ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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Could not find function list_fields() #273

Closed watrbeans closed 11 months ago

watrbeans commented 11 months ago

Hello!

I'm having trouble with the list_fileds() function. I've updated rfishbase and R to the latest version, but continue to get the following error code when running list_fields(): Error in list_fields() : could not find function "list_fields". What reasons might there be for this?

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.3.1 (2023-06-16) os macOS Sonoma 14.0 system aarch64, darwin20 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/New_York date 2023-10-29 rstudio 2023.06.1+524 Mountain Hydrangea (desktop) pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

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[1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

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list_fields()

> Error in list_fields(): could not find function "list_fields"

cboettig commented 11 months ago

correct, it is deprecated now that rfishbase supports all ~ 211 different tables, listing all the columns of all the tables in a function call doesn't serve users particularly well. Eventually we hope to have a more user friendly solution, but for now users are best querying the column names of the most likely tables of interest rather than be confronted with a list of 211 tables, many with upwards of 50 columns.