[med-svn] [r-cran-rotl] 11/12: Updated version 3.0.3 from 'upstream/3.0.3'

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-cran-rotl.

commit fdeee26d4745b842e930b3639c87219916187129
Merge: dde42d1 3521108
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 23 08:17:30 2017 +0200

    Updated version 3.0.3 from 'upstream/3.0.3'
    
    with Debian dir 653f8cf9e0b67af4d09a99549c8e381ac73237be

 DESCRIPTION                             |   8 +-
 LICENSE                                 |   2 +-
 MD5                                     | 106 ++++++++++++------------
 NAMESPACE                               |   3 +
 NEWS.md                                 |  23 ++++++
 R/api-studies.R                         |   9 +-
 R/deduplicate_labels.R                  |   3 +-
 R/is_in_tree.R                          |  50 ++++++++++++
 R/studies.R                             |  56 ++++++++-----
 R/tax_utils.R                           |   7 ++
 README.md                               | 140 ++++++++++++--------------------
 build/vignette.rds                      | Bin 316 -> 315 bytes
 inst/CITATION                           |  75 ++++++++++++-----
 inst/doc/data_mashups.html              |  22 ++---
 inst/doc/how-to-use-rotl.R              |  15 ++--
 inst/doc/how-to-use-rotl.Rmd            |  46 +++++++----
 inst/doc/how-to-use-rotl.html           |  92 +++++++++++++--------
 inst/doc/meta-analysis.R                |   3 +-
 inst/doc/meta-analysis.Rmd              |   5 +-
 inst/doc/meta-analysis.html             |  20 ++---
 inst/extdata/protist_mutation_rates.csv |   0
 man/get_study.Rd                        |   1 -
 man/get_study_meta.Rd                   |  13 ++-
 man/get_study_subtree.Rd                |  29 +++++--
 man/get_study_tree.Rd                   |   9 +-
 man/is_in_tree.Rd                       |  40 +++++++++
 man/list_trees.Rd                       |   1 -
 man/match_names-methods.Rd              |   5 +-
 man/match_names.Rd                      |   3 +-
 man/source_list.Rd                      |   1 -
 man/strip_ott_ids.Rd                    |   1 -
 man/studies_find_studies.Rd             |   1 -
 man/studies_find_trees.Rd               |   1 -
 man/studies_properties.Rd               |   1 -
 man/study_external_IDs.Rd               |   1 -
 man/synonyms.match_names.Rd             |   1 -
 man/tax_lineage.Rd                      |   1 -
 man/taxon_external_IDs.Rd               |   1 -
 man/taxonomy-methods.Rd                 |   7 +-
 man/taxonomy_about.Rd                   |   1 -
 man/taxonomy_mrca.Rd                    |  13 ++-
 man/taxonomy_subtree.Rd                 |   1 -
 man/taxonomy_taxon_info.Rd              |  15 ++--
 man/tnrs_contexts.Rd                    |   1 -
 man/tnrs_infer_context.Rd               |   1 -
 man/tnrs_match_names.Rd                 |   1 -
 man/tol_about.Rd                        |   7 +-
 man/tol_induced_subtree.Rd              |   1 -
 man/tol_mrca.Rd                         |  11 ++-
 man/tol_node_info.Rd                    |  13 ++-
 man/tol_subtree.Rd                      |   1 -
 tests/testthat/test-match_names.R       |  14 ++--
 tests/testthat/test-studies.R           |  57 ++++++++-----
 tests/testthat/test-taxonomy.R          |  38 ++++++++-
 vignettes/how-to-use-rotl.Rmd           |  46 +++++++----
 vignettes/meta-analysis.Rmd             |   5 +-
 56 files changed, 632 insertions(+), 396 deletions(-)

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