I have no idea what is going on here, and this seems baffling to me.
I'm sorting through some taxonomy with the taxize package; I need to do something like this:
fung = taxize::fg_name_search("Xanthoparmelia ionnis-simae")
new_name = fung$current_name
I noticed that for some records it would return a number instead of a name, and I noticed one of the column names was "current_name_record_number". It seems to be automatically assuming that I mean "current_name_record_number" instead of "current_name". It's filling in the name automatically inside of the console.
colnames(fung)
[1] "name_of_fungus" "authors"
[3] "specific_epithet" "infraspecific_rank"
[5] "orthography_comment" "year_of_publication"
[7] "editorial_comment" "sts_flag"
[9] "record_number" "basionym_record_number"
[11] "protonym_record_number" "name_of_fungus_fundic_record_number"
[13] "current_name_record_number" "updatedby"
[15] "updateddate" "addeddate"
[17] "uuid"
fung$current_name[1]
[1] "343913"
fung$current_name_record_number[1]
[1] "343913"
I tested this on a dummy data frame and it does the same thing.
df = data.frame(current_name_record_number="343913")
df$current_name
[1] "343913"
This is deadly behavior and shouldn't exist. I don't understand how this is possible and needs to be fixed. Or maybe I've done something wrong? I need help to understand this issue and how it can be solved.
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5.2
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] taxize_0.9.100
loaded via a namespace (and not attached):
[1] crayon_1.5.2 conditionz_0.1.0 nlme_3.1-162 cli_3.6.1 rlang_1.1.1
[6] crul_1.4.0 stringi_1.7.12 jsonlite_1.8.7 data.table_1.14.8 zoo_1.8-12
[11] glue_1.6.2 httpcode_0.3.0 bold_1.3.0 grid_4.3.1 foreach_1.5.2
[16] ape_5.7-1 lifecycle_1.0.3 stringr_1.5.0 compiler_4.3.1 codetools_0.2-19
[21] Rcpp_1.0.11 rstudioapi_0.15.0 lattice_0.21-8 digest_0.6.33 R6_2.5.1
[26] curl_5.0.1 parallel_4.3.1 magrittr_2.0.3 uuid_1.1-1 tools_4.3.1
[31] iterators_1.0.14 xml2_1.3.6