Error in retrieving GBIF backbone taxon ID using get_gbifid()

[OndrejMottl]

I got the following error trying to retrieve GBIF ID using get_gbifid():

r$> taxize::get_gbifid(
      sci = "Tithonia subg. Mirasolia Carl Heinrich 'Bipontinus' Schultz, 1856"   
    )
==  1 queries  ===============

Retrieving data for taxon 'Tithonia subg. Mirasolia Carl Heinrich 'Bipontinus' Sc'

Error in `[.data.frame`(x, , c(cols, other)) : undefined columns selected

Neither this works:

r$> taxize::get_gbifid_(
      sci = "Tithonia subg. Mirasolia Carl Heinrich 'Bipontinus' Schultz, 1856"   
    )

Retrieving data for taxon 'Tithonia subg. Mirasolia Carl Heinrich 'Bipontinus' Sc'

Error in `[.data.frame`(x, , c(cols, other)) : undefined columns selected

The name ( "Tithonia subg. Mirasolia Carl Heinrich 'Bipontinus' Schultz, 1856") was obtained directly from taxize::resolve().

Session info

- Session info -----------------------------------------------------------------
 setting  value
 version  R version 4.2.3 (2023-03-15 ucrt)
 os       Windows 10 x64 (build 22631)
 system   x86_64, mingw32
 ui       RTerm
 language (EN)
 collate  English_United Kingdom.1252
 ctype    English_United Kingdom.1252
 tz       Europe/Prague
 date     2024-04-08
 pandoc   3.1.4 @ C:\\Users\\ondre\\AppData\\Local\\Pandoc\\pandoc.exe

- Packages ---------------------------------------------------------------------  
 !  package     * version  date (UTC) lib source
    ape           5.7-1    2023-03-13 [1] CRAN (R 4.2.3)
    assertthat    0.2.1    2019-03-21 [1] CRAN (R 4.2.3)
    bold          1.3.0    2023-05-02 [1] CRAN (R 4.2.3)
    brio          1.1.4    2023-12-10 [1] CRAN (R 4.2.3)
    cachem        1.0.8    2023-05-01 [1] CRAN (R 4.2.3)
    cli           3.6.1    2023-03-23 [1] CRAN (R 4.2.3)
    codetools     0.2-19   2023-02-01 [2] CRAN (R 4.2.3)
    conditionz    0.1.0    2019-04-24 [1] CRAN (R 4.2.3)
    crayon        1.5.2    2022-09-29 [1] CRAN (R 4.2.3)
    crul          1.4.0    2023-05-17 [1] CRAN (R 4.2.3)
    curl          5.1.0    2023-10-02 [1] CRAN (R 4.2.3)
    data.table    1.15.2   2024-02-29 [1] CRAN (R 4.2.3)
    desc          1.4.3    2023-12-10 [1] CRAN (R 4.2.3)
    devtools      2.4.5    2022-10-11 [1] CRAN (R 4.2.3)
    digest        0.6.31   2022-12-11 [1] CRAN (R 4.2.3)
    dplyr         1.1.4    2023-11-17 [1] CRAN (R 4.2.3)
    ellipsis      0.3.2    2021-04-29 [1] CRAN (R 4.2.3)
    fansi         1.0.5    2023-10-08 [1] CRAN (R 4.2.3)
    fastmap       1.1.1    2023-02-24 [1] CRAN (R 4.2.3)
    foreach       1.5.2    2022-02-02 [1] CRAN (R 4.2.3)
    fs            1.6.3    2023-07-20 [1] CRAN (R 4.2.3)
    generics      0.1.3    2022-07-05 [1] CRAN (R 4.2.3)
    glue          1.6.2    2022-02-24 [1] CRAN (R 4.2.3)
    hms           1.1.3    2023-03-21 [1] CRAN (R 4.2.3)
    htmltools     0.5.8    2024-03-25 [1] CRAN (R 4.2.3)
    htmlwidgets   1.6.4    2023-12-06 [1] CRAN (R 4.2.3)
    httpcode      0.3.0    2020-04-10 [1] CRAN (R 4.2.3)
    httpuv        1.6.11   2023-05-11 [1] CRAN (R 4.2.3)
    iterators     1.0.14   2022-02-05 [1] CRAN (R 4.2.3)
    janitor       2.2.0    2023-02-02 [1] CRAN (R 4.2.3)
    jsonlite      1.8.7    2023-06-29 [1] CRAN (R 4.2.3)
    later         1.3.1    2023-05-02 [1] CRAN (R 4.2.3)
    lattice       0.20-45  2021-09-22 [2] CRAN (R 4.2.3)
    lifecycle     1.0.4    2023-11-07 [1] CRAN (R 4.2.3)
    lubridate     1.9.2    2023-02-10 [1] CRAN (R 4.2.3)
    magrittr      2.0.3    2022-03-30 [1] CRAN (R 4.2.3)
    memoise       2.0.1    2021-11-26 [1] CRAN (R 4.2.3)
    mime          0.12     2021-09-28 [1] CRAN (R 4.2.0)
    miniUI        0.1.1.1  2018-05-18 [1] CRAN (R 4.2.3)
    nlme          3.1-162  2023-01-31 [2] CRAN (R 4.2.3)
    pillar        1.9.0    2023-03-22 [1] CRAN (R 4.2.3)
    pkgbuild      1.4.3    2023-12-10 [1] CRAN (R 4.2.3)
    pkgconfig     2.0.3    2019-09-22 [1] CRAN (R 4.2.3)
    pkgload       1.3.4    2024-01-16 [1] CRAN (R 4.2.3)
    profvis       0.3.8    2023-05-02 [1] CRAN (R 4.2.3)
    promises      1.2.0.1  2021-02-11 [1] CRAN (R 4.2.3)
    purrr         1.0.2    2023-08-10 [1] CRAN (R 4.2.3)
    R6            2.5.1    2021-08-19 [1] CRAN (R 4.2.3)
    Rcpp          1.0.11   2023-07-06 [1] CRAN (R 4.2.3)
    readr         2.1.4    2023-02-10 [1] CRAN (R 4.2.3)
    remotes       2.4.2.1  2023-07-18 [1] CRAN (R 4.2.3)
    rlang         1.1.2    2023-11-04 [1] CRAN (R 4.2.3)
    rprojroot     2.0.4    2023-11-05 [1] CRAN (R 4.2.3)
    rstudioapi    0.15.0   2023-07-07 [1] CRAN (R 4.2.3)
    sessioninfo   1.2.2    2021-12-06 [1] CRAN (R 4.2.3)
    shiny         1.7.4    2022-12-15 [1] CRAN (R 4.2.3)
    snakecase     0.11.1   2023-08-27 [1] CRAN (R 4.2.3)
    stringi       1.8.1    2023-11-13 [1] CRAN (R 4.2.3)
    stringr       1.5.1    2023-11-14 [1] CRAN (R 4.2.3)
    taxize        0.9.100  2022-04-22 [1] CRAN (R 4.2.3)
 VP taxospace   * 0.0.9003 2023-07-12 [?] load_all() (on disk 0.0.0.9000)
    testthat    * 3.2.1    2023-12-02 [1] CRAN (R 4.2.3)
    tibble        3.2.1    2023-03-20 [1] CRAN (R 4.2.3)
    tidyr         1.3.0    2023-01-24 [1] CRAN (R 4.2.3)
    tidyselect    1.2.0    2022-10-10 [1] CRAN (R 4.2.3)
    timechange    0.2.0    2023-01-11 [1] CRAN (R 4.2.3)
    triebeard     0.4.1    2023-03-04 [1] CRAN (R 4.2.3)
    tzdb          0.4.0    2023-05-12 [1] CRAN (R 4.2.3)
    urlchecker    1.0.1    2021-11-30 [1] CRAN (R 4.2.3)
    urltools      1.7.3    2019-04-14 [1] CRAN (R 4.2.3)
    usethis       2.2.3    2024-02-19 [1] CRAN (R 4.2.3)
    utf8          1.2.4    2023-10-22 [1] CRAN (R 4.2.3)
    uuid          1.2-0    2024-01-14 [1] CRAN (R 4.2.3)
    vctrs         0.6.4    2023-10-12 [1] CRAN (R 4.2.3)
    withr         3.0.0    2024-01-16 [1] CRAN (R 4.2.3)
    xml2          1.3.4    2023-04-27 [1] CRAN (R 4.2.3)
    xtable        1.8-4    2019-04-21 [1] CRAN (R 4.2.3)
    zoo           1.8-12   2023-04-13 [1] CRAN (R 4.2.3)

 [1] C:/Users/ondre/AppData/Local/R/win-library/4.2
 [2] C:/Program Files/R/R-4.2.3/library

 V -- Loaded and on-disk version mismatch.
 P -- Loaded and on-disk path mismatch.

[ggrittz]

This issue is related to both quotation marks (') in Bipontinus. They need to be escaped with backslashes because of regex

> taxize::get_gbifid(
+   sci = "Tithonia subg. Mirasolia Carl Heinrich \\'Bipontinus\\' Schultz, 1856"   
+ )
══  1 queries  ═══════════════

Retrieving data for taxon 'Tithonia subg. Mirasolia Carl Heinrich \'Bipontinus\' Schultz, 1856'





More than one GBIF ID found for taxon 'Tithonia subg. Mirasolia Carl Heinrich \'Bipontinus\' Schultz, 1856'!

            Enter rownumber of taxon (other inputs will return 'NA'):

    gbifid                         scientificname  rank   status matchtype
1  8892593 Mirasolia Sch.Bip. ex Benth. & Hook.f. genus  SYNONYM     EXACT
2 11114626        Mirasolita Hermsen et al., 2014 genus ACCEPTED     FUZZY