Man pages for bomeara/chapter2
Creates an Initial Report for a Clade
| aggregate_category | Aggregate count by category |
| aggregate_phydo_traits | Aggregate phydo traits |
| check_continuous | Check a data.frame to see which columns are continuous |
| check_numeric_vector | Check a vector to see if the elements are numeric |
| construct_phydo_targets | Do phydo analysis with targets |
| contrasts_correlations | All pairwise correlations |
| convert_continuous_to_discrete | Continuous to discrete |
| eol_data | Query Encyclopedia of Life with a URL to return all data for... |
| eol_traits | Collapse the data frame produced by eol_data to a single row... |
| eol_traits2 | Collapse the data frame produced by eol_data to a single row... |
| fishbase_genus_query | Get information on fish localities rfishbase |
| fishbase_species_query | Get information on fish localities rfishbase |
| gbif_species_query | Query gbif to return latitude and longitude for a vector of... |
| gbif_taxon_query | Query gbif to return latitude and longitude for members of a... |
| get_combie_image_summary | Get Wikipedia images |
| get_datelife_all | Get all tree from datelife |
| get_datelife_biggest | Get biggest tree from datelife |
| get_descendant_species | Get all descendant species of the taxon |
| get_eol | Get info from Encyclopedia of Life |
| get_genbank_count | Information about the number of species in the clade in... |
| get_genbank_count_by_gene | Get the count of number of sequences for different genes for... |
| get_location_realm_biome | Get location, realm, and biome |
| get_otol | Get info from Open Tree of Life |
| get_phydo_data | Get phydo raw data |
| get_pubmed | Get information on the clade from pubmed |
| get_pubmed_count_only | Get information on the count of papers from pubmed |
| get_pubmed_info_on_OTOL | Aggregate pubmed data down OToLtree |
| get_wikipedia_pics | Get Wikipedia images |
| get_wikipedia_summary | Get Wikipedia summary |
| locality_add_habitat_biome | Uses info from... |
| locality_clean | Clean locality information |
| match_data | Get a tree and data, resolve to same set of taxa, and make a... |
| pbdb_taxon_query | Get information on specimens from the paleobiology data base... |
| phydo_convert_to_Beaulieu_data | Convert the phydo format to one usable for Beaulieu-style |
| phydo_drop_type | Return a phydo object with only the selected kind of traits |
| phydo_fitGeiger | Try geiger's fitContinuous or fitDiscrete on all the... |
| plot_gis | Plot a map of points |
| plot_pubmed_info_on_OTOL | Plot pubmed data down OToLtree |
| reconstruct_apomorphy | Reconstruct an apomorphy down a tree using parsimony |
| render_phydo | Create a file of results |
| render_quarto | Create a file of results |
| reroot.tree | Root a tree |
| run_biogeobears | Run biogeobears analyses |
| run_corHMM | Run a corHMM analysis |
| run_misse | Run misse analysis |
| run_phydo | Do phydo analysis |
| spocc_taxon_query | Query many sources at once using spocc to get latitude and... |
| WWFload | Use azizka/speciesgeocodeR/ and WWF data to encode locations... |
