Skip to contents

Internal function

Source: R/site_model_to_xml_prior.R
site_model_to_xml_prior_distr.Rd

Converts a site model to XML, used in the prior section

Usage

site_model_to_xml_prior_distr(site_model, beauti_options)

Arguments

site_model

a site model, as returned by create_site_model

beauti_options

one BEAUti options object, as returned by create_beauti_options

Value

the site model as XML text

Author

Richèl J.C. Bilderbeek

Examples

site_model_to_xml_prior_distr(
  site_model = create_jc69_site_model(id = 1),
  beauti_options = create_beauti_options()
)
#> NULL
site_model_to_xml_prior_distr(
  site_model = create_hky_site_model(
    id = 1,
    kappa_prior_distr = create_uniform_distr(id = 2)
  ),
  beauti_options = create_beauti_options()
)
#> [1] "<prior id=\"KappaPrior.s:1\" name=\"distribution\" x=\"@kappa.s:1\">"
#> [2] "    <Uniform id=\"Uniform.2\" name=\"distr\" upper=\"Infinity\"/>"   
#> [3] "</prior>"                                                            
site_model_to_xml_prior_distr(
  site_model = create_tn93_site_model(
    id = 1,
    kappa_1_prior_distr = create_uniform_distr(id = 2),
    kappa_2_prior_distr = create_uniform_distr(id = 3)
  ),
  beauti_options = create_beauti_options()
)
#> [1] "<prior id=\"kappa1Prior.s:1\" name=\"distribution\" x=\"@kappa1.s:1\">"
#> [2] "    <Uniform id=\"Uniform.2\" name=\"distr\" upper=\"Infinity\"/>"     
#> [3] "</prior>"                                                              
#> [4] "<prior id=\"kappa2Prior.s:1\" name=\"distribution\" x=\"@kappa2.s:1\">"
#> [5] "    <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"Infinity\"/>"     
#> [6] "</prior>"                                                              
site_model_to_xml_prior_distr(
  site_model = create_gtr_site_model(
    id = 1,
    rate_ac_prior_distr = create_uniform_distr(id = 2),
    rate_ag_prior_distr = create_uniform_distr(id = 3),
    rate_at_prior_distr = create_uniform_distr(id = 4),
    rate_cg_prior_distr = create_uniform_distr(id = 5),
    rate_gt_prior_distr = create_uniform_distr(id = 6)
  ),
  beauti_options = create_beauti_options()
)
#>  [1] "<prior id=\"RateACPrior.s:1\" name=\"distribution\" x=\"@rateAC.s:1\">"
#>  [2] "    <Uniform id=\"Uniform.2\" name=\"distr\" upper=\"Infinity\"/>"     
#>  [3] "</prior>"                                                              
#>  [4] "<prior id=\"RateAGPrior.s:1\" name=\"distribution\" x=\"@rateAG.s:1\">"
#>  [5] "    <Uniform id=\"Uniform.3\" name=\"distr\" upper=\"Infinity\"/>"     
#>  [6] "</prior>"                                                              
#>  [7] "<prior id=\"RateATPrior.s:1\" name=\"distribution\" x=\"@rateAT.s:1\">"
#>  [8] "    <Uniform id=\"Uniform.4\" name=\"distr\" upper=\"Infinity\"/>"     
#>  [9] "</prior>"                                                              
#> [10] "<prior id=\"RateCGPrior.s:1\" name=\"distribution\" x=\"@rateCG.s:1\">"
#> [11] "    <Uniform id=\"Uniform.5\" name=\"distr\" upper=\"Infinity\"/>"     
#> [12] "</prior>"                                                              
#> [13] "<prior id=\"RateGTPrior.s:1\" name=\"distribution\" x=\"@rateGT.s:1\">"
#> [14] "    <Uniform id=\"Uniform.6\" name=\"distr\" upper=\"Infinity\"/>"     
#> [15] "</prior>"