[med-svn] [r-cran-taxize] branch master updated (dbf8984 -> 366cfad)
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 change to branch master
in repository r-cran-taxize.
from dbf8984 Moved packaging from SVN to Git
new e376bf0 New upstream version 0.9.0
new 249b174 Updated version 0.9.0 from 'upstream/0.9.0'
new 21446ce New upstream version
new e340650 Standards-Version: 4.1.1
new 5fa74ac Add debian/README.source to document binary data files
new 366cfad New Build-Depends: r-cran-wikitaxa
The 6 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
debian/README.source | 28 ++
debian/changelog | 7 +-
debian/control | 5 +-
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 +++++++++++++++-----------
231 files changed, 5794 insertions(+), 2950 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 debian/README.source
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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