Skip to content

Unclear error when using input data.frame of more than 2 columns #13

@Rekyt

Description

@Rekyt

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
#> NULL

Created 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)
#>  digest        0.6.31     2022-12-11 [1] CRAN (R 4.2.2)
#>  evaluate      0.20       2023-01-17 [1] CRAN (R 4.2.2)
#>  fastmap       1.1.0      2021-01-25 [1] CRAN (R 4.2.0)
#>  fs            1.6.0      2023-01-23 [1] CRAN (R 4.2.2)
#>  glue          1.6.2      2022-02-24 [1] CRAN (R 4.2.0)
#>  htmltools     0.5.4      2022-12-07 [1] CRAN (R 4.2.2)
#>  httr          1.4.4      2022-08-17 [1] CRAN (R 4.2.1)
#>  jsonlite      1.8.4      2022-12-06 [1] CRAN (R 4.2.2)
#>  knitr         1.42       2023-01-25 [1] CRAN (R 4.2.2)
#>  lifecycle     1.0.3      2022-10-07 [1] CRAN (R 4.2.1)
#>  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

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions