Man pages for richelbilderbeek/beastscriptr
'BEAUti' from R

are_equivalent_xml_linesDetermine if XML lines result in equivalent trees
are_equivalent_xml_lines_allDetermine if XML lines result in equivalent trees
are_equivalent_xml_lines_loggersDetermine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_operatorsDetermine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_sectionDetermine if XML lines result in equivalent trees
bd_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
cbs_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
ccp_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
cep_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
create_alpha_paramCreate a parameter called alpha
create_bd_tree_priorCreate a Birth-Death tree prior
create_beast2_inputCreate a BEAST2 XML input text
create_beast2_input_1_12Create a BEAST2 XML input text, interface of v1.12
create_beast2_input_distr_lhCreates the likelihood section in the distribution section of...
create_beast2_input_distr_priorCreates the prior section in the distribution section of a...
create_beast2_input_fileCreate a BEAST2 input file
create_beast2_input_file_1_12Create a BEAST2 input file, interface of v1.12. This...
create_beast2_input_screenlogCreates the screenlog section of the logger section of a...
create_beast2_input_tracelogCreates the tracelog section of the logger section of a...
create_beast2_input_treelogsCreates the tracelog section of the logger section of a...
create_beast2_input_xmlCreates the xml section of a BEAST2 XML parameter file
create_beta_distrCreate a beta distribution
create_beta_paramCreate a parameter called beta
create_cbs_tree_priorCreate a Coalescent Bayesian Skyline tree prior
create_ccp_tree_priorCreate a Coalescent Constant Population tree prior
create_cep_tree_priorCreate a Coalescent Exponential Population tree prior
create_clock_modelGeneral function to create a clock model
create_clock_modelsCreates all supported clock models, which is just a list of...
create_clock_rate_paramCreate a parameter called 'clock_rate', as needed by...
create_distrGeneral function to create a distribution.
create_exp_distrCreate an exponential distribution
create_gamma_distrCreate a gamma distribution
create_gamma_site_modelCreate a gamma site model, part of a site model
create_gtr_site_modelCreate a GTR site model
create_hky_site_modelCreate an HKY site model
create_inv_gamma_distrCreate an inverse gamma distribution
create_jc69_site_modelCreate a JC69 site model
create_jc69_site_modelsCreates a JC69_site_model for each ID
create_kappa_1_paramCreate a parameter called kappa 1
create_kappa_2_paramCreate a parameter called kappa 2
create_lambda_paramCreate a parameter called lambda
create_laplace_distrCreate a Laplace distribution
create_log_normal_distrCreate a log-normal distribution
create_mcmcFunction to create the MCMC options, as in the BEAUti MCMC...
create_mean_paramCreate a parameter called mean
create_misc_optionsFunction to create a misc_options, containing miscellaneous...
create_m_paramCreate a parameter called m
create_mrca_priorCreate a Most Recent Common Ancestor prior
create_mu_paramCreate a parameter called mu
create_normal_distrCreate an normal distribution
create_one_div_x_distrCreate a 1/x distribution
create_paramGeneral function to create a parameter.
create_poisson_distrCreate a Poisson distribution
create_rate_ac_paramCreate a parameter called 'rate AC'
create_rate_ag_paramCreate a parameter called 'rate AG'
create_rate_at_paramCreate a parameter called 'rate AT'
create_rate_cg_paramCreate a parameter called 'rate CG'
create_rate_ct_paramCreate a parameter called 'rate CT'
create_rate_gt_paramCreate a parameter called 'rate GT'
create_rln_clock_modelCreate a relaxed log-normal clock model
create_rnd_alpha_paramCreate a random alpha parameter
create_rnd_bd_tree_priorCreate a random BD tree prior
create_rnd_beta_distrCreate a random beta distribution
create_rnd_beta_paramCreate a random beta parameter
create_rnd_boolCreate a random boolean
create_rnd_cbs_tree_priorCreate a random CBS tree prior
create_rnd_ccp_tree_priorCreate a random CCP tree prior
create_rnd_cep_tree_priorCreate a random CEP tree prior
create_rnd_clock_modelCreate a random clock model
create_rnd_clock_rate_paramCreate a random clock rate parameter
create_rnd_distrCreate a random distribution
create_rnd_estimateCreate a random value for 'estimate', which must be TRUE or...
create_rnd_exp_distrCreate a random exponential distribution
create_rnd_freq_equilibriumCreate a random value for 'freq equilibrium', which can be...
create_rnd_gamma_distrCreate a random gamma distribution
create_rnd_gamma_site_modelCreate a random gamma site model
create_rnd_gtr_site_modelCreate a random GTR site model
create_rnd_hky_site_modelCreate a random HKY site model
create_rnd_inv_gamma_distrCreate a random inverse-gamma distribution
create_rnd_jc69_site_modelCreate a random JC69 distribution
create_rnd_kappa_1_paramCreate a random kappa 1 parameter
create_rnd_kappa_2_paramCreate a random kappa 2 parameter
create_rnd_lambda_paramCreate a random lambda parameter
create_rnd_laplace_distrCreate a random Laplace distribution
create_rnd_log_normal_distrCreate a random log-normal distribution
create_rnd_mean_paramCreate a random mean parameter
create_rnd_m_paramCreate a random m parameter
create_rnd_mrca_priorCreate a random MRCA prior
create_rnd_mrca_priorsCreates a random MRCA prior option. This is either zero, one...
create_rnd_mu_paramCreate a random mu parameter
create_rnd_normal_distrCreate a random normal distribution
create_rnd_one_div_x_distrCreate a random 1/x distribution
create_rnd_paramCreate a random parameter
create_rnd_poisson_distrCreate a random Poisson distribution
create_rnd_rate_ac_paramCreate a random rate AC parameter
create_rnd_rate_ag_paramCreate a random rate AG parameter
create_rnd_rate_at_paramCreate a random rate AT parameter
create_rnd_rate_cg_paramCreate a random rate CG parameter
create_rnd_rate_ct_paramCreate a random rate CT parameter
create_rnd_rate_gt_paramCreate a random rate GT parameter
create_rnd_rln_clock_modelCreate a random RLN clock model
create_rnd_scale_paramCreate a random scale parameter
create_rnd_sigma_paramCreate a random sigma parameter
create_rnd_site_modelCreate a random site model
create_rnd_s_paramCreate a random s parameter
create_rnd_strict_clock_modelCreate a random strict clock model
create_rnd_tn93_site_modelCreate a random TN93 site model
create_rnd_tree_priorCreate a random tree prior
create_rnd_two_mrca_priorsCreates two MRCA priors, checked to be compatible
create_rnd_uniform_distrCreate a random uniform distribution
create_rnd_yule_tree_priorCreate a random Yule tree prior
create_scale_paramCreate a parameter called scale
create_sigma_paramCreate a parameter called sigma
create_site_modelGeneral function to create a site model.
create_site_modelsCreates all supported site models which is just a list of the...
create_s_paramCreate a parameter called s
create_strict_clock_modelCreate a strict clock model
create_strict_clock_modelsCreates n strict clock_models
create_tn93_site_modelCreate a TN93 site model
create_tree_priorInternal function to create a tree prior
create_tree_priorsCreates all supported tree priors, which is just a list of...
create_uniform_distrCreate a uniform distribution
create_yule_tree_priorCreate a Yule tree prior
create_yule_tree_priorsCreates n Yule tree priors
default_params_docThis function does nothing. It is intended to inherit is...
distr_to_xml_betaConverts a beta distribution to XML
distr_to_xml_expConverts an exponential distribution to XML
distr_to_xml_gammaConverts a gamma distribution to XML
distr_to_xml_inv_gammaConverts a inv_gamma distribution to XML
distr_to_xml_laplaceConverts a laplace distibution to XML
distr_to_xml_log_normalConverts a log-normal distribution to XML
distr_to_xml_normalConverts a normal distribution to XML
distr_to_xml_one_div_xConverts a 1/x distribution to XML
distr_to_xml_poissonConverts a poisson distribution to XML
distr_to_xml_uniformConverts a uniform distribution to XML
fastas_to_phylosCreate a random phylogeny, with the same taxa names as the...
fasta_to_phyloCreate a random phylogeny, with the same taxa names as the...
get_alignment_idGet the alignment ID from a FASTA filename
get_beautier_pathGet the full path of a file in the 'inst/extdata' folder
get_beautier_pathsGet the full paths of files in the 'inst/extdata' folder
get_fasta_filenameGet the path of a FASTA file used in testing
get_idConclude the ID from a FASTA filename
get_idsConclude the IDs from one or more FASTA filenames
get_taxa_namesExtract the names of taxa from a file
init_bd_tree_priorInitializes a Birth-Death tree prior
init_ccp_tree_priorInitializes a Coalescent Constant Population tree prior
init_cep_tree_priorInitializes a Coalescent Exponential Population tree prior
init_gtr_site_modelInitializes a GTR site model
init_hky_site_modelInitializes an HKY site model
init_jc69_site_modelInitializes a JC69 site model
init_rln_clock_modelInitializes a Relaxed Log-Normal clock model
init_strict_clock_modelInitializes a strict clock model
init_tn93_site_modelInitializes a TN93 site model
init_yule_tree_priorInitializes a Yule tree prior
is_init_beta_distrDetermine if x is an initialized beta distribution object as...
is_init_cep_tree_priorDetermine if x is an initialized Coalescent Exponential...
is_init_exp_distrDetermine if x is an initialized exponential distribution...
is_init_gamma_distrDetermine if x is an initialized gamma distribution object
is_init_inv_gamma_distrDetermine if x is an initialized inv_gamma distribution...
is_init_laplace_distrDetermine if x is an initialized laplace distribution object...
is_init_log_normal_distrDetermine if x is an initialized log_normal distribution...
is_init_normal_distrDetermine if x is an initialized normal distribution object...
is_init_one_div_x_distrDetermine if x is an initialized one_div_x distribution...
is_init_poisson_distrDetermine if x is an initialized poisson distribution object...
is_init_uniform_distrDetermine if x is an initialized uniform distribution object...
parameter_to_xml_alphaConverts an alpha parameter to XML
parameter_to_xml_betaConverts a beta parameter to XML
parameter_to_xml_clock_rateConverts a 'clockRate' parameter to XML
parameter_to_xml_kappa_1Converts a kappa 1 parameter to XML
parameter_to_xml_kappa_2Converts a kappa 2 parameter to XML
parameter_to_xml_lambdaConverts a lambda parameter to XML
parameter_to_xml_mConverts a m parameter to XML
parameter_to_xml_meanConverts a mean parameter to XML
parameter_to_xml_muConverts a mu parameter to XML
parameter_to_xml_rate_acConverts a 'rate AC' parameter to XML
parameter_to_xml_rate_agConverts a 'rate AG' parameter to XML
parameter_to_xml_rate_atConverts a 'rate AT' parameter to XML
parameter_to_xml_rate_cgConverts a 'rate CG' parameter to XML
parameter_to_xml_rate_ctConverts a 'rate CT' parameter to XML
parameter_to_xml_rate_gtConverts a 'rate GT' parameter to XML
parameter_to_xml_sConverts a s parameter to XML
parameter_to_xml_scaleConverts a scale parameter to XML
parameter_to_xml_sigmaConverts a sigma parameter to XML
yule_tree_prior_to_xml_prior_distrCreates the 'prior' section in the prior section of the prior...
richelbilderbeek/beastscriptr documentation built on May 19, 2018, 7:22 p.m.