bootstrap: Runs a bootstrapping on a DAISIE model to determine parameter...

In tece-lab/DAISIEutils: Utility Functions for the DAISIE Package

Runs a bootstrapping on a DAISIE model to determine parameter precision

Description

Runs a bootstrapping on a DAISIE model to determine parameter precision

Usage

bootstrap(
  daisie_data,
  data_name,
  model,
  array_index,
  cond,
  methode = "lsodes",
  optimmethod = "subplex",
  results_dir = NULL,
  test = FALSE
)

Arguments

daisie_data	A list, conforming to the DAISIE object format. Usually preprocessed by DAISIE::DAISIE_dataprep(), see it's documentation for details. Otherwise it may be generated via simulations, using DAISIE::DAISIE_sim_cr() and friends.
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.
cond	An integer specifying conditioning, as described in DAISIE::DAISIE_ML_CS().
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.
results_dir	A string with the path to the directory where results are to be stored or can be found. For example, if the data in question is (to be) stored in ⁠folder_with_res/$data_name⁠, then results_dir should be "folder_with_res". Defaults to NULL, which indicates the default directories are to be used. Default directories are: * ⁠$HOME/results/$data_name⁠ if on the cluster * ⁠getwd()/results/$data_name⁠ if called from another environment If is.na(results_dir), then the object is returned to the R session and not saved to file.
test	A boolean, defaults to FALSE. Set to TRUE for testing purposes, to fix the seed.

Value

Nothing. Writes bootstrapping results to a .rds file. This file is stored in ⁠$HOME/results/data_name⁠ if running on the cluster or ⁠/results/data_name⁠ if running locally. The directory is created if it doesn't exist.

Examples

## Not run: 
data(Galapagos_datalist, package = "DAISIE")
bootstrap(
  daisie_data = Galapagos_datalist,
  data_name = "Galapagos_datalist",
  model = "cr_dd",
  array_index = 1,
  cond = 1
)

## End(Not run)

tece-lab/DAISIEutils documentation built on Jan. 31, 2024, 12:09 p.m.