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Description
Hi TNRS maintainers 👋
I really like the feature that let's the user submit a data.frame to the TNRS() function so that they can be easily referred in other contexts.
However, I had a 3 columns data.frame that also included some additional info on the names, then the function output a strange error.
I perfectly understand why TNRS() would only accept 2 columns data.frame and I have an easy fix for that, but maybe the error message could be clearer.
reprex:
# Works fine with a 2 columns dataset
TNRS::TNRS(data.frame(ID = 1, name = "Helianthus annuus"))
#> ID Name_submitted Overall_score Name_matched_id Name_matched
#> 1 1 Helianthus annuus 1 51089 Helianthus annuus
#> Name_score Name_matched_rank Author_submitted Author_matched Author_score
#> 1 1 species NA
#> Canonical_author Name_matched_accepted_family Genus_submitted Genus_matched
#> 1 L. Asteraceae Helianthus Helianthus
#> Genus_score Specific_epithet_submitted Specific_epithet_matched
#> 1 1 annuus annuus
#> Specific_epithet_score Family_submitted Family_matched Family_score
#> 1 1 NA
#> Infraspecific_rank Infraspecific_epithet_matched Infraspecific_epithet_score
#> 1 NA
#> Infraspecific_rank_2 Infraspecific_epithet_2_matched
#> 1
#> Infraspecific_epithet_2_score Annotations Unmatched_terms
#> 1 NA
#> Name_matched_url Name_matched_lsid Phonetic
#> 1 http://www.tropicos.org/Name/2700851 Y
#> Taxonomic_status Accepted_name Accepted_species Accepted_name_author
#> 1 Accepted Helianthus annuus Helianthus annuus L.
#> Accepted_name_id Accepted_name_rank Accepted_name_url
#> 1 51089 species http://www.tropicos.org/Name/2700851
#> Accepted_name_lsid Accepted_family Overall_score_order Highertaxa_score_order
#> 1 Asteraceae 1 1
#> Source Warnings
#> 1 tropicos 0
# Strange error message when having more than 2 columns
TNRS::TNRS(data.frame(ID = 1, name = "Helianthus annuus", other_name = "bla"))
#> Problem with the API: HTTP Status 400
#> NULLCreated on 2023-02-08 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.0 (2022-04-22 ucrt)
#> os Windows 10 x64 (build 19045)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate fr_FR.UTF-8
#> ctype fr_FR.UTF-8
#> tz Europe/Berlin
#> date 2023-02-08
#> pandoc 3.0.1 @ C:/Users/ke76dimu/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0)
#> curl 5.0.0 2023-01-12 [1] CRAN (R 4.2.2)
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#> evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.2)
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#> fs 1.6.0 2023-01-23 [1] CRAN (R 4.2.2)
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#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
#> purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.2)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.1)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
#> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.2.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> rlang 1.0.6.9000 2022-10-11 [1] Github (r-lib/rlang@28a40b5)
#> rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.2)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
#> styler 1.9.0 2023-01-15 [1] CRAN (R 4.2.2)
#> TNRS 0.3.3 2023-01-11 [1] CRAN (R 4.2.2)
#> vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.0)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
#> xfun 0.36 2022-12-21 [1] CRAN (R 4.2.2)
#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.2)
#>
#> [1] C:/Users/ke76dimu/Documents/R/R-4.2.0/library
#>
#> ──────────────────────────────────────────────────────────────────────────────Metadata
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