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Creates the distribution section of a BEAST2 XML parameter file.

Source: R/create_beast2_input_distr.R
create_beast2_input_distr.Rd

Creates the distribution section of a BEAST2 XML parameter file.

Usage

create_beast2_input_distr(inference_model)

Arguments

inference_model

a Bayesian phylogenetic inference model. An inference model is the complete model setup in which a site model, clock model, tree prior and more are specified. Use create_inference_model to create an inference model. Use check_inference_model to check if an inference model is valid. Use rename_inference_model_filenames to rename the files in an inference model.

Value

lines of XML text

Note

this function is not intended for regular use, thus its long name length is accepted

See also

create_beast2_input

Author

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

inference_model <- init_inference_model(
  input_filename = get_fasta_filename(),
  inference_model = create_inference_model(
    beauti_options = create_beauti_options_v2_4()
  )
)
create_beast2_input_distr(
  inference_model = inference_model
)
#>  [1] "<distribution id=\"posterior\" spec=\"util.CompoundDistribution\">"                                                                                                                
#>  [2] "    <distribution id=\"prior\" spec=\"util.CompoundDistribution\">"                                                                                                                
#>  [3] "        <distribution id=\"YuleModel.t:test_output_0\" spec=\"beast.evolution.speciation.YuleModel\" birthDiffRate=\"@birthRate.t:test_output_0\" tree=\"@Tree.t:test_output_0\"/>"
#>  [4] "        <prior id=\"YuleBirthRatePrior.t:test_output_0\" name=\"distribution\" x=\"@birthRate.t:test_output_0\">"                                                                  
#>  [5] "            <Uniform id=\"Uniform.100\" name=\"distr\" upper=\"Infinity\"/>"                                                                                                       
#>  [6] "        </prior>"                                                                                                                                                                  
#>  [7] "    </distribution>"                                                                                                                                                               
#>  [8] "    <distribution id=\"likelihood\" spec=\"util.CompoundDistribution\" useThreads=\"true\">"                                                                                       
#>  [9] "        <distribution id=\"treeLikelihood.test_output_0\" spec=\"ThreadedTreeLikelihood\" data=\"@test_output_0\" tree=\"@Tree.t:test_output_0\">"                                 
#> [10] "            <siteModel id=\"SiteModel.s:test_output_0\" spec=\"SiteModel\">"                                                                                                       
#> [11] "                <parameter id=\"mutationRate.s:test_output_0\" estimate=\"false\" name=\"mutationRate\">1.0</parameter>"                                                           
#> [12] "                <parameter id=\"gammaShape.s:test_output_0\" estimate=\"false\" name=\"shape\">1.0</parameter>"                                                                    
#> [13] "                <parameter id=\"proportionInvariant.s:test_output_0\" estimate=\"false\" lower=\"0.0\" name=\"proportionInvariant\" upper=\"1.0\">0.0</parameter>"                 
#> [14] "                <substModel id=\"JC69.s:test_output_0\" spec=\"JukesCantor\"/>"                                                                                                    
#> [15] "            </siteModel>"                                                                                                                                                          
#> [16] "            <branchRateModel id=\"StrictClock.c:test_output_0\" spec=\"beast.evolution.branchratemodel.StrictClockModel\">"                                                        
#> [17] "                <parameter id=\"clockRate.c:test_output_0\" estimate=\"false\" name=\"clock.rate\">1.0</parameter>"                                                                
#> [18] "            </branchRateModel>"                                                                                                                                                    
#> [19] "        </distribution>"                                                                                                                                                           
#> [20] "    </distribution>"                                                                                                                                                               
#> [21] "</distribution>"                                                                                                                                                                   
 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()