Files in ropensci/taxize
Taxonomic Information from Around the Web

.Rbuildignore

.gitattributes

.github/CONTRIBUTING.md .github/issue_template.md .github/pull_request_template.md

.github/workflows/R-CMD-check.yaml

.github/workflows/revdep-check.yaml

.gitignore

DESCRIPTION

LICENSE

LICENSE.md

Makefile

NAMESPACE

NEWS.md R/aaa.R R/apg.R R/apg_lookup.R R/bold_downstream.R R/bold_search.R R/children.R R/class2tree.R R/classification.R R/col.R R/comm2sci.R R/downstream-utils.R R/downstream.R R/eol_dataobjects.R R/eol_hierarchy.R R/eol_invasive.R R/eol_pages.R R/eol_search.R R/eol_utiils.R R/eubon.R R/eubon_capabilities.R R/eubon_children.R R/eubon_hierarchy.R R/fungorum.R R/gbif_downstream.R R/gbif_helpers.R R/gbif_name_usage.R R/gbif_parse.R R/genbank2uid.R R/get-id-details.R R/get_boldid.R R/get_eolid.R R/get_gbifid.R R/get_ids.R R/get_iucn.R R/get_natservid.R R/get_nbnid.R R/get_pow.R R/get_tolid.R R/get_tpsid.R R/get_tsn.R R/get_ubioid.R R/get_uid.R R/get_utils.R R/get_wiki.R R/get_wormsid.R R/getkey.R R/gisd_isinvasive.R R/globals.R R/gn_parse.R R/gni_details.R R/gni_helpers.R R/gni_parse.R R/gni_search.R R/gnr_datasources.R R/gnr_resolve.R R/http.R R/id2name.R R/ion.R R/iplant_resolve.R R/ipni_search.R R/itis_acceptname.R R/itis_downstream.R R/itis_getrecord.R R/itis_hierarchy.R R/itis_kingdomnames.R R/itis_lsid.R R/itis_name.R R/itis_native.R R/itis_refs.R R/itis_taxrank.R R/itis_terms.R R/iucn_getname.R R/iucn_id.R R/iucn_summary.R R/key_helpers.R R/limited_print.R R/lowest_common.R R/messages.R R/names_list.r R/nbn_classification.R R/nbn_search.R R/nbn_synonyms.R R/ncbi_children.R R/ncbi_downstream.R R/ncbi_get_taxon_summary.R R/ncbi_getbyid.R R/ncbi_getbyname.R R/ncbi_search.R R/onload.R R/phylomatic_format.R R/phylomatic_tree.R R/ping.R R/plantminer.R R/pow_search.R R/progressor.R R/rankagg.R R/rename.R R/resolve.R R/sci2comm.R R/scrapenames.r R/status_codes.R R/synonyms.R R/tax_agg.R R/tax_name.R R/tax_rank.R R/taxize-authentication.R R/taxize-package.R R/taxize-params.R R/taxize_capwords.r R/taxize_cite.R R/taxize_ldfast.R R/taxize_options.R R/taxon_state.R R/tnrs.R R/tnrs_sources.r R/tol_id2name.R R/tol_resolve.R R/tp_accnames.R R/tp_classification.R R/tp_dist.R R/tp_refs.R R/tp_search.R R/tp_summary.R R/tp_synonyms.R R/tpl_families.r R/tpl_get.r R/tpl_search.r R/ubio_classification.R R/ubio_classification_search.R R/ubio_id.R R/ubio_search.R R/ubio_synonyms.R R/upstream.R R/vascan_search.r R/worms_downstream.R R/zzz.R README.Rmd README.md

_pkgdown.yml

codemeta.json

cran-comments.md

data/apg_families.RData

data/apg_orders.RData

data/plantGenusNames.RData

data/plantNames.RData

data/rank_ref.RData

data/rank_ref_zoo.RData

data/species_plantarum_binomials.rda

data/theplantlist.RData

data/worrms_ranks.RData

inst/CITATION

inst/examples/species.txt

inst/ignore/aou_notes.R inst/ignore/apg_script.R inst/ignore/nature_serve.R inst/ignore/phylomatic_tree2.R inst/ignore/phytools_fxns_touse.r inst/ignore/rank_ref_script.R inst/ignore/rbladj.r inst/ignore/taxonclass.R inst/ignore/taxonclass2.R inst/ignore/taxonid.R inst/ignore/tests/test-ubio_classification.R inst/ignore/tests/test-ubio_id.R inst/ignore/tests/test-ubio_namebank.R inst/ignore/tests/test-ubio_search.R inst/ignore/tests/test-ubio_synonyms.R inst/ignore/try_with_timeout.R log.Rmd man-roxygen/getreturn.R man-roxygen/ncbi.R man/apg.Rd man/apg_families.Rd man/apg_lookup.Rd man/apg_orders.Rd man/bold_children.Rd man/bold_downstream.Rd man/bold_search.Rd man/children.Rd man/class2tree.Rd man/classification.Rd man/col-defunct.Rd man/comm2sci.Rd man/downstream.Rd man/eol_dataobjects.Rd man/eol_hierarchy-defunct.Rd man/eol_invasive-defunct.Rd man/eol_pages.Rd man/eol_search.Rd man/eubon-defunct.Rd man/eubon_capabilities.Rd man/eubon_children.Rd man/eubon_hierarchy.Rd man/eubon_search.Rd

man/figures/screencast.png

man/fungorum.Rd man/gbif_downstream.Rd man/gbif_name_usage.Rd man/gbif_parse.Rd man/genbank2uid.Rd man/get_boldid.Rd man/get_eolid.Rd man/get_gbifid.Rd man/get_genes-defunct.Rd man/get_genes_avail-defunct.Rd man/get_id_details.Rd man/get_ids.Rd man/get_iucn.Rd man/get_natservid.Rd man/get_nbnid.Rd man/get_pow.Rd man/get_seqs-defunct.Rd man/get_tolid.Rd man/get_tpsid.Rd man/get_tsn.Rd man/get_ubioid-defunct.Rd man/get_uid.Rd man/get_wiki.Rd man/get_wormsid.Rd man/getkey.Rd man/gisd_invasive-defunct.Rd man/gn_parse.Rd man/gni_details.Rd man/gni_parse.Rd man/gni_search.Rd man/gnr_datasources.Rd man/gnr_resolve.Rd man/id2name.Rd man/ion.Rd man/iplant_resolve.Rd man/ipni_search.Rd man/itis_acceptname.Rd man/itis_downstream.Rd man/itis_getrecord.Rd man/itis_hierarchy.Rd man/itis_kingdomnames.Rd man/itis_lsid.Rd man/itis_name-deprecated.Rd man/itis_native.Rd man/itis_refs.Rd man/itis_taxrank.Rd man/itis_terms.Rd man/iucn_getname.Rd man/iucn_id.Rd man/iucn_status.Rd man/iucn_summary.Rd man/iucn_summary_id-defunct.Rd man/key_helpers.Rd man/limited_print.Rd man/lowest_common.Rd man/names_list.Rd man/nbn_classification.Rd man/nbn_search.Rd man/nbn_synonyms.Rd man/ncbi_children.Rd man/ncbi_downstream.Rd man/ncbi_get_taxon_summary.Rd man/ncbi_getbyid-defunct.Rd man/ncbi_getbyname-defunct.Rd man/ncbi_search-defunct.Rd man/phylomatic_format-defunct.Rd man/phylomatic_tree-defunct.Rd man/ping.Rd man/plantGenusNames.Rd man/plantNames.Rd man/plantminer.Rd man/pow_lookup.Rd man/pow_search.Rd man/pow_synonyms.Rd man/progressor.Rd man/rank_ref.Rd man/rank_ref_zoo.Rd man/rankagg.Rd man/resolve.Rd man/sci2comm.Rd man/scrapenames.Rd man/species_plantarum_binomials.Rd man/status_codes.Rd man/synonyms.Rd man/tax_agg.Rd man/tax_name.Rd man/tax_rank.Rd man/taxize-authentication.Rd man/taxize-defunct.Rd man/taxize-package.Rd man/taxize-params.Rd man/taxize_capwords.Rd man/taxize_cite.Rd man/taxize_ldfast.Rd man/taxize_options.Rd man/taxon-state.Rd man/taxon_state.Rd man/theplantlist.Rd man/tnrs-defunct.Rd man/tnrs_sources-defunct.Rd man/tol_resolve.Rd man/tp_acceptednames-deprecated.Rd man/tp_accnames.Rd man/tp_classification-defunct.Rd man/tp_dist.Rd man/tp_namedistributions-deprecated.Rd man/tp_namereferences-deprecated.Rd man/tp_refs.Rd man/tp_search.Rd man/tp_summary.Rd man/tp_synonyms.Rd man/tpl_families.Rd man/tpl_get.Rd man/tpl_search-defunct.Rd man/ubio_classification-defunct.Rd man/ubio_classification_search-defunct.Rd man/ubio_id-defunct.Rd man/ubio_ping-defunct.Rd man/ubio_search-defunct.Rd man/ubio_synonyms-defunct.Rd man/upstream.Rd man/use_eol-defunct.Rd man/vascan_search.Rd man/worms_downstream.Rd man/worrms_ranks.Rd

tests/fixtures/apgFamilies.yml

tests/fixtures/apgOrders.yml

tests/fixtures/bold_children.yml

tests/fixtures/bold_children_no_results.yml

tests/fixtures/bold_downstream.yml

tests/fixtures/bold_downstream_intermediate.yml

tests/fixtures/bold_ping.yml

tests/fixtures/bold_search.yml

tests/fixtures/children_ambiguous_ncbi.yml

tests/fixtures/children_bold.yml

tests/fixtures/children_itis_types.yml

tests/fixtures/children_no_results.yml

tests/fixtures/children_no_results_structure_ncbi_x.yml

tests/fixtures/children_no_results_structure_ncbi_y.yml

tests/fixtures/children_no_results_structure_x.yml

tests/fixtures/children_no_results_structure_y.yml

tests/fixtures/children_rows_param.yml

tests/fixtures/children_warn_on_db_mismatch.yml

tests/fixtures/children_with_id.yml

tests/fixtures/children_with_name.yml

tests/fixtures/children_worms_marine_only.yml

tests/fixtures/class2tree_classification_call.yml

tests/fixtures/class2tree_classification_dup_call.yml

tests/fixtures/class2tree_internal_fxns.yml

tests/fixtures/classification.yml

tests/fixtures/classification_cbind_rbind.yml

tests/fixtures/classification_fetches_merged_taxon.yml

tests/fixtures/classification_gbif.yml

tests/fixtures/classification_gbif_get_fxn.yml

tests/fixtures/classification_gbif_ranks_below_species_subsp.yml

tests/fixtures/classification_gbif_ranks_below_species_var.yml

tests/fixtures/classification_gbif_ranks_correct_order.yml

tests/fixtures/classification_get_fxn.yml

tests/fixtures/classification_no_results.yml

tests/fixtures/classification_passing_id.yml

tests/fixtures/classification_pow.yml

tests/fixtures/classification_pow_cbind_rbind.yml

tests/fixtures/classification_pow_get_fxn.yml

tests/fixtures/classification_pow_more_name_egs.yml

tests/fixtures/classification_pow_no_results.yml

tests/fixtures/classification_pow_passing_id.yml

tests/fixtures/classification_rank_is_lowercase.yml

tests/fixtures/classification_rows_param.yml

tests/fixtures/classification_variety_of_names.yml

tests/fixtures/classification_warn_on_db_mismatch.yml

tests/fixtures/comm2sci.yml

tests/fixtures/comm2sci_warn_on_db_mismatch.yml

tests/fixtures/downstream.yml

tests/fixtures/downstream_bold.yml

tests/fixtures/downstream_id_input.yml

tests/fixtures/downstream_multiple_data_sources.yml

tests/fixtures/downstream_rows_param.yml

tests/fixtures/downstream_warn_on_db_mismatch.yml

tests/fixtures/downstream_worms_marine_only_para.yml

tests/fixtures/eol_dataobjects.yml

tests/fixtures/eol_dataobjects_taxonomy_param.yml

tests/fixtures/eol_pages.yml

tests/fixtures/eol_pages2.yml

tests/fixtures/eol_search.yml

tests/fixtures/eubon_search.yml

tests/fixtures/fg_author_search.yml

tests/fixtures/fg_epithet_search.yml

tests/fixtures/fg_name_by_key.yml

tests/fixtures/fg_name_full_by_lsid.yml

tests/fixtures/fg_name_search.yml

tests/fixtures/gbif_downstream.yml

tests/fixtures/gbif_downstream_intermediate.yml

tests/fixtures/gbif_downstream_pagination.yml

tests/fixtures/gbif_parse.yml

tests/fixtures/gbif_ping.yml

tests/fixtures/genbank2uid.yml

tests/fixtures/genbank2uid_fails.yml

tests/fixtures/genbank2uid_gi_numbers.yml

tests/fixtures/get_boldid.yml

tests/fixtures/get_boldid_ask_false.yml

tests/fixtures/get_boldid_no_parent_name.yml

tests/fixtures/get_colid.yml

tests/fixtures/get_colid_ask_arg.yml

tests/fixtures/get_eolid.yml

tests/fixtures/get_eolid_ask_param.yml

tests/fixtures/get_gbifid.yml

tests/fixtures/get_gbifid_ask_arg.yml

tests/fixtures/get_gbifid_class_doesnt_matter.yml

tests/fixtures/get_gbifid_method_param.yml

tests/fixtures/get_gbifid_phylum_param.yml

tests/fixtures/get_gbifid_state.yml

tests/fixtures/get_natservid.yml

tests/fixtures/get_natservid_ask_arg.yml

tests/fixtures/get_pow.yml

tests/fixtures/get_pow_accepted_no_results.yml

tests/fixtures/get_pow_ask_arg.yml

tests/fixtures/get_tolid.yml

tests/fixtures/get_tolid_ask_arg.yml

tests/fixtures/get_tpsid.yml

tests/fixtures/get_tpsid_ask_arg.yml

tests/fixtures/get_tpsid_warnings_dots.yml

tests/fixtures/get_tpsid_warnings_subspecific.yml

tests/fixtures/get_tsn.yml

tests/fixtures/get_tsn_ask_verbose_args.yml

tests/fixtures/get_uid.yml

tests/fixtures/get_uid_ask_arg.yml

tests/fixtures/get_uid_filtering_division.yml

tests/fixtures/get_uid_filtering_rank.yml

tests/fixtures/get_uid_name_modifiers.yml

tests/fixtures/get_uid_rank_modifiers.yml

tests/fixtures/get_wormsid.yml

tests/fixtures/get_wormsid_ask_arg.yml

tests/fixtures/get_wormsid_fail_with_rows_unknown.yml

tests/fixtures/get_wormsid_fuzzy.yml

tests/fixtures/get_wormsid_marine_only.yml

tests/fixtures/get_wormsid_multiple_exact_matches_found.yml

tests/fixtures/get_wormsid_query_modifiers.yml

tests/fixtures/gn_parse.yml

tests/fixtures/gni_details.yml

tests/fixtures/gni_parse.yml

tests/fixtures/gni_parse_not_parsed.yml

tests/fixtures/gni_search.yml

tests/fixtures/gnr_datasources.yml

tests/fixtures/id2name_warn_on_db_mismatch.yml

tests/fixtures/ion.yml

tests/fixtures/ion_fails_well.yml

tests/fixtures/ipni_search.yml

tests/fixtures/ipni_search_no_results.yml

tests/fixtures/ipni_search_output_formats.yml

tests/fixtures/itis_acceptname.yml

tests/fixtures/itis_acceptname_non_accepted_tsn.yml

tests/fixtures/itis_downstream.yml

tests/fixtures/itis_getrecord.yml

tests/fixtures/itis_hierarchy.yml

tests/fixtures/itis_kingdomnames.yml

tests/fixtures/itis_kingdomnames_fail_well.yml

tests/fixtures/itis_kingdomnames_with_tsns.yml

tests/fixtures/itis_lsid.yml

tests/fixtures/itis_native.yml

tests/fixtures/itis_ping.yml

tests/fixtures/itis_ping_http_code_200.yml

tests/fixtures/itis_ping_http_code_503.yml

tests/fixtures/itis_refs.yml

tests/fixtures/itis_taxrank.yml

tests/fixtures/itis_terms.yml

tests/fixtures/iucn_getname.yml

tests/fixtures/iucn_id.yml

tests/fixtures/iucn_id_fail.yml

tests/fixtures/iucn_summary.yml

tests/fixtures/iucn_summary_other_egs.yml

tests/fixtures/nbn_ping.yml

tests/fixtures/ncbi_children.yml

tests/fixtures/ncbi_children_ambiguous.yml

tests/fixtures/ncbi_children_id_class_check.yml

tests/fixtures/ncbi_downstream.yml

tests/fixtures/ncbi_downstream_ambiguous_false.yml

tests/fixtures/ncbi_downstream_ambiguous_true.yml

tests/fixtures/ncbi_downstream_handles_self_ids.yml

tests/fixtures/ncbi_downstream_intermediate.yml

tests/fixtures/ncbi_get_taxon_summary.yml

tests/fixtures/ncbi_get_taxon_summary_many_ids_long.yml

tests/fixtures/ncbi_get_taxon_summary_many_ids_short.yml

tests/fixtures/ncbi_ping.yml

tests/fixtures/plantminer.yml

tests/fixtures/plantminer_not_found.yml

tests/fixtures/pow_lookup.yml

tests/fixtures/pow_lookup_include_param.yml

tests/fixtures/pow_search.yml

tests/fixtures/sci2comm.yml

tests/fixtures/sci2comm_warn_on_db_mismatch.yml

tests/fixtures/synonyms_itis.yml

tests/fixtures/synonyms_name_found_but_no_synonyms.yml

tests/fixtures/synonyms_name_found_but_no_synonyms_redlist.yml

tests/fixtures/synonyms_name_not_found.yml

tests/fixtures/synonyms_name_not_found_redlist.yml

tests/fixtures/synonyms_warn_on_db_mismatch.yml

tests/fixtures/synonyms_worms.yml

tests/fixtures/tax_name_arg_arg.yml

tests/fixtures/tax_name_itis.yml

tests/fixtures/tax_name_na.yml

tests/fixtures/tax_name_ncbi.yml

tests/fixtures/tax_name_no_data.yml

tests/fixtures/tax_name_rows_Arg.yml

tests/fixtures/tax_name_throws_warning.yml

tests/fixtures/tax_rank.yml

tests/fixtures/tax_rank_get_star_input.yml

tests/fixtures/taxon_state_get_gbifid.yml

tests/fixtures/taxon_state_get_uid.yml

tests/fixtures/tnrs.yml

tests/fixtures/tnrs_order_row_names.yml

tests/fixtures/tnrs_sources.yml

tests/fixtures/tol_resolve.yml

tests/fixtures/tol_resolve_context_name.yml

tests/fixtures/tol_resolve_do_approximate_matching.yml

tests/fixtures/tol_resolve_do_approximate_matching_false.yml

tests/fixtures/tp_accnames.yml

tests/fixtures/tp_dist.yml

tests/fixtures/tp_refs.yml

tests/fixtures/tp_search.yml

tests/fixtures/tp_search_warnings_dots.yml

tests/fixtures/tp_search_warnings_subspecific.yml

tests/fixtures/tp_summary.yml

tests/fixtures/tp_synonyms.yml

tests/fixtures/trpicos_ping.yml

tests/fixtures/upstream.yml

tests/fixtures/vascan_ping.yml

tests/fixtures/vascan_search.yml

tests/fixtures/worms_downstream.yml

tests/fixtures/worms_downstream_intermediate_param.yml

tests/fixtures/worms_downstream_marine_only_para.yml

tests/fixtures/worms_downstream_previously_unaccounted_for_ranks.yml

tests/fixtures/worms_downstream_start_param.yml

tools/screencast.png

vignettes/case_study.Rmd

vignettes/case_study.Rmd.og

vignettes/datasources.Rmd

vignettes/datasources.Rmd.og

vignettes/infotable.Rmd

vignettes/margins.sty

vignettes/name_cleaning.Rmd

vignettes/name_cleaning.Rmd.og

vignettes/taxize.Rmd

vignettes/taxize.Rmd.og

vignettes/taxonomic_ranks.Rmd

vignettes/taxonomic_ranks.Rmd.og

ropensci/taxize documentation built on Jan. 25, 2024, 6:49 p.m.

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ropensci/taxize
Taxonomic Information from Around the Web

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Taxonomic Information from Around the Web

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ropensci/taxize Taxonomic Information from Around the Web

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ropensci/taxize
Taxonomic Information from Around the Web

Files in ropensci/taxize
Taxonomic Information from Around the Web