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The package was\noriginally developed to support the 'Propensity to Cycle Tool',\na publicly available strategic cycle network planning tool\n(Lovelace et al. 2017) , but has\nsince been extended to support public transport routing and\naccessibility analysis (Moreno-Monroy et al. 2017)\n and routing with locally\nhosted routing engines such as 'OSRM' (Lowans et al. 2023)\n. The main functions are\nfor creating and manipulating geographic \"desire lines\" from\norigin-destination (OD) data (building on the 'od' package);\ncalculating routes on the transport network locally and via\ninterfaces to routing services such as\n (Desjardins et al. 2021)\n; and calculating route segment\nattributes such as bearing. The package implements the 'travel\nflow aggregration' method described in Morgan and Lovelace\n(2020) and the 'OD jittering'\nmethod described in Lovelace et al. (2022)\n. 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*[Stable]*","topics":["vis_drake_graph"]},{"page":"which_clean","title":"Which targets will 'clean()' invalidate? *[Stable]*","topics":["which_clean"]}],"_pkglogo":"https://github.com/ropensci/drake/raw/main/man/figures/logo.svg","_readme":"https://github.com/ropensci/drake/raw/main/README.md","_rundeps":["backports","base64url","cli","cpp11","digest","filelock","glue","igraph","lattice","lifecycle","magrittr","Matrix","pkgconfig","R6","rlang","storr","tidyselect","txtq","vctrs","withr"],"_score":11.437714415509445,"_indexed":true,"_nocasepkg":"drake","_universes":["ropensci","wlandau"]} {"Package":"MODIStsp","Title":"Find, Download and Process MODIS Land Products Data","Type":"Package","Version":"2.1.0","Authors@R":"c(person(\"Lorenzo\", \"Busetto\", \nrole = c(\"aut\"),\ncomment = c(ORCID = '0000-0001-9634-6038')),\nperson(\"Luigi\", \"Ranghetti\",\nemail = \"rpackages.ranghetti@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = '0000-0001-6207-5188')),\nperson(\"Leah\", 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Call the 'Cloud Translation' API\n for detection and\ntranslation of text, the 'Natural Language' API\n to analyse text\nfor sentiment, entities or syntax, the 'Cloud Speech' API\n to transcribe sound files to\ntext and the 'Cloud Text-to-Speech' API\n to turn text into\nsound files.","URL":"http://code.markedmondson.me/googleLanguageR/,\nhttps://github.com/ropensci/googleLanguageR,\nhttps://docs.ropensci.org/googleLanguageR/","BugReports":"https://github.com/ropensci/googleLanguageR/issues","License":"MIT + file LICENSE","Encoding":"UTF-8","RoxygenNote":"7.2.3","VignetteBuilder":"knitr","Config/pak/sysreqs":"make libssl-dev","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/googleLanguageR","RemoteRef":"master","RemoteSha":"7c6f93b0977ac7ac2189a6b5648362b12509c953","NeedsCompilation":"no","Packaged":{"Date":"2024-11-14 04:59:57 UTC","User":"root"},"Author":"Aleksander Dietrichson [ctb],\nMark Edmondson [aut, cre],\nJohn Muschelli [ctb],\nNeal 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The work loop\ntechnique is used to evaluate the mechanical work and power\noutput of muscle. Josephson (1985) \nmodernized the technique for application in comparative\nbiomechanics. Although our initial motivation was to provide\nfunctions to analyze work loop experiment data, as we developed\nthe package we incorporated the ability to analyze data from\nexperiments that are often complementary to work loops. There\nare currently three supported experiment types: work loops,\nsimple twitches, and tetanus trials. Data can be imported\ndirectly from .ddf files or via an object constructor function.\nThrough either method, data can then be cleaned or transformed\nvia methods typically used in studies of muscle physiology.\nData can then be analyzed to determine the timing and magnitude\nof force development and relaxation (for isometric trials) or\nthe magnitude of work, net power, and instantaneous power among\nother things (for work loops). 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prior.","topics":["check_mrca_prior"]},{"page":"check_mrca_prior_name","title":"Check if 'mrca_prior_name' is a valid MRCA prior name.","topics":["check_mrca_prior_name"]},{"page":"check_mrca_prior_names","title":"Check if the MRCA prior, which is a list, has all the named elements.","topics":["check_mrca_prior_names"]},{"page":"check_mrca_prior_taxa_names","title":"Check the MRCA prior's taxon names are valid.","topics":["check_mrca_prior_taxa_names"]},{"page":"check_ns_mcmc","title":"Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.","topics":["check_mcmc_nested_sampling","check_nested_sampling_mcmc","check_ns_mcmc"]},{"page":"check_param","title":"Check if the parameter is a valid parameter","topics":["check_param"]},{"page":"check_param_names","title":"Check if the 'param' has the list elements of a valid 'param' object.","topics":["check_param_names"]},{"page":"check_param_types","title":"Check if the 'param' has the list elements of the right type for a valid 'param' object.","topics":["check_param_types"]},{"page":"check_phylogeny","title":"Check if the phylogeny is a valid phylogeny object.","topics":["check_phylogeny"]},{"page":"check_rename_fun","title":"Check if the rename function is a valid filename rename function","topics":["check_rename_fun"]},{"page":"check_rln_clock_model","title":"Check if the clock model is a valid clock model.","topics":["check_rln_clock_model"]},{"page":"check_screenlog","title":"Check if a 'screenlog' is valid.","topics":["check_screenlog"]},{"page":"check_screenlog_names","title":"Check if the 'screenlog' has the list elements of a valid 'screenlog' object.","topics":["check_screenlog_names"]},{"page":"check_screenlog_values","title":"Check if the screenlog has the list elements with valid values for being a valid screenlog object.","topics":["check_screenlog_values"]},{"page":"check_site_model","title":"Check if the site model is a valid site model","topics":["check_site_model"]},{"page":"check_site_model_names","title":"Check if the 'site_model' has the list elements of a valid 'site_model' object.","topics":["check_site_model_names"]},{"page":"check_site_model_types","title":"Check if the 'site_model' has the list elements of the right type for a valid 'site_model' object.","topics":["check_site_model_types"]},{"page":"check_site_models","title":"Check if the object is a list of one or more site models.","topics":["check_site_models"]},{"page":"check_store_every","title":"Check if 'store_every' holds a valid value","topics":["check_store_every"]},{"page":"check_strict_clock_model","title":"Check if the clock model is a valid clock model.","topics":["check_strict_clock_model"]},{"page":"check_tn93_site_model","title":"Check if the 'tn93_site_model' is a valid TN93 nucleotide substitution model.","topics":["check_tn93_site_model"]},{"page":"check_tn93_site_model_names","title":"Check if the 'tn93_site_model' has the list elements of a valid 'tn93_site_model' object.","topics":["check_tn93_site_model_names"]},{"page":"check_tracelog","title":"Check if a 'tracelog' is valid.","topics":["check_tracelog"]},{"page":"check_tracelog_names","title":"Check if the 'tracelog' has the list elements of a valid 'tracelog' object.","topics":["check_tracelog_names"]},{"page":"check_tracelog_values","title":"Check if the tracelog has the list elements with valid values for being a valid tracelog object.","topics":["check_tracelog_values"]},{"page":"check_tree_prior","title":"Check if the tree prior is a valid tree prior","topics":["check_tree_prior"]},{"page":"check_tree_priors","title":"Check if the object is a list of one or more tree priors.","topics":["check_tree_priors"]},{"page":"check_treelog","title":"Check if a 'treelog' is valid.","topics":["check_treelog"]},{"page":"check_treelog_names","title":"Check if the 'treelog' has the list elements of a valid 'treelog' object.","topics":["check_treelog_names"]},{"page":"check_treelog_values","title":"Check if the treelog has the list elements with valid values for being a valid treelog object.","topics":["check_treelog_values"]},{"page":"clock_model_to_xml_operators","title":"Internal function","topics":["clock_model_to_xml_operators"]},{"page":"clock_model_to_xml_prior_distr","title":"Internal function","topics":["clock_model_to_xml_prior_distr"]},{"page":"clock_model_to_xml_state","title":"Internal function","topics":["clock_model_to_xml_state"]},{"page":"clock_model_to_xml_tracelog","title":"Internal function","topics":["clock_model_to_xml_tracelog"]},{"page":"clock_model_to_xml_treelogger","title":"Convert a clock model to the XML of the 'TreeLogger'","topics":["clock_model_to_xml_treelogger"]},{"page":"clock_rate_param_to_xml","title":"Internal function","topics":["clock_rate_param_to_xml"]},{"page":"compare_lines","title":"Internal function","topics":["compare_lines"]},{"page":"count_trailing_spaces","title":"Count the number of spaces before the first character","topics":["count_trailing_spaces"]},{"page":"create_alpha_param","title":"Create a parameter called alpha","topics":["create_alpha_param","create_param_alpha"]},{"page":"create_b_pop_sizes_param","title":"Create a parameter called `b_pop_sizes`.","topics":["create_b_pop_sizes_param","create_param_b_pop_sizes"]},{"page":"create_bd_tree_prior","title":"Create a Birth-Death tree prior","topics":["create_bd_tree_prior","create_tree_prior_bd"]},{"page":"create_beast2_beast_xml","title":"Create the '' XML","topics":["create_beast2_beast_xml"]},{"page":"create_beast2_input","title":"Create a BEAST2 XML input text","topics":["create_beast2_input"]},{"page":"create_beast2_input_beast","title":"Creates the XML text for the 'beast' tag of a BEAST2 parameter file.","topics":["create_beast2_input_beast"]},{"page":"create_beast2_input_data","title":"Creates the 'data' section of a BEAST2 XML parameter file","topics":["create_beast2_input_data"]},{"page":"create_beast2_input_data_sequences","title":"Creates the data section of a BEAST2 XML parameter file","topics":["create_beast2_input_data_sequences"]},{"page":"create_beast2_input_distr","title":"Creates the distribution section of a BEAST2 XML parameter file.","topics":["create_beast2_input_distr"]},{"page":"create_beast2_input_distr_lh","title":"Creates the XML text for the 'distribution' tag with the 'likelihood' ID, of a BEAST2 parameter file.","topics":["create_beast2_input_distr_lh"]},{"page":"create_beast2_input_distr_prior","title":"Creates the prior section in the distribution section of a BEAST2 XML parameter file","topics":["create_beast2_input_distr_prior"]},{"page":"create_beast2_input_file","title":"Create a BEAST2 input file","topics":["create_beast2_input_file"]},{"page":"create_beast2_input_file_from_model","title":"Create a BEAST2 input file from an inference model","topics":["create_beast2_input_file_from_model"]},{"page":"create_beast2_input_from_model","title":"Create a BEAST2 XML input text from an inference model","topics":["create_beast2_input_from_model"]},{"page":"create_beast2_input_init","title":"Creates the 'init' section of a BEAST2 XML parameter file","topics":["create_beast2_input_init"]},{"page":"create_beast2_input_map","title":"Creates the map section of a BEAST2 XML parameter file","topics":["create_beast2_input_map"]},{"page":"create_beast2_input_operators","title":"Creates the operators section of a BEAST2 XML parameter file","topics":["create_beast2_input_operators"]},{"page":"create_beast2_input_run","title":"Creates the ''run'' section of a BEAST2 XML parameter file","topics":["create_beast2_input_run"]},{"page":"create_beast2_input_state","title":"Creates the ''state'' section of a BEAST2 XML parameter file","topics":["create_beast2_input_state"]},{"page":"create_beauti_options","title":"Function to create a set of `BEAUti` options.","topics":["create_beauti_options"]},{"page":"create_beauti_options_v2_4","title":"Function to create the BEAUti options for version 2.4.","topics":["create_beauti_options_v2_4"]},{"page":"create_beauti_options_v2_6","title":"Function to create the BEAUti options for version 2.6.","topics":["create_beauti_options_v2_6"]},{"page":"create_beautier_tempfolder","title":"Create the default `beautier` temporary folder","topics":["create_beautier_tempfolder"]},{"page":"create_beta_distr","title":"Create a beta distribution","topics":["create_beta_distr","create_distr_beta"]},{"page":"create_beta_param","title":"Create a parameter called beta","topics":["create_beta_param","create_param_beta"]},{"page":"create_branch_rate_model_xml","title":"Internal function to create the 'branchRateModel' section of the XML as text.","topics":["create_branch_rate_model_xml"]},{"page":"create_cbs_tree_prior","title":"Create a Coalescent Bayesian Skyline tree prior","topics":["create_cbs_tree_prior","create_tree_prior_cbs"]},{"page":"create_ccp_tree_prior","title":"Create a Coalescent Constant Population tree prior","topics":["create_ccp_tree_prior","create_tree_prior_ccp"]},{"page":"create_cep_tree_prior","title":"Create a Coalescent Exponential Population tree prior","topics":["create_cep_tree_prior","create_tree_prior_cep"]},{"page":"create_clock_model","title":"General function to create a clock model","topics":["create_clock_model"]},{"page":"create_clock_model_from_name","title":"Create a clock model from name","topics":["create_clock_model_from_name"]},{"page":"create_clock_models","title":"Creates all supported clock models, which is a list of the types returned by 'create_rln_clock_model', and 'create_strict_clock_model'","topics":["create_clock_models"]},{"page":"create_clock_models_from_names","title":"Create clock models from their names","topics":["create_clock_models_from_names"]},{"page":"create_clock_rate_param","title":"Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'","topics":["create_clock_rate_param","create_param_clock_rate"]},{"page":"create_clock_rate_state_node_parameter_xml","title":"Internal function","topics":["create_clock_rate_state_node_parameter_xml"]},{"page":"create_data_xml","title":"Create the '' XML","topics":["create_data_xml"]},{"page":"create_distr","title":"General function to create a distribution.","topics":["create_distr"]},{"page":"create_exp_distr","title":"Create an exponential distribution","topics":["create_distr_exp","create_exp_distr"]},{"page":"create_freq_param","title":"Create a parameter called freq","topics":["create_freq_param","create_param_freq"]},{"page":"create_gamma_distr","title":"Create a gamma distribution","topics":["create_distr_gamma","create_gamma_distr"]},{"page":"create_gamma_site_model","title":"Create a gamma site model, part of a site model","topics":["create_gamma_site_model"]},{"page":"create_gtr_site_model","title":"Create a GTR site model","topics":["create_gtr_site_model","create_site_model_gtr"]},{"page":"create_gtr_subst_model_xml","title":"Converts a GTR site model to XML, used in the 'substModel' section","topics":["create_gtr_subst_model_xml"]},{"page":"create_hky_site_model","title":"Create an HKY site model","topics":["create_hky_site_model","create_site_model_hky"]},{"page":"create_hky_subst_model_xml","title":"Converts a site model to XML, used in the 'substModel' section","topics":["create_hky_subst_model_xml"]},{"page":"create_inference_model","title":"Create a Bayesian phylogenetic inference model.","topics":["create_inference_model"]},{"page":"create_inv_gamma_distr","title":"Create an inverse-gamma distribution","topics":["create_distr_inv_gamma","create_inv_gamma_distr"]},{"page":"create_jc69_site_model","title":"Create a JC69 site model","topics":["create_jc69_site_model","create_site_model_jc69"]},{"page":"create_jc69_subst_model_xml","title":"Converts a JC69 site model to XML, used in the 'substModel' section","topics":["create_jc69_subst_model_xml"]},{"page":"create_kappa_1_param","title":"Create a parameter called kappa 1","topics":["create_kappa_1_param","create_param_kappa_1"]},{"page":"create_kappa_2_param","title":"Create a parameter called kappa 2","topics":["create_kappa_2_param","create_param_kappa_2"]},{"page":"create_kappa_param","title":"Create a parameter called kappa","topics":["create_kappa_param","create_param_kappa"]},{"page":"create_lambda_param","title":"Create a parameter called lambda","topics":["create_lambda_param","create_param_lambda"]},{"page":"create_laplace_distr","title":"Create a Laplace distribution","topics":["create_distr_laplace","create_laplace_distr"]},{"page":"create_log_normal_distr","title":"Create a log-normal distribution","topics":["create_distr_log_normal","create_log_normal_distr"]},{"page":"create_loggers_xml","title":"Creates the three logger sections of a BEAST2 XML parameter file","topics":["create_loggers_xml"]},{"page":"create_m_param","title":"Create a parameter called m","topics":["create_m_param","create_param_m"]},{"page":"create_mcmc","title":"Create an MCMC configuration.","topics":["create_mcmc"]},{"page":"create_mean_param","title":"Create a parameter called mean","topics":["create_mean_param","create_param_mean"]},{"page":"create_mrca_prior","title":"Create a Most Recent Common Ancestor prior","topics":["create_mrca_prior"]},{"page":"create_mu_param","title":"Create a parameter called mu","topics":["create_mu_param","create_param_mu"]},{"page":"create_normal_distr","title":"Create an normal distribution","topics":["create_distr_normal","create_normal_distr"]},{"page":"create_ns_inference_model","title":"Create an inference model to measure the evidence of.","topics":["create_ns_inference_model"]},{"page":"create_ns_mcmc","title":"Create an MCMC object to estimate the marginal likelihood using Nested Sampling.","topics":["create_mcmc_nested_sampling","create_ns_mcmc"]},{"page":"create_one_div_x_distr","title":"Create a 1/x distribution","topics":["create_distr_one_div_x","create_one_div_x_distr"]},{"page":"create_param","title":"General function to create a parameter.","topics":["create_param"]},{"page":"create_poisson_distr","title":"Create a Poisson distribution","topics":["create_distr_poisson","create_poisson_distr"]},{"page":"create_rate_ac_param","title":"Create a parameter called 'rate AC'","topics":["create_param_rate_ac","create_rate_ac_param"]},{"page":"create_rate_ag_param","title":"Create a parameter called 'rate AG'","topics":["create_param_rate_ag","create_rate_ag_param"]},{"page":"create_rate_at_param","title":"Create a parameter called 'rate AT'","topics":["create_param_rate_at","create_rate_at_param"]},{"page":"create_rate_categories_state_node_xml","title":"Internal function","topics":["create_rate_categories_state_node_xml"]},{"page":"create_rate_cg_param","title":"Create a parameter called 'rate CG'","topics":["create_param_rate_cg","create_rate_cg_param"]},{"page":"create_rate_ct_param","title":"Create a parameter called 'rate CT'","topics":["create_param_rate_ct","create_rate_ct_param"]},{"page":"create_rate_gt_param","title":"Create a parameter called 'rate GT'","topics":["create_param_rate_gt","create_rate_gt_param"]},{"page":"create_rln_clock_branch_rate_model_xml","title":"Internal function","topics":["create_rln_clock_branch_rate_model_xml"]},{"page":"create_rln_clock_model","title":"Create a relaxed log-normal clock model","topics":["create_clock_model_rln","create_rln_clock_model"]},{"page":"create_s_param","title":"Create a parameter called s","topics":["create_param_s","create_s_param"]},{"page":"create_scale_param","title":"Create a parameter called scale","topics":["create_param_scale","create_scale_param"]},{"page":"create_screenlog","title":"Create a 'screenlog' object","topics":["create_screenlog"]},{"page":"create_screenlog_xml","title":"Creates the 'screenlog' section of the 'logger' section of a BEAST2 XML parameter file","topics":["create_screenlog_xml"]},{"page":"create_sigma_param","title":"Create a parameter called sigma","topics":["create_param_sigma","create_sigma_param"]},{"page":"create_site_model","title":"General function to create a site model.","topics":["create_site_model"]},{"page":"create_site_model_from_name","title":"Create a site model from name","topics":["create_site_model_from_name"]},{"page":"create_site_model_parameters_xml","title":"Internal function to creates the XML text for the 'parameter's within the 'siteModel' section of a BEAST2 parameter file.","topics":["create_site_model_parameters_xml"]},{"page":"create_site_model_xml","title":"Internal function to creates the XML text for the 'siteModel' tag of a BEAST2 parameter file.","topics":["create_site_model_xml"]},{"page":"create_site_models","title":"Creates all supported site models which is a list of the types returned by 'create_gtr_site_model', 'create_hky_site_model', 'create_jc69_site_model' and 'create_tn93_site_model'","topics":["create_site_models"]},{"page":"create_site_models_from_names","title":"Create site models from their names","topics":["create_site_models_from_names"]},{"page":"create_strict_clock_branch_rate_model_xml","title":"Internal function.","topics":["create_strict_clock_branch_rate_model_xml"]},{"page":"create_strict_clock_model","title":"Create a strict clock model","topics":["create_clock_model_strict","create_strict_clock_model"]},{"page":"create_strict_clock_rate_scaler_operator_xml","title":"Internal function","topics":["create_strict_clock_rate_scaler_operator_xml"]},{"page":"create_subst_model_xml","title":"Internal function to create the 'substModel' section","topics":["create_subst_model_xml"]},{"page":"create_temp_screenlog_filename","title":"Create a filename for a temporary `screenlog` file","topics":["create_temp_screenlog_filename"]},{"page":"create_temp_tracelog_filename","title":"Create a filename for a temporary `tracelog` file","topics":["create_temp_tracelog_filename"]},{"page":"create_temp_treelog_filename","title":"Create a filename for a temporary `treelog` file","topics":["create_temp_treelog_filename"]},{"page":"create_test_inference_model","title":"Create a testing inference model.","topics":["create_test_inference_model"]},{"page":"create_test_mcmc","title":"Create an MCMC configuration for testing.","topics":["create_test_mcmc"]},{"page":"create_test_ns_inference_model","title":"Create an inference model to be tested by Nested Sampling","topics":["create_test_ns_inference_model"]},{"page":"create_test_ns_mcmc","title":"Create an NS MCMC object for testing","topics":["create_test_ns_mcmc"]},{"page":"create_test_screenlog","title":"Create a 'screenlog' object, to be used in testing","topics":["create_test_screenlog"]},{"page":"create_test_tracelog","title":"Create a 'tracelog' object, as used for testing","topics":["create_test_tracelog"]},{"page":"create_test_treelog","title":"Create a 'treelog' object to be used in testing","topics":["create_test_treelog"]},{"page":"create_tn93_site_model","title":"Create a TN93 site model","topics":["create_site_model_tn93","create_tn93_site_model"]},{"page":"create_tn93_subst_model_xml","title":"Converts a TN93 site model to XML, used in the 'substModel' section","topics":["create_tn93_subst_model_xml"]},{"page":"create_tracelog","title":"Create a 'tracelog' object","topics":["create_tracelog"]},{"page":"create_tracelog_xml","title":"Internal function","topics":["create_tracelog_xml"]},{"page":"create_trait_set_string","title":"Create a trait set string.","topics":["create_trait_set_string"]},{"page":"create_tree_likelihood_distr_xml","title":"Creates the XML text for the 'distribution' tag with the 'treeLikelihood' ID, of a BEAST2 parameter file.","topics":["create_tree_likelihood_distr_xml"]},{"page":"create_tree_prior","title":"Internal function to create a tree prior","topics":["create_tree_prior"]},{"page":"create_tree_priors","title":"Creates all supported tree priors, which is a list of the types returned by 'create_bd_tree_prior', 'create_cbs_tree_prior', 'create_ccp_tree_prior', 'create_cep_tree_prior' and 'create_yule_tree_prior'","topics":["create_tree_priors"]},{"page":"create_treelog","title":"Create a 'treelog' object","topics":["create_treelog"]},{"page":"create_treelog_xml","title":"Creates the XML text for the `logger` tag with ID `treelog`. This section has these elements: ``` # nolint indeed long # nolint indeed long ```","topics":["create_treelog_xml"]},{"page":"create_ucld_mean_state_node_param_xml","title":"Internal function","topics":["create_ucld_mean_state_node_param_xml"]},{"page":"create_ucld_stdev_state_node_param_xml","title":"Internal function","topics":["create_ucld_stdev_state_node_param_xml"]},{"page":"create_uniform_distr","title":"Create a uniform distribution","topics":["create_distr_uniform","create_uniform_distr"]},{"page":"create_xml_declaration","title":"Create the XML declaration of the BEAST2 XML input file","topics":["create_xml_declaration"]},{"page":"create_yule_tree_prior","title":"Create a Yule tree prior","topics":["create_tree_prior_yule","create_yule_tree_prior"]},{"page":"default_parameters_doc","title":"Documentation of parameters (for example, 'create_param'. This function does nothing. It is intended to inherit documentation from.","topics":["default_parameters_doc"]},{"page":"default_params_doc","title":"Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.","topics":["default_params_doc"]},{"page":"distr_to_xml","title":"Internal function","topics":["distr_to_xml"]},{"page":"distr_to_xml_beta","title":"Internal function","topics":["distr_to_xml_beta"]},{"page":"distr_to_xml_exp","title":"Internal function","topics":["distr_to_xml_exp"]},{"page":"distr_to_xml_inv_gamma","title":"Internal function","topics":["distr_to_xml_inv_gamma"]},{"page":"distr_to_xml_laplace","title":"Internal function","topics":["distr_to_xml_laplace"]},{"page":"distr_to_xml_log_normal","title":"Internal function","topics":["distr_to_xml_log_normal"]},{"page":"distr_to_xml_normal","title":"Internal function","topics":["distr_to_xml_normal"]},{"page":"distr_to_xml_one_div_x","title":"Internal function","topics":["distr_to_xml_one_div_x"]},{"page":"distr_to_xml_poisson","title":"Internal function","topics":["distr_to_xml_poisson"]},{"page":"distr_to_xml_uniform","title":"Internal function","topics":["distr_to_xml_uniform"]},{"page":"extract_xml_loggers_from_lines","title":"Extract everything between first loggers and last loggers line","topics":["extract_xml_loggers_from_lines"]},{"page":"extract_xml_operators_from_lines","title":"Extract everything between first operators and last operators line","topics":["extract_xml_operators_from_lines"]},{"page":"extract_xml_section_from_lines","title":"Get the lines of an XML section, including the section tags","topics":["extract_xml_section_from_lines"]},{"page":"fasta_file_to_sequences","title":"Convert a FASTA file to a table of sequences","topics":["fasta_file_to_sequences"]},{"page":"find_clock_model","title":"Finds a clock model with a certain ID","topics":["find_clock_model"]},{"page":"find_first_regex_line","title":"Find the first line that satisfies a regex","topics":["find_first_regex_line"]},{"page":"find_first_xml_opening_tag_line","title":"Find the line number of the first section's opening tag","topics":["find_first_xml_opening_tag_line"]},{"page":"find_last_regex_line","title":"Find the index of the last line that matches a regex","topics":["find_last_regex_line"]},{"page":"find_last_xml_closing_tag_line","title":"Find the highest line number of a section's closing tag","topics":["find_last_xml_closing_tag_line"]},{"page":"freq_equilibrium_to_xml","title":"Creates the 'freq_equilibrium' as XML","topics":["freq_equilibrium_to_xml"]},{"page":"freq_param_to_xml","title":"Internal function","topics":["freq_param_to_xml"]},{"page":"gamma_distr_to_xml","title":"Internal function","topics":["gamma_distr_to_xml"]},{"page":"gamma_site_model_to_xml_prior_distr","title":"Internal function.","topics":["gamma_site_model_to_xml_prior_distr"]},{"page":"gamma_site_model_to_xml_state","title":"Converts a gamma site model to XML, used in the 'state' section","topics":["gamma_site_model_to_xml_state"]},{"page":"gamma_site_models_to_xml_prior_distr","title":"Deprecated function","topics":["gamma_site_models_to_xml_prior_distr"]},{"page":"get_alignment_id","title":"Conclude the ID from a FASTA filename.","topics":["get_alignment_id"]},{"page":"get_alignment_ids","title":"Get the alignment IDs from one or more files.","topics":["get_alignment_ids"]},{"page":"get_alignment_ids_from_fasta_filenames","title":"Get the alignment ID from one or more FASTA filenames.","topics":["get_alignment_ids_from_fasta_filenames"]},{"page":"get_beautier_folder","title":"Get the path to the beautier temporary files folder","topics":["get_beautier_folder"]},{"page":"get_beautier_path","title":"Get the full path of a file in the 'inst/extdata' folder","topics":["get_beautier_path"]},{"page":"get_beautier_paths","title":"Get the full paths of files in the 'inst/extdata' folder","topics":["get_beautier_paths"]},{"page":"get_beautier_tempfilename","title":"Get a temporary filename","topics":["get_beautier_tempfilename"]},{"page":"get_clock_model_name","title":"Get the BEAUti name for a clock model","topics":["get_clock_model_name"]},{"page":"get_clock_model_names","title":"Get the clock model names","topics":["get_clock_model_names"]},{"page":"get_clock_models_ids","title":"Collect the IDs of the list of clock models","topics":["get_clock_models_ids"]},{"page":"get_crown_age","title":"Obtain the crown age of a phylogeny.","topics":["get_crown_age"]},{"page":"get_default_beast_namespace","title":"Get the default `namespace` element value of the `beast` XML tag.","topics":["get_default_beast_namespace"]},{"page":"get_default_beast_namespace_v2_4","title":"Get the default `namespace` element value of the `beast` XML tag for BEAST 2.4","topics":["get_default_beast_namespace_v2_4"]},{"page":"get_default_beast_namespace_v2_6","title":"Get the default `namespace` element value of the `beast` XML tag for BEAST 2.6","topics":["get_default_beast_namespace_v2_6"]},{"page":"get_distr_n_params","title":"Get the number of parameters a distribution uses","topics":["get_distr_n_params"]},{"page":"get_distr_names","title":"Get the distribution names","topics":["get_distr_names"]},{"page":"get_fasta_filename","title":"Get the path of a FASTA file used in testing","topics":["get_fasta_filename"]},{"page":"get_file_base_sans_ext","title":"Get the base of the filename base without extension","topics":["get_file_base_sans_ext"]},{"page":"get_freq_equilibrium_names","title":"Returns valid values for the 'freq_equilibrium' argument","topics":["get_freq_equilibrium_names"]},{"page":"get_gamma_site_model_n_distrs","title":"Get the number of distributions in a gamma site model","topics":["get_gamma_site_model_n_distrs"]},{"page":"get_gamma_site_model_n_params","title":"Get the number of distributions a site model has","topics":["get_gamma_site_model_n_params"]},{"page":"get_has_non_strict_clock_model","title":"Determines if there is at least one non-strict clock model in the list of one or more clock models","topics":["get_has_non_strict_clock_model"]},{"page":"get_inference_model_filenames","title":"Get the filenames stored in an inference model.","topics":["get_inference_model_filenames"]},{"page":"get_log_modes","title":"Get the possible log modes","topics":["get_log_modes"]},{"page":"get_log_sorts","title":"Get the possible log sorts","topics":["get_log_sorts"]},{"page":"get_mcmc_filenames","title":"Get the filenames stored in an MCMC.","topics":["get_mcmc_filenames"]},{"page":"get_n_taxa","title":"Extract the number of taxa from a file","topics":["get_n_taxa"]},{"page":"get_operator_id_pre","title":"Get the prefix of operator IDs","topics":["get_operator_id_pre"]},{"page":"get_param_names","title":"Get the parameter names","topics":["get_param_names"]},{"page":"get_remove_dir_fun","title":"Get a function that, from a filename, returns the part without the directory.","topics":["get_remove_dir_fun"]},{"page":"get_remove_hex_fun","title":"Get a function that removes the hex string from filenames.","topics":["get_remove_hex_fun"]},{"page":"get_replace_dir_fun","title":"Get a function to replace the directory of a filename","topics":["get_replace_dir_fun"]},{"page":"get_site_model_n_distrs","title":"Get the number of distributions a site model has","topics":["get_site_model_n_distrs"]},{"page":"get_site_model_n_params","title":"Get the number of distributions a site model has","topics":["get_site_model_n_params"]},{"page":"get_site_model_names","title":"Get the site models' names","topics":["get_site_model_names"]},{"page":"get_site_models_n_distrs","title":"Get the number of distributions a site model has","topics":["get_site_models_n_distrs"]},{"page":"get_site_models_n_params","title":"Get the number of distributions one or more site models have","topics":["get_site_models_n_params"]},{"page":"get_taxa_names","title":"Extract the names of taxa from a file","topics":["get_taxa_names"]},{"page":"get_tree_prior_n_distrs","title":"Get the number of distributions a tree prior has","topics":["get_tree_prior_n_distrs"]},{"page":"get_tree_prior_n_params","title":"Get the number of parameters a tree prior has","topics":["get_tree_prior_n_params"]},{"page":"get_tree_prior_names","title":"Get the tree prior names","topics":["get_tree_prior_names"]},{"page":"get_tree_priors_n_distrs","title":"Get the number of distributions a tree prior has","topics":["get_tree_priors_n_distrs"]},{"page":"get_tree_priors_n_params","title":"Get the number of parameters a list of tree priors has","topics":["get_tree_priors_n_params"]},{"page":"get_xml_closing_tag","title":"Get the XML closing tag","topics":["get_xml_closing_tag"]},{"page":"get_xml_opening_tag","title":"Get the XML opening tag","topics":["get_xml_opening_tag"]},{"page":"gtr_site_model_to_xml_prior_distr","title":"Internal function","topics":["gtr_site_model_to_xml_prior_distr"]},{"page":"gtr_site_model_to_xml_state","title":"Converts a site model to XML, used in the 'state' section","topics":["gtr_site_model_to_xml_state"]},{"page":"has_mrca_prior","title":"Determines if the inference model has an MRCA prior.","topics":["has_mrca_prior"]},{"page":"has_mrca_prior_with_distr","title":"See if the inference model has one MRCA prior with a distribution","topics":["has_mrca_prior_with_distr"]},{"page":"has_rln_clock_model","title":"Determine if the 'inference_model' uses a relaxed log-normal clock model.","topics":["has_rln_clock_model"]},{"page":"has_strict_clock_model","title":"Determine if the 'inference_model' uses a strict clock model.","topics":["has_strict_clock_model"]},{"page":"has_tip_dating","title":"Determine if the 'inference_model' uses tip dating.","topics":["has_tip_dating"]},{"page":"has_xml_closing_tag","title":"Is an XML closing tag with the value of 'section' present among the lines of the text?","topics":["has_xml_closing_tag"]},{"page":"has_xml_opening_tag","title":"Is an XML opening tag with value 'section' present among the lines of the text?","topics":["has_xml_opening_tag"]},{"page":"has_xml_short_closing_tag","title":"Is an XML closing tag with short closing text in one of the lines of the text?","topics":["has_xml_short_closing_tag"]},{"page":"hky_site_model_to_xml_prior_distr","title":"Internal function","topics":["hky_site_model_to_xml_prior_distr"]},{"page":"hky_site_model_to_xml_state","title":"Converts a site model to XML, used in the 'state' section","topics":["hky_site_model_to_xml_state"]},{"page":"indent","title":"Indent text for a certain number of spaces. If the text is only whitespace, leave it as such","topics":["indent"]},{"page":"init_bd_tree_prior","title":"Initializes a Birth-Death tree prior","topics":["init_bd_tree_prior"]},{"page":"init_beta_distr","title":"Initializes a beta distribution","topics":["init_beta_distr"]},{"page":"init_ccp_tree_prior","title":"Initializes a Coalescent Constant Population tree prior","topics":["init_ccp_tree_prior"]},{"page":"init_cep_tree_prior","title":"Initializes a Coalescent Exponential Population tree prior","topics":["init_cep_tree_prior"]},{"page":"init_clock_models","title":"Initializes all clock models","topics":["init_clock_models"]},{"page":"init_distr","title":"Initializes a distribution","topics":["init_distr"]},{"page":"init_exp_distr","title":"Initializes an exponential distribution","topics":["init_exp_distr"]},{"page":"init_gamma_distr","title":"Initializes a gamma distribution","topics":["init_gamma_distr"]},{"page":"init_gamma_site_model","title":"Initializes a gamma site model","topics":["init_gamma_site_model"]},{"page":"init_gtr_site_model","title":"Initializes a GTR site model","topics":["init_gtr_site_model"]},{"page":"init_hky_site_model","title":"Initializes an HKY site model","topics":["init_hky_site_model"]},{"page":"init_inference_model","title":"Initialize an inference model","topics":["init_inference_model"]},{"page":"init_inv_gamma_distr","title":"Initializes an inverse gamma distribution","topics":["init_inv_gamma_distr"]},{"page":"init_jc69_site_model","title":"Initializes a JC69 site model","topics":["init_jc69_site_model"]},{"page":"init_laplace_distr","title":"Initializes an Laplace distribution","topics":["init_laplace_distr"]},{"page":"init_log_normal_distr","title":"Initializes an log-normal distribution","topics":["init_log_normal_distr"]},{"page":"init_mrca_prior","title":"Initialize the MRCA prior.","topics":["init_mrca_prior"]},{"page":"init_mrca_priors","title":"Initializes all MRCA priors","topics":["init_mrca_priors"]},{"page":"init_normal_distr","title":"Initializes an normal distribution","topics":["init_normal_distr"]},{"page":"init_one_div_x_distr","title":"Initializes an one-divided-by-x distribution","topics":["init_one_div_x_distr"]},{"page":"init_param","title":"Initializes a parameter","topics":["init_param"]},{"page":"init_poisson_distr","title":"Initializes an Poisson distribution","topics":["init_poisson_distr"]},{"page":"init_rln_clock_model","title":"Initializes a Relaxed Log-Normal clock model","topics":["init_rln_clock_model"]},{"page":"init_site_models","title":"Initializes all site models","topics":["init_site_models"]},{"page":"init_strict_clock_model","title":"Initializes a strict clock model","topics":["init_strict_clock_model"]},{"page":"init_tn93_site_model","title":"Initializes a TN93 site model","topics":["init_tn93_site_model"]},{"page":"init_tree_priors","title":"Initializes all tree priors","topics":["init_tree_priors"]},{"page":"init_uniform_distr","title":"Initializes a uniform distribution","topics":["init_uniform_distr"]},{"page":"init_yule_tree_prior","title":"Initializes a Yule tree prior","topics":["init_yule_tree_prior"]},{"page":"interspace","title":"Puts spaces in between the lines","topics":["interspace"]},{"page":"is_alpha_param","title":"Determine if the object is a valid alpha parameter","topics":["is_alpha_param"]},{"page":"is_b_pop_sizes_param","title":"Determine if the object is a valid b_pop_sizes parameter","topics":["is_b_pop_sizes_param"]},{"page":"is_bd_tree_prior","title":"Determine if the object is a valid Birth Death tree prior","topics":["is_bd_tree_prior"]},{"page":"is_beauti_options","title":"Determine if the object is a valid 'beauti_options'","topics":["is_beauti_options"]},{"page":"is_beta_distr","title":"Determine if the object is a valid beta distribution, as created by 'create_beta_distr'","topics":["is_beta_distr"]},{"page":"is_beta_param","title":"Determine if the object is a valid beta parameter","topics":["is_beta_param"]},{"page":"is_cbs_tree_prior","title":"Determine if the object is a valid constant coalescent Bayesian skyline prior","topics":["is_cbs_tree_prior"]},{"page":"is_ccp_tree_prior","title":"Determine if the object is a valid constant coalescence population tree prior","topics":["is_ccp_tree_prior"]},{"page":"is_cep_tree_prior","title":"Determine if the object is a valid coalescent exponential population tree prior","topics":["is_cep_tree_prior"]},{"page":"is_clock_model","title":"Determine if the object is a valid clock_model","topics":["is_clock_model"]},{"page":"is_clock_model_name","title":"Determines if the name is a valid clock model name","topics":["is_clock_model_name"]},{"page":"is_clock_rate_param","title":"Determine if the object is a valid clock_rate parameter","topics":["is_clock_rate_param"]},{"page":"is_default_mcmc","title":"Determine if the MCMC is a default MCMC","topics":["is_default_mcmc"]},{"page":"is_distr","title":"Determine if the object is a valid distribution","topics":["is_distr"]},{"page":"is_distr_name","title":"Determines if the name is a valid distribution name","topics":["is_distr_name"]},{"page":"is_exp_distr","title":"Determine if the object is a valid exponential distribution as created by 'create_exp_distr'","topics":["is_exp_distr"]},{"page":"is_freq_equilibrium_name","title":"Checks if 'name' is a valid 'freq_equilibrium' argument value","topics":["is_freq_equilibrium_name"]},{"page":"is_freq_param","title":"Determine if the object is a valid freq parameter","topics":["is_freq_param"]},{"page":"is_gamma_distr","title":"Determine if the object is a valid gamma distribution, as created by 'create_gamma_distr'","topics":["is_gamma_distr"]},{"page":"is_gamma_site_model","title":"Is object x a gamma site model?","topics":["is_gamma_site_model"]},{"page":"is_gtr_site_model","title":"Determine if the object is a valid GTR site model, as created by 'create_gtr_site_model'","topics":["is_gtr_site_model"]},{"page":"is_hky_site_model","title":"Determine if the object is a valid HKY site model, as created by 'create_hky_site_model'","topics":["is_hky_site_model"]},{"page":"is_id","title":"Determine if the object is a valid ID","topics":["is_id"]},{"page":"is_in_patterns","title":"Is there at least one regular expression having a match with the line?","topics":["is_in_patterns"]},{"page":"is_inference_model","title":"Determine if the input is an inference model","topics":["is_inference_model"]},{"page":"is_init_bd_tree_prior","title":"Determine if x is an initialized Birth-Death tree_prior object","topics":["is_init_bd_tree_prior"]},{"page":"is_init_beta_distr","title":"Determine if x is an initialized beta distribution object as created by 'create_beta_distr'","topics":["is_init_beta_distr"]},{"page":"is_init_cbs_tree_prior","title":"Determine if x is an initialized Coalescent Bayesian Skyline tree_prior object","topics":["is_init_cbs_tree_prior"]},{"page":"is_init_ccp_tree_prior","title":"Determine if x is an initialized Coalescent Constant Population tree_prior object","topics":["is_init_ccp_tree_prior"]},{"page":"is_init_cep_tree_prior","title":"Determine if x is an initialized Coalescent Exponential Population tree_prior object","topics":["is_init_cep_tree_prior"]},{"page":"is_init_clock_model","title":"Determine if x is an initialized clock_model object, as created by 'create_clock_model'","topics":["is_init_clock_model"]},{"page":"is_init_distr","title":"Determine if x is an initialized distribution object as created by 'create_distr'","topics":["is_init_distr"]},{"page":"is_init_exp_distr","title":"Determine if x is an initialized exponential distribution object as created by 'create_exp_distr'","topics":["is_init_exp_distr"]},{"page":"is_init_gamma_distr","title":"Determine if x is an initialized gamma distribution object","topics":["is_init_gamma_distr"]},{"page":"is_init_gamma_site_model","title":"Determine if x is an initialized gamma site model, as created by 'create_gamma_site_model'","topics":["is_init_gamma_site_model"]},{"page":"is_init_gtr_site_model","title":"Determine if x is an initialized GTR site model as created by 'create_gtr_site_model'","topics":["is_init_gtr_site_model"]},{"page":"is_init_hky_site_model","title":"Determine if x is an initialized HKY site model as created by 'create_hky_site_model'","topics":["is_init_hky_site_model"]},{"page":"is_init_inv_gamma_distr","title":"Determine if x is an initialized inverse-gamma distribution as created by 'create_inv_gamma_distr'","topics":["is_init_inv_gamma_distr"]},{"page":"is_init_jc69_site_model","title":"Determine if x is an initialized JC69 site model as created by 'create_jc69_site_model'","topics":["is_init_jc69_site_model"]},{"page":"is_init_laplace_distr","title":"Determine if x is an initialized Laplace distribution as created by 'create_laplace_distr'","topics":["is_init_laplace_distr"]},{"page":"is_init_log_normal_distr","title":"Determine if x is an initialized log_normal distribution object as created by 'create_log_normal_distr'","topics":["is_init_log_normal_distr"]},{"page":"is_init_mrca_prior","title":"Determine if x is an initialized MRCA prior","topics":["is_init_mrca_prior"]},{"page":"is_init_normal_distr","title":"Determine if x is an initialized normal distribution object as created by 'create_normal_distr'","topics":["is_init_normal_distr"]},{"page":"is_init_one_div_x_distr","title":"Determine if x is an initialized one_div_x distribution object as created by 'create_one_div_x_distr'","topics":["is_init_one_div_x_distr"]},{"page":"is_init_param","title":"Determine if x is an initialized parameter, as created by create_param","topics":["is_init_param"]},{"page":"is_init_poisson_distr","title":"Determine if x is an initialized Poisson distribution object as created by 'create_poisson_distr'","topics":["is_init_poisson_distr"]},{"page":"is_init_rln_clock_model","title":"Determine if x is an initialized relaxed log-normal clock_model object","topics":["is_init_rln_clock_model"]},{"page":"is_init_site_model","title":"Determine if x is an initialized site model, as created by 'create_site_model'","topics":["is_init_site_model"]},{"page":"is_init_strict_clock_model","title":"Determine if x is an initialized strict clock_model object","topics":["is_init_strict_clock_model"]},{"page":"is_init_tn93_site_model","title":"Determine if x is an initialized tn93 site model as created by 'create_tn93_site_model'","topics":["is_init_tn93_site_model"]},{"page":"is_init_tree_prior","title":"Determine if x is an initialized tree_prior objects","topics":["is_init_tree_prior"]},{"page":"is_init_uniform_distr","title":"Determine if x is an initialized uniform distribution object as created by 'create_uniform_distr'","topics":["is_init_uniform_distr"]},{"page":"is_init_yule_tree_prior","title":"Determine if x is an initialized Yule tree_prior object","topics":["is_init_yule_tree_prior"]},{"page":"is_inv_gamma_distr","title":"Determine if the object is a valid inverse-gamma distribution as created by 'create_inv_gamma_distr'","topics":["is_inv_gamma_distr"]},{"page":"is_jc69_site_model","title":"Determine if the object is a valid JC69 site model","topics":["is_jc69_site_model"]},{"page":"is_kappa_1_param","title":"Determine if the object is a valid kappa 1 parameter","topics":["is_kappa_1_param"]},{"page":"is_kappa_2_param","title":"Determine if the object is a valid kappa 2 parameter","topics":["is_kappa_2_param"]},{"page":"is_kappa_param","title":"Determine if the object is a valid kappa parameter","topics":["is_kappa_param"]},{"page":"is_lambda_param","title":"Determine if the object is a valid lambda parameter","topics":["is_lambda_param"]},{"page":"is_laplace_distr","title":"Determine if the object is a valid Laplace distribution, as created by 'create_laplace_distr'","topics":["is_laplace_distr"]},{"page":"is_log_normal_distr","title":"Determine if the object is a valid log-normal distribution, as created by 'create_log_normal_distr'","topics":["is_log_normal_distr"]},{"page":"is_m_param","title":"Determine if the object is a valid m parameter","topics":["is_m_param"]},{"page":"is_mcmc","title":"Determine if the object is a valid MCMC","topics":["is_mcmc"]},{"page":"is_mcmc_nested_sampling","title":"Determine if the object is a valid Nested-Sampling MCMC, as used in [1]","topics":["is_mcmc_nested_sampling","is_nested_sampling_mcmc"]},{"page":"is_mean_param","title":"Determine if the object is a valid mean parameter","topics":["is_mean_param"]},{"page":"is_mrca_align_id_in_fasta","title":"Determine if an MRCA prior's alignment IDs is present in the FASTA file","topics":["is_mrca_align_id_in_fasta"]},{"page":"is_mrca_align_ids_in_fastas","title":"Determine if an MRCA prior's alignment IDs are present in the FASTA files","topics":["is_mrca_align_ids_in_fastas"]},{"page":"is_mrca_prior","title":"Determine of the object is an empty ('NA') or valid MRCA prior.","topics":["is_mrca_prior"]},{"page":"is_mrca_prior_with_distr","title":"See if x is one MRCA prior with a distribution","topics":["is_mrca_prior_with_distr"]},{"page":"is_mu_param","title":"Determine if the object is a valid mu parameter","topics":["is_mu_param"]},{"page":"is_normal_distr","title":"Determine if the object is a valid normal distribution as created by 'create_normal_distr'","topics":["is_normal_distr"]},{"page":"is_on_appveyor","title":"Determines if the environment is AppVeyor","topics":["is_on_appveyor"]},{"page":"is_on_ci","title":"Determines if the environment is a continuous integration service","topics":["is_on_ci"]},{"page":"is_on_github_actions","title":"Determines if the environment is GitHub Actions","topics":["is_on_github_actions"]},{"page":"is_on_travis","title":"Determines if the environment is Travis CI","topics":["is_on_travis"]},{"page":"is_one_bool","title":"Check if the argument is one boolean","topics":["is_one_bool"]},{"page":"is_one_div_x_distr","title":"Determine if the object is a valid 1/x distribution, as created by 'create_one_div_x_distr'","topics":["is_one_div_x_distr"]},{"page":"is_one_double","title":"Determines if the argument is a double","topics":["is_one_double"]},{"page":"is_one_empty_string","title":"Determine if an object is one empty string","topics":["is_one_empty_string"]},{"page":"is_one_int","title":"Determines if the argument is a whole number","topics":["is_one_int"]},{"page":"is_one_na","title":"Determines if x is one NA","topics":["is_one_na"]},{"page":"is_one_string","title":"Determines if the argument is one string","topics":["is_one_string"]},{"page":"is_one_string_that_is_a_number","title":"General function to create a distribution.","topics":["is_one_string_that_is_a_number"]},{"page":"is_param","title":"Determine if the object is a valid parameter","topics":["is_param"]},{"page":"is_param_name","title":"Determines if the name is a valid parameter name","topics":["is_param_name"]},{"page":"is_phylo","title":"Checks if the input is a phylogeny","topics":["is_phylo"]},{"page":"is_poisson_distr","title":"Determine if the object is a valid Poisson distribution as created by 'create_poisson_distr'","topics":["is_poisson_distr"]},{"page":"is_rate_ac_param","title":"Determine if the object is a valid 'rate AC' parameter","topics":["is_rate_ac_param"]},{"page":"is_rate_ag_param","title":"Determine if the object is a valid 'rate AG' parameter","topics":["is_rate_ag_param"]},{"page":"is_rate_at_param","title":"Determine if the object is a valid 'rate AT' parameter","topics":["is_rate_at_param"]},{"page":"is_rate_cg_param","title":"Determine if the object is a valid 'rate CG' parameter","topics":["is_rate_cg_param"]},{"page":"is_rate_ct_param","title":"Determine if the object is a valid 'rate CT' parameter","topics":["is_rate_ct_param"]},{"page":"is_rate_gt_param","title":"Determine if the object is a valid 'rate GT' parameter","topics":["is_rate_gt_param"]},{"page":"is_rln_clock_model","title":"Determine if the object is a valid relaxed log normal clock model","topics":["is_rln_clock_model"]},{"page":"is_s_param","title":"Determine if the object is a valid s parameter","topics":["is_s_param"]},{"page":"is_scale_param","title":"Determine if the object is a valid scale parameter","topics":["is_scale_param"]},{"page":"is_sigma_param","title":"Determine if the object is a valid sigma parameter","topics":["is_sigma_param"]},{"page":"is_site_model","title":"Determine if the object is a valid site_model","topics":["is_site_model"]},{"page":"is_site_model_name","title":"Determines if the name is a valid site_model name","topics":["is_site_model_name"]},{"page":"is_strict_clock_model","title":"Determine if the object is a valid strict clock model, as returned by 'create_strict_clock_model'","topics":["is_strict_clock_model"]},{"page":"is_tn93_site_model","title":"Determine if the object is a valid TN93 site model,","topics":["is_tn93_site_model"]},{"page":"is_tree_prior","title":"Determine if an object is a valid tree prior","topics":["is_tree_prior"]},{"page":"is_tree_prior_name","title":"Determines if the name is a valid tree prior name","topics":["is_tree_prior_name"]},{"page":"is_uniform_distr","title":"Determine if the object is a valid uniform distribution as created by 'create_uniform_distr'","topics":["is_uniform_distr"]},{"page":"is_xml","title":"Checks if the 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Measures can be\ncalculated in groups or individually. The calculated measure or\nthe resulting vector in table format should help practitioners\nmake more informed decisions. Methods used in this package are\nfrom: 1. Chang, E. J., Guerra, S. M., de Souza Penaloza, R. A.\n& Tabak, B. M. (2005) \"Banking concentration: the Brazilian\ncase\". 2. Cobham, A. and A. Summer (2013). \"Is It All About\nthe Tails? The Palma Measure of Income Inequality\". 3. Garcia\nAlba Idunate, P. (1994). \"Un Indice de dominancia para el\nanalisis de la estructura de los mercados\". 4. Ginevicius, R.\nand S. Cirba (2009). \"Additive measurement of market\nconcentration\" . 5.\nHerfindahl, O. C. (1950), \"Concentration in the steel industry\"\n(PhD thesis). 6. Hirschmann, A. O. (1945), \"National power and\nstructure of foreign trade\". 7. Melnik, A., O. Shy, and R.\nStenbacka (2008), \"Assessing market dominance\"\n. 8. Palma, J. G. (2006).\n\"Globalizing Inequality: 'Centrifugal' and 'Centripetal' Forces\nat Work\". 9. Shannon, C. E. (1948). \"A Mathematical Theory of\nCommunication\". 10. Simpson, E. H. (1949). \"Measurement of\nDiversity\" .","License":"GPL (>= 3)","URL":"https://github.com/ropensci/concstats/,\nhttps://docs.ropensci.org/concstats/(website)","BugReports":"https://github.com/ropensci/concstats/issues/","VignetteBuilder":"knitr, rmarkdown","Encoding":"UTF-8","Language":"en-US","LazyData":"true","Roxygen":"list(markdown = TRUE)","RoxygenNote":"7.3.1","Config/testthat/edition":"3","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/concstats","RemoteRef":"master","RemoteSha":"c450c9e1713c2ce7b9ca44323e462112f6feefd8","NeedsCompilation":"no","Packaged":{"Date":"2024-10-31 22:09:57 UTC","User":"root"},"Author":"Andreas Schneider [aut, cre] (),\nSebastian Wojcik [rev],\nChristopher T. 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comment=c(ORCID = \"0000-0003-1444-9135\")),\nperson(\"David\", \"Beckett\", role = c(\"cph\")),\nperson(\"University of Bristol\", role = c(\"cph\")),\nperson(\"Regents of the University of California\", role = c(\"cph\"))\n)","Date":"2024-02-23","VignetteBuilder":"knitr","Description":"Provides methods to parse, query and serialize information\nstored in the Resource Description Framework (RDF). RDF is\ndescribed at . This package\nsupports RDF by implementing an R interface to the Redland RDF\nC library, described at\n. In brief, RDF\nprovides a structured graph consisting of Statements composed\nof Subject, Predicate, and Object Nodes.","SystemRequirements":"Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>=\n1.0.14), librdf0-dev (>= 1.0.14)","Collate":"'redland.R' 'World.R' 'Node.R' 'Statement.R' 'Storage.R'\n'Model.R' 'Parser.R' 'Query.R' 'QueryResults.R' 'Serializer.R'\n'mergeNamespace_roclet.R' 'redland-package.R' 'util.R'","License":"Apache License 2.0","Copyright":"See file (inst/)COPYRIGHTS.","BugReports":"https://github.com/ropensci/redland-bindings/issues","RoxygenNote":"7.2.3","URL":"https://github.com/ropensci/redland-bindings/tree/master/R/redland\nhttps://github.com/ropensci/redland-bindings/tree/master/R","Encoding":"UTF-8","Language":"en-US","Roxygen":"list(roclets = c(\"collate\", \"rd\", \"namespace\",\n\"mergeNamespace_roclet\"), markdown=TRUE)","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/redland-bindings","RemoteRef":"master","RemoteSha":"8f0d0d569372501126e3c8bc0cc3497f363eec7a","NeedsCompilation":"yes","Packaged":{"Date":"2024-10-26 05:42:15 UTC","User":"root"},"Author":"Matthew B. Jones [aut, cre] (),\nPeter Slaughter [aut] (),\nJeroen Ooms [aut] (),\nCarl Boettiger [aut] (),\nScott Chamberlain [ctb] (),\nDavid Beckett [cph],\nUniversity of Bristol [cph],\nRegents of the University of California [cph]","Maintainer":"Matthew B. 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message from log entry.","topics":["librdf_log_message_message"]},{"page":"librdf_model_add","title":"Create and add a new statement about a resource to the model.","topics":["librdf_model_add"]},{"page":"librdf_model_add_statement","title":"Add a statement to the model.","topics":["librdf_model_add_statement"]},{"page":"librdf_model_add_statements","title":"Add a stream of statements to the model.","topics":["librdf_model_add_statements"]},{"page":"librdf_model_add_string_literal_statement","title":"Create and add a new statement about a literal to the model.","topics":["librdf_model_add_string_literal_statement"]},{"page":"librdf_model_add_typed_literal_statement","title":"Create and add a new statement about a typed literal to the model.","topics":["librdf_model_add_typed_literal_statement"]},{"page":"librdf_model_as_stream","title":"List the model contents as a stream of statements.","topics":["librdf_model_as_stream"]},{"page":"librdf_model_contains_context","title":"Check for a 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Collating\nand manipulating data from CliFlo (hence clifro) and importing\ninto R for further analysis, exploration and visualisation is\nnow straightforward and coherent. The user is required to have\nan internet connection, and a current CliFlo subscription\n(free) if data from stations, other than the public Reefton\nelectronic weather station, is sought.","URL":"https://docs.ropensci.org/clifro/,\nhttps://github.com/ropensci/clifro","BugReports":"https://github.com/ropensci/clifro/issues","License":"GPL-2","Encoding":"UTF-8","Collate":"'dataFrame.R' 'cfStation.R' 'cfData.R' 'cfDataList.R'\n'cfData-plotMethods.R' 'cfDatatype.R' 'cfQuery.R' 'cfUser.R'\n'findStations.R'","RoxygenNote":"7.2.3","Language":"en-GB","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/clifro","RemoteRef":"master","RemoteSha":"46c72d399ee3d6069cfffa87a4452f85794bdef9","NeedsCompilation":"no","Packaged":{"Date":"2024-10-28 06:06:58 UTC","User":"root"},"Author":"Blake Seers [aut, cre] ()","Maintainer":"Blake Seers ","MD5sum":"70ac79d54140f1c40a0d38021d5ec406","_user":"ropensci","_file":"clifro_3.2-5.9003.tar.gz","_fileid":"621a8a019b4e2a4f912cc92b15d9c076b07b8391170338d9d4bb305dd1193387","_filesize":2089305,"_sha256":"621a8a019b4e2a4f912cc92b15d9c076b07b8391170338d9d4bb305dd1193387","_created":"2024-10-28T06:06:58.000Z","_published":"2024-10-28T06:10:12.624Z","_buildurl":"https://github.com/r-universe/ropensci/actions/runs/11548285962","_status":"success","_windevel":"failure","_linuxdevel":"failure","_wasmbinary":"success","_macbinary":"failure","_winbinary":"failure","_pkgdocs":"success","_upstream":"https://github.com/ropensci/clifro","_commit":{"id":"46c72d399ee3d6069cfffa87a4452f85794bdef9","author":"Seers, Blake (Environment, Aspendale) ","committer":"Seers, Blake (Environment, Aspendale) ","message":"Update documentation for the calm_wind argument in the windrose function. 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data from another format into a viewr object","topics":["as_viewr"]},{"page":"bind_viewr_objects","title":"Bind viewr objects","topics":["bind_viewr_objects"]},{"page":"calc_min_dist_box","title":"Calculate minimum distance to lateral and end walls in a box-shaped experimental tunnel","topics":["calc_min_dist_box"]},{"page":"calc_min_dist_v","title":"Calculate minimum distance to lateral and end walls in a V-shaped experimental tunnel","topics":["calc_min_dist_v"]},{"page":"clean_by_span","title":"Remove file_sub_traj entries that do not span the full region of interest","topics":["clean_by_span"]},{"page":"clean_viewr","title":"All-in-one function to clean imported objects","topics":["clean_viewr"]},{"page":"clean_viewr_batch","title":"Batch clean viewr files","topics":["clean_viewr_batch"]},{"page":"deg_2_rad","title":"Convert degrees to radians","topics":["deg_2_rad"]},{"page":"exclude_by_velocity","title":"Remove trajectories entirely, based on velocity thresholds","topics":["exclude_by_velocity"]},{"page":"fill_traj_gaps","title":"Interpolate gaps within trajectories","topics":["fill_traj_gaps"]},{"page":"find_curve_elbow","title":"Find the \"elbow\" of a curve.","topics":["find_curve_elbow"]},{"page":"gather_tunnel_data","title":"Gather data columns into key-value pairs","topics":["gather_tunnel_data"]},{"page":"get_2d_angle","title":"Compute an angle in 2D space","topics":["get_2d_angle"]},{"page":"get_3d_angle","title":"Compute an angle in 3D space","topics":["get_3d_angle"]},{"page":"get_3d_cross_prod","title":"Compute the cross product of two 3D vectors","topics":["get_3d_cross_prod"]},{"page":"get_dist_point_line","title":"Compute distance between a point and a line","topics":["get_dist_point_line"]},{"page":"get_full_trajectories","title":"Retain trajectories that span a selected region of interest","topics":["get_full_trajectories"]},{"page":"get_header_viewr","title":"Extract header info from imported viewr object","topics":["get_header_viewr"]},{"page":"get_sf","title":"Estimate the spatial frequency of visual stimuli from the subject's perspective in an experimental tunnel.","topics":["get_sf"]},{"page":"get_traj_velocities","title":"Recompute trajectory-specific velocities","topics":["get_traj_velocities"]},{"page":"get_velocity","title":"Get instantaneous velocity for subjects","topics":["get_velocity"]},{"page":"get_vis_angle","title":"Estimate visual angles from a subject's perspective in an experimental tunnel","topics":["get_vis_angle"]},{"page":"import_and_clean_batch","title":"Batch import and clean files","topics":["import_and_clean_batch"]},{"page":"import_and_clean_viewr","title":"Import + clean_viewr()","topics":["import_and_clean_viewr"]},{"page":"import_batch","title":"Batch import of files for either Motive or Flydra (but not a mix of both)","topics":["import_batch"]},{"page":"insert_treatments","title":"Inserts treatment and experiment information","topics":["insert_treatments"]},{"page":"plot_by_subject","title":"Plot trajectories and density plots of position by subject","topics":["plot_by_subject"]},{"page":"plot_viewr_trajectories","title":"Plot each trajectory within a viewr object","topics":["plot_viewr_trajectories"]},{"page":"quick_separate_trajectories","title":"Quick version of separate_trajectories()","topics":["quick_separate_trajectories"]},{"page":"rad_2_deg","title":"Convert radians to degrees","topics":["rad_2_deg"]},{"page":"read_flydra_mat","title":"Import data from a MAT file exported from Flydra software","topics":["read_flydra_mat"]},{"page":"read_motive_csv","title":"Import data from a CSV exported from Optitrack's Motive software","topics":["read_motive_csv"]},{"page":"redefine_tunnel_center","title":"\"Center\" the tunnel data, i.e. translation but no rotation","topics":["redefine_tunnel_center"]},{"page":"relabel_viewr_axes","title":"Relabel the dimensions as length, width, and height","topics":["relabel_viewr_axes"]},{"page":"remove_duplicate_frames","title":"Remove any duplicates or aliased frames within trajectories","topics":["remove_duplicate_frames"]},{"page":"remove_vel_anomalies","title":"Remove any rows which show sharp shifts in velocity that are likely due to tracking errors","topics":["remove_vel_anomalies"]},{"page":"rename_viewr_characters","title":"Rename subjects in the data via pattern detection","topics":["rename_viewr_characters"]},{"page":"rescale_tunnel_data","title":"Rescale position data within a 'viewr' object","topics":["rescale_tunnel_data"]},{"page":"rm_by_trajnum","title":"Remove subjects by trajectory number","topics":["rm_by_trajnum"]},{"page":"rotate_tunnel","title":"Rotate a tunnel so that perches are approximately aligned","topics":["rotate_tunnel"]},{"page":"section_tunnel_by","title":"Bin data along a specified axis","topics":["section_tunnel_by"]},{"page":"select_x_percent","title":"Select a region of interest within the 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