[med-svn] [r-cran-taxize] branch upstream updated (fc801b9 -> e376bf0)
Andreas Tille
tille at debian.org
Mon Oct 2 12:34:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository r-cran-taxize.
from fc801b9 New upstream version 0.8.4
new e376bf0 New upstream version 0.9.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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(-)
create mode 100644 R/downstream-utils.R
create mode 100644 R/get-id-details.R
create mode 100644 R/get_iucn.R
create mode 100644 R/get_utils.R
create mode 100644 R/get_wiki.R
create mode 100644 R/ncbi_downstream.R
create mode 100644 man/get_id_details.Rd
create mode 100644 man/get_iucn.Rd
create mode 100644 man/get_wiki.Rd
create mode 100644 man/ncbi_downstream.Rd
create mode 100644 tests/testthat/helper-taxize.R
create mode 100644 tests/testthat/test-genbank2uid.R
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