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Set up DAISIE_ML arguments

Source: R/setup_2type_model.R
setup_2type_model.Rd

Set up DAISIE_ML arguments

Usage

setup_2type_model(model, prop_type2_pool, low_rates = FALSE)

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

prop_type2_pool

A numeric determining the proportion of the mainland species pool that is composed on type 2 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.

Value

A named list with DAISIE::DAISIE_ML() arguments.

Author

Luis M Valente, Pedro Santos Neves, Joshua W. Lambert

Examples

model <- "cr_dd"
setup_model(
  model = model
)
#> $ddmodel
#> [1] 11
#> 
#> $idparsopt
#> lac  mu   k gam laa 
#>   1   2   3   4   5 
#> 
#> $parsfix
#> NULL
#> 
#> $idparsfix
#> NULL
#> 
#> $idparsnoshift
#> [1]  6  7  8  9 10
#> 
#> $initparsopt
#>          lac           mu            k          gam          laa 
#>   1.42422100   0.11442169 104.17502013   0.04743772   2.06825583 
#> 
#> $cs_version
#> [1] 1
#>