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This is small potatoes, but I thought it couldn't hurt to mention. And mostly I'm curious about why this is happening.
I had reason to mix search_scientific and scientific_name for a large list of taxa and wanted to join the results on combinedName. But search_scientific returns a column named combinedName, while scientific_name returns a field called combinedname (lowercase n). After closer inspection, the unitname fields are also inconsistently capitalized. So the request is that these functions return the same names so the tables can be easily joined.
But I couldn't find where the names with the lowercase n were being defined. The scientific_namefunction explicitly namescombinedName. The capital N seems to be consistent with what the ITIS API returns and what the full record function returns (see below).
I reinstalled from github, in case I had overlooked some commit, but the mystery remains. Is this by design, or am I overlooking something simple?
pick_cols() is used all over the codebase, so I'm guessing that the original motivation behind lowercasing was to make this utility as flexible as possible.
I agree that it would be nicer for the field names to have consistent capitalization no matter which path you took to getting the information. As you point out, that makes it easier to join outputs from different functions. I can also see the merit in making the capitalization consistent with the ITIS API.
However, since pick_cols() is such a widespread piece of infrastructure in this package, rethinking its behavior is a bit of an undertaking. I'm tagging this as a feature request, but I likely won't be able to get to it super soon (contributions welcome!).
jcblum
changed the title
inconsistent capitalization in column names returned by scientific_name and search_scientific
Make output column capitalization consistent with ITIS API for functions using pick_cols()Dec 1, 2023
Excellent detective work! I did not figure this out yet; I appreciate you following up on it. I don't have time to work on this in the next couple months, but I'll put it in the queue for the new year.
This is small potatoes, but I thought it couldn't hurt to mention. And mostly I'm curious about why this is happening.
I had reason to mix
search_scientific
andscientific_name
for a large list of taxa and wanted to join the results oncombinedName
. Butsearch_scientific
returns a column namedcombinedName
, whilescientific_name
returns a field calledcombinedname
(lowercase n). After closer inspection, theunitname
fields are also inconsistently capitalized. So the request is that these functions return the same names so the tables can be easily joined.But I couldn't find where the names with the lowercase n were being defined. The
scientific_name
function explicitly namescombinedName
. The capital N seems to be consistent with what the ITIS API returns and what the full record function returns (see below).I reinstalled from github, in case I had overlooked some commit, but the mystery remains. Is this by design, or am I overlooking something simple?
Session Info
```rR version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ritis_1.0.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 fansi_1.0.4 utf8_1.2.3 dplyr_1.1.0 plyr_1.8.8 crul_1.3 R6_2.5.1
[8] jsonlite_1.8.4 lifecycle_1.0.3 magrittr_2.0.3 pillar_1.8.1 rlang_1.0.6 cli_3.6.0 curl_5.0.0
[15] rstudioapi_0.14 xml2_1.3.3 vctrs_0.5.2 generics_0.1.3 urltools_1.7.3 tools_4.2.1 glue_1.6.2
[22] triebeard_0.3.0 compiler_4.2.1 pkgconfig_2.0.3 tidyselect_1.2.0 tibble_3.1.8 solrium_1.2.0 httpcode_0.3.0
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