[med-svn] [r-cran-rotl] 05/12: Updated version 3.0.1 from 'upstream/3.0.1'

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

commit 3ccac273cdf66cf449c0b85b2820d9e5c6a1ab72
Merge: 6c1b25d 8624bd0
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 23 08:11:46 2017 +0200

    Updated version 3.0.1 from 'upstream/3.0.1'
    
    with Debian dir 7f91caf8c678edfc2f1f4e46ebcef3a64a00507c

 DESCRIPTION                              |  32 ++
 LICENSE                                  |   2 +
 MD5                                      |  87 ++++
 NAMESPACE                                | 116 ++++++
 NEWS.md                                  | 104 +++++
 R/api-collections.R                      |  28 ++
 R/api-studies.R                          | 163 ++++++++
 R/api-taxonomy.R                         |  68 ++++
 R/api-tnrs.R                             |  70 ++++
 R/api-tol.R                              | 126 ++++++
 R/base.R                                 | 204 ++++++++++
 R/deduplicate_labels.R                   |  39 ++
 R/external_data.R                        | 119 ++++++
 R/match_names.R                          | 361 +++++++++++++++++
 R/methods.R                              |  93 +++++
 R/rotl-package.R                         |  50 +++
 R/studies-methods.R                      |  88 ++++
 R/studies-utils.R                        |  77 ++++
 R/studies.R                              | 461 +++++++++++++++++++++
 R/tax_utils.R                            |  73 ++++
 R/taxonomy.R                             | 325 +++++++++++++++
 R/tnrs.R                                 | 250 ++++++++++++
 R/tol.R                                  | 668 +++++++++++++++++++++++++++++++
 R/tree_to_labels.R                       |  48 +++
 README.md                                | 155 +++++++
 build/vignette.rds                       | Bin 0 -> 316 bytes
 inst/CITATION                            |  20 +
 inst/doc/data_mashups.R                  |  61 +++
 inst/doc/data_mashups.Rmd                | 222 ++++++++++
 inst/doc/data_mashups.html               | 362 +++++++++++++++++
 inst/doc/how-to-use-rotl.R               |  75 ++++
 inst/doc/how-to-use-rotl.Rmd             | 283 +++++++++++++
 inst/doc/how-to-use-rotl.html            | 446 +++++++++++++++++++++
 inst/doc/meta-analysis.R                 |  66 +++
 inst/doc/meta-analysis.Rmd               | 231 +++++++++++
 inst/doc/meta-analysis.html              | 216 ++++++++++
 inst/extdata/egg.csv                     |  66 +++
 inst/extdata/protist_mutation_rates.csv  |   7 +
 man/get_study.Rd                         |  60 +++
 man/get_study_meta.Rd                    |  80 ++++
 man/get_study_subtree.Rd                 |  44 ++
 man/get_study_tree.Rd                    |  61 +++
 man/list_trees.Rd                        |  41 ++
 man/match_names-methods.Rd               |  60 +++
 man/match_names.Rd                       |  77 ++++
 man/rotl.Rd                              |  56 +++
 man/source_list.Rd                       |  31 ++
 man/strip_ott_ids.Rd                     |  32 ++
 man/studies_find_studies.Rd              |  71 ++++
 man/studies_find_trees.Rd                |  80 ++++
 man/studies_properties.Rd                |  39 ++
 man/study_external_IDs.Rd                |  43 ++
 man/synonyms.match_names.Rd              |  55 +++
 man/tax_lineage.Rd                       |  32 ++
 man/taxon_external_IDs.Rd                |  32 ++
 man/taxonomy-methods.Rd                  |  43 ++
 man/taxonomy_about.Rd                    |  44 ++
 man/taxonomy_mrca.Rd                     |  73 ++++
 man/taxonomy_subtree.Rd                  |  68 ++++
 man/taxonomy_taxon_info.Rd               |  85 ++++
 man/tnrs_contexts.Rd                     |  32 ++
 man/tnrs_infer_context.Rd                |  35 ++
 man/tnrs_match_names.Rd                  |  82 ++++
 man/tol_about.Rd                         | 123 ++++++
 man/tol_induced_subtree.Rd               |  50 +++
 man/tol_mrca.Rd                          | 157 ++++++++
 man/tol_node_info.Rd                     | 146 +++++++
 man/tol_subtree.Rd                       |  46 +++
 tests/test-all.R                         |   3 +
 tests/testthat/test-API.R                | 195 +++++++++
 tests/testthat/test-api-studies.R        | 195 +++++++++
 tests/testthat/test-api-taxonomy.R       |  87 ++++
 tests/testthat/test-api-tnrs.R           |  66 +++
 tests/testthat/test-api-tol.R            |  69 ++++
 tests/testthat/test-base.R               |  55 +++
 tests/testthat/test-deduplicate_labels.R |  45 +++
 tests/testthat/test-external.R           |  39 ++
 tests/testthat/test-match_names.R        | 408 +++++++++++++++++++
 tests/testthat/test-studies.R            | 484 ++++++++++++++++++++++
 tests/testthat/test-taxonomy.R           | 341 ++++++++++++++++
 tests/testthat/test-tnrs.R               |  67 ++++
 tests/testthat/test-tol.R                | 456 +++++++++++++++++++++
 tests/testthat/test-tree_to_labels.R     |  51 +++
 tests/tree_of_life.json                  | 111 +++++
 vignettes/data_mashups.Rmd               | 222 ++++++++++
 vignettes/how-to-use-rotl.Rmd            | 283 +++++++++++++
 vignettes/meta-analysis.Rmd              | 231 +++++++++++
 vignettes/vignette.css                   | 207 ++++++++++
 88 files changed, 11355 insertions(+)

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