[med-svn] [r-cran-taxize] 02/06: Updated version 0.9.0 from 'upstream/0.9.0'
Andreas Tille
tille at debian.org
Mon Oct 2 12:34:48 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-taxize.
commit 249b1742d05864cd2f8504296253657520124910
Merge: dbf8984 e376bf0
Author: Andreas Tille <tille at debian.org>
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(-)
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