default_params_doc: Default parameters documentation
In tece-lab/DAISIEutils: Utility Functions for the DAISIE Package

default_params_doc

R Documentation

Default parameters documentation

Description

Default parameters documentation

Usage

default_params_doc(
  model,
  data_name,
  results_root_folder,
  daisie_data,
  array_index,
  file_path,
  results,
  cond,
  optimmethod,
  methode,
  model_1,
  model_2,
  model_1_lik_res,
  model_2_lik_res,
  model_lik_res,
  lik_res,
  data_names,
  full_output,
  seed,
  test,
  logs_path,
  results_dir,
  overall_results,
  sumstats,
  ylim4,
  title,
  ddmodel,
  verbose,
  island_ontogeny,
  eqmodel,
  tol,
  maxiter,
  x_E,
  x_I,
  mainland_n,
  low_rates,
  rep_index,
  res,
  prop_type2_pool,
  par_upper_bound
)

Arguments

`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
`data_name`	String. Will be used for the name of the created output folder.
`results_root_folder`	Character. A path to the root folder containing subfolders. Each subfolder contains result files for analysis runs.
`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.
`array_index`	A single numeric with the array index. It is used for naming the output file.
`file_path`	The system directory where the output files will be stored.
`results`	A data frame containing model results as created by `run_daisie_ml()`. These results are the `DAISIE::DAISIE_ML_CS()` and the bic, and they're saved as an RDS file by `run_daisie_ml()`.
`cond`	An integer specifying conditioning, as described in `DAISIE::DAISIE_ML_CS()`.
`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.
`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}()⁠`.
`model_1`	A string with model that should run. For a list of options see documentation for `model` parameter in `run_daisie_ml()`.
`model_2`	A string with model that should run. For a list of options see documentation for `model` parameter in `run_daisie_ml()`.
`model_1_lik_res`	A data frame with results from a DAISIE maximum likelihood model.
`model_2_lik_res`	A data frame with results from a DAISIE maximum likelihood model.
`model_lik_res`	A data frame with results from a DAISIE maximum likelihood model.
`lik_res`	A data frame with results from a DAISIE maximum likelihood model.
`data_names`	A vector of strings with the names of the data sets you want to compare sensitivity.
`full_output`	A boolean determining whether the full model output is returned.
`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.
`test`	A boolean, defaults to `FALSE`. Set to `TRUE` for testing purposes, to fix the seed.
`logs_path`	Character with path to the folder containing logs. Only log files should be present, in plain text format.
`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.
`overall_results`	summary results obtained with `summarize_bootstrap_results()`.
`sumstats`	vector with the number of species, number of colonization, size of the largest clade and the rank of the largest clade in the empirical data
`ylim4`	maximum of the plot of the rank of the largest clade.
`title`	title of the plot.
`ddmodel`	Sets the model of diversity-dependence: `ddmodel = 0`: no diversity dependence `ddmodel = 1`: linear dependence in speciation rate `ddmodel = 11`: linear dependence in speciation rate and in immigration rate `ddmodel = 2`: exponential dependence in speciation rate `ddmodel = 21`: exponential dependence in speciation rate and in immigration rate
`verbose`	In simulation and dataprep functions a logical, `Default = TRUE` gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed, `Default = 0` does not print, `verbose = 1` prints intermediate output of the parameters and loglikelihood, `verbose = 2` means also intermediate progress during loglikelihood computation is shown.
`island_ontogeny`	In `DAISIE_sim_time_dep()`, `DAISIE_ML_CS` and plotting a string describing the type of island ontogeny. Can be `"const"`, `"beta"` for a beta function describing area through time. In all other functions a numeric describing the type of island ontogeny. Can be `0` for constant, `1` for a beta function describing area through time. In ML functions `island_ontogeny = NA` assumes constant ontogeny. Time dependent estimation is not yet available as development is still ongoing. Will return an error if called in that case.
`eqmodel`	Sets the equilibrium constraint that can be used during the likelihood optimization. Only available for datatype = 'single'. eqmodel = 0 : no equilibrium is assumed eqmodel = 13 : near-equilibrium is assumed on endemics using deterministic equation for endemics and immigrants. Endemics must be within x_E of the equilibrium value eqmodel = 15 : near-equilibrium is assumed on endemics and immigrants using deterministic equation for endemics and immigrants. Endemics must be within x_E of the equilibrium value, while non-endemics must be within x_I of the equilibrium value.
`tol`	Sets the tolerances in the optimization. Consists of: `reltolx` - relative tolerance of parameter values in optimization. `reltolf` - relative tolerance of function value in optimization. `abstolx` - absolute tolerance of parameter values in optimization.
`maxiter`	Sets the maximum number of iterations in the optimization.
`x_E`	Sets the fraction of the equlibrium endemic diversity above which the endemics are assumed to be in equilibrium; only active for `eqmodel = 13` or `15`.
`x_I`	Sets the fraction of the equlibrium non-endemic diversity above which the system is assumed to be in equilibrium; only active for `eqmodel = 15`.
`mainland_n`	A numeric stating the number of mainland species, that is the number of species that can potentially colonize the island. If using a clade-specific diversity dependence, this value is set to 1 internally in the simulation. If using an island-wide diversity dependence, this value is set to the number of mainland species.
`low_rates`	Boolean determining whether the random sampling of initial parameter estimates should be sampled from a broad range (FALSE) or from a restricted range where the initial rates a ensured to be smaller (TRUE). The latter helps when using large datasets that may fail the initial likelihood computation with higher rates that could be sampled from the broad range of rates.
`rep_index`	A string which by default is "NULL" (it is a string and not a true NULL due to being passed from the command line), or can be a string of a numeric which is used to detect whether multiple data set from the same data source is being run. This is the case, for example, when fitting a DAISIE model to a posterior distribution of data.
`res`	A numeric determining the resolution of the likelihood calculations, it sets the limit for the maximum number of species for which a probability must be computed, which must be larger than the size of the largest clade.
`prop_type2_pool`	A numeric determining the proportion of the mainland species pool that is composed on type 2 species.
`par_upper_bound`	A numeric defining the upper limit of the integration of a parameter when fitting the relaxed-rate DAISIE model. If the DAISIE model being applied is not the relaxed-rate model, this parameter can be ignored and left as its default as it does not influence the model.