author

Pedro Santos Neves, Luis Valente, Joshua W. Lambert

Examples

if (FALSE) {
print_metadata(
  data_name = "Galapagos_datalist",
  model = "cr_di",
  array_index = 1,
  seed = 1
)
}