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commit 249b1742d05864cd2f8504296253657520124910 Merge: dbf8984 e376bf0 Author: Andreas Tille <[email protected]> Date: Mon Oct 2 14:15:40 2017 +0200 Updated version 0.9.0 from 'upstream/0.9.0' with Debian dir 9e0faa1c515b513f402703b136a8a7a33e784583 DESCRIPTION | 20 +- MD5 | 442 +++++++++++++++--------------- NAMESPACE | 43 ++- NEWS.md | 318 ++++++++++++++------- R/children.R | 4 +- R/class2tree.R | 74 ++--- R/classification.R | 166 ++++++++--- R/col_children.R | 19 +- R/col_downstream.R | 66 +++-- R/col_search.R | 18 +- R/comm2sci.R | 227 ++++++++------- R/downstream-utils.R | 14 + R/downstream.R | 123 ++++++--- R/eol_search.R | 31 ++- R/eubon.R | 6 +- R/eubon_capabilities.R | 2 +- R/eubon_children.R | 4 +- R/eubon_hierarchy.R | 4 +- R/gbif_downstream.R | 24 +- R/genbank2uid.R | 78 ++++-- R/get-id-details.R | 70 +++++ R/get_boldid.R | 84 +++--- R/get_colid.R | 63 +++-- R/get_eolid.R | 17 +- R/get_gbifid.R | 72 +++-- R/get_iucn.R | 175 ++++++++++++ R/get_natservid.R | 45 ++- R/get_nbnid.R | 126 ++++++--- R/get_tolid.R | 48 ++-- R/get_tpsid.R | 61 +++-- R/get_tsn.R | 59 ++-- R/get_uid.R | 171 +++++++----- R/get_utils.R | 50 ++++ R/get_wiki.R | 303 ++++++++++++++++++++ R/get_wormsid.R | 32 ++- R/gnr_resolve.R | 142 +++++++--- R/itis_getrecord.R | 2 +- R/iucn_getname.R | 3 +- R/iucn_id.R | 31 +-- R/iucn_summary.R | 182 +++++++++--- R/nbn_classification.R | 16 +- R/nbn_search.R | 67 +++-- R/nbn_synonyms.R | 12 +- R/ncbi_downstream.R | 89 ++++++ R/ping.R | 27 +- R/plantminer.R | 4 +- R/sci2comm.R | 153 +++++++---- R/scrapenames.r | 79 +++--- R/synonyms.R | 57 +++- R/tax_agg.R | 2 +- R/tax_name.R | 13 +- R/tax_rank.R | 154 ++++++----- R/taxize-package.R | 19 +- R/tnrs.R | 32 ++- R/tpl_get.r | 1 + R/upstream.R | 2 +- R/zzz.R | 58 ++-- README.md | 97 +++++-- build/vignette.rds | Bin 282 -> 282 bytes data/rank_ref.RData | Bin 531 -> 470 bytes inst/doc/name_cleaning.Rmd | 105 ++++--- inst/doc/name_cleaning.html | 105 ++++--- inst/doc/taxize_infotable.Rmd | 34 ++- inst/doc/taxize_infotable.html | 72 ++++- inst/doc/taxize_vignette.Rmd | 389 +++++++++++++++----------- inst/doc/taxize_vignette.html | 392 ++++++++++++++------------ inst/vign/name_cleaning.md | 72 +++-- inst/vign/taxize_infotable.Rmd | 34 ++- inst/vign/taxize_infotable.md | 34 ++- inst/vign/taxize_vignette.md | 70 ++--- man/apg.Rd | 3 +- man/apg_families.Rd | 3 +- man/apg_lookup.Rd | 1 - man/apg_orders.Rd | 3 +- man/bold_search.Rd | 1 - man/children.Rd | 11 +- man/class2tree.Rd | 58 ++-- man/classification.Rd | 102 ++++--- man/col_children.Rd | 10 +- man/col_classification-defunct.Rd | 1 - man/col_downstream.Rd | 4 +- man/col_search.Rd | 1 - man/comm2sci.Rd | 48 ++-- man/downstream.Rd | 84 +++--- man/eol_dataobjects.Rd | 1 - man/eol_hierarchy-defunct.Rd | 1 - man/eol_invasive-defunct.Rd | 1 - man/eol_pages.Rd | 1 - man/eol_search.Rd | 13 +- man/eubon.Rd | 7 +- man/eubon_capabilities.Rd | 5 +- man/eubon_children.Rd | 5 +- man/eubon_hierarchy.Rd | 5 +- man/fungorum.Rd | 9 +- man/gbif_downstream.Rd | 9 +- man/gbif_name_usage.Rd | 1 - man/gbif_parse.Rd | 7 +- man/genbank2uid.Rd | 14 +- man/get_boldid.Rd | 60 ++-- man/get_colid.Rd | 50 ++-- man/get_eolid.Rd | 51 ++-- man/get_gbifid.Rd | 52 ++-- man/get_genes-defunct.Rd | 1 - man/get_genes_avail-defunct.Rd | 1 - man/get_id_details.Rd | 78 ++++++ man/get_ids.Rd | 10 +- man/get_iucn.Rd | 97 +++++++ man/get_natservid.Rd | 50 ++-- man/get_nbnid.Rd | 92 ++++--- man/get_seqs-defunct.Rd | 1 - man/get_tolid.Rd | 43 ++- man/get_tpsid.Rd | 50 ++-- man/get_tsn.Rd | 52 ++-- man/get_ubioid-defunct.Rd | 10 +- man/get_uid.Rd | 135 +++++---- man/get_wiki.Rd | 114 ++++++++ man/get_wormsid.Rd | 45 ++- man/getkey.Rd | 1 - man/gisd_invasive-defunct.Rd | 1 - man/gni_details.Rd | 7 +- man/gni_parse.Rd | 1 - man/gni_search.Rd | 7 +- man/gnr_datasources.Rd | 7 +- man/gnr_resolve.Rd | 81 ++++-- man/ion.Rd | 1 - man/iplant_resolve.Rd | 1 - man/ipni_search.Rd | 1 - man/itis_acceptname.Rd | 1 - man/itis_downstream.Rd | 1 - man/itis_getrecord.Rd | 3 +- man/itis_hierarchy.Rd | 1 - man/itis_kingdomnames.Rd | 1 - man/itis_lsid.Rd | 1 - man/itis_name-deprecated.Rd | 1 - man/itis_native.Rd | 1 - man/itis_refs.Rd | 1 - man/itis_taxrank.Rd | 1 - man/itis_terms.Rd | 1 - man/iucn_getname.Rd | 4 +- man/iucn_id.Rd | 9 +- man/iucn_status.Rd | 1 - man/iucn_summary.Rd | 36 ++- man/lowest_common.Rd | 7 +- man/names_list.Rd | 1 - man/nbn_classification.Rd | 23 +- man/nbn_search.Rd | 51 ++-- man/nbn_synonyms.Rd | 13 +- man/ncbi_children.Rd | 7 +- man/ncbi_downstream.Rd | 57 ++++ man/ncbi_get_taxon_summary.Rd | 1 - man/ncbi_getbyid-defunct.Rd | 1 - man/ncbi_getbyname-defunct.Rd | 1 - man/ncbi_search-defunct.Rd | 1 - man/phylomatic_format-defunct.Rd | 1 - man/phylomatic_tree-defunct.Rd | 1 - man/ping.Rd | 13 +- man/plantGenusNames.Rd | 1 - man/plantNames.Rd | 1 - man/plantminer.Rd | 5 +- man/rank_ref.Rd | 17 +- man/rankagg.Rd | 1 - man/resolve.Rd | 1 - man/sci2comm.Rd | 32 ++- man/scrapenames.Rd | 62 +++-- man/status_codes.Rd | 1 - man/synonyms.Rd | 24 +- man/tax_agg.Rd | 5 +- man/tax_name.Rd | 10 +- man/tax_rank.Rd | 56 ++-- man/taxize-defunct.Rd | 3 +- man/taxize-package.Rd | 4 +- man/taxize_capwords.Rd | 1 - man/taxize_cite.Rd | 1 - man/taxize_ldfast.Rd | 1 - man/theplantlist.Rd | 1 - man/tnrs.Rd | 26 +- man/tnrs_sources.Rd | 1 - man/tol_resolve.Rd | 9 +- man/tp_acceptednames-deprecated.Rd | 1 - man/tp_accnames.Rd | 1 - man/tp_classification-defunct.Rd | 1 - man/tp_dist.Rd | 1 - man/tp_namedistributions-deprecated.Rd | 1 - man/tp_namereferences-deprecated.Rd | 1 - man/tp_refs.Rd | 1 - man/tp_search.Rd | 1 - man/tp_summary.Rd | 1 - man/tp_synonyms.Rd | 1 - man/tpl_families.Rd | 7 +- man/tpl_get.Rd | 8 +- man/tpl_search-defunct.Rd | 1 - man/ubio_classification-defunct.Rd | 1 - man/ubio_classification_search-defunct.Rd | 1 - man/ubio_id-defunct.Rd | 1 - man/ubio_ping-defunct.Rd | 1 - man/ubio_search-defunct.Rd | 1 - man/ubio_synonyms-defunct.Rd | 1 - man/upstream.Rd | 7 +- man/vascan_search.Rd | 7 +- tests/testthat/Rplots.pdf | Bin 4797 -> 4732 bytes tests/testthat/helper-taxize.R | 1 + tests/testthat/test-bold_search.R | 14 +- tests/testthat/test-class2tree.R | 6 +- tests/testthat/test-classification.R | 3 +- tests/testthat/test-comm2sci.R | 15 + tests/testthat/test-downstream.R | 14 + tests/testthat/test-genbank2uid.R | 89 ++++++ tests/testthat/test-get_boldid.R | 32 +++ tests/testthat/test-get_colid.R | 33 +++ tests/testthat/test-get_eolid.R | 15 + tests/testthat/test-get_gbifid.R | 33 +++ tests/testthat/test-get_natservid.R | 6 + tests/testthat/test-get_tpsid.R | 23 ++ tests/testthat/test-get_tsn.R | 35 ++- tests/testthat/test-get_uid.R | 33 ++- tests/testthat/test-get_wormsid.R | 13 +- tests/testthat/test-itis_getrecord.R | 3 +- tests/testthat/test-itis_lsid.R | 4 +- tests/testthat/test-iucn_summary.R | 18 +- tests/testthat/test-sci2comm.R | 6 +- tests/testthat/test-synonyms.R | 4 +- tests/testthat/test-tax_name.R | 24 +- tests/testthat/test-tax_rank.R | 45 ++- tests/testthat/test-tnrs.R | 38 ++- tests/testthat/test-tp_summary.R | 2 +- vignettes/name_cleaning.Rmd | 105 ++++--- vignettes/taxize_infotable.Rmd | 34 ++- vignettes/taxize_vignette.Rmd | 389 +++++++++++++++----------- 228 files changed, 5759 insertions(+), 2945 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-cran-taxize.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
