ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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fishbase dataset present in 3.1.9. is missing from v. 4.0.0 #243

Closed wmorgan485 closed 1 year ago

wmorgan485 commented 2 years ago

The fishbase dataset (A table of all the the species found in FishBase, including taxonomic classification and the Species Code (SpecCode) by which the species is identified in FishBase.) is listed in the Documentation for package rfishbase version 4.0.0 Help Pages. However, when the rfishbase package is loaded, this dataset is not listed using the data() command (see below).

Session Info ```r sessionInfo() # R version 4.1.0 (2021-05-18) # Platform: x86_64-apple-darwin17.0 (64-bit) # Running under: macOS Big Sur 11.6.1 # # Matrix products: default # LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib # # locale: # [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 # # attached base packages: # [1] stats graphics grDevices utils datasets methods # [7] base # # other attached packages: # [1] rfishbase_4.0.0 # # loaded via a namespace (and not attached): # [1] pillar_1.6.4 compiler_4.1.0 dbplyr_2.1.1 # [4] prettyunits_1.1.1 tools_4.1.0 progress_1.2.2 # [7] bit_4.0.4 contentid_0.0.15 jsonlite_1.7.2 # [10] memoise_2.0.0 lifecycle_1.0.1 tibble_3.1.5 # [13] pkgconfig_2.0.3 rlang_0.4.12 rstudioapi_0.13 # [16] DBI_1.1.1 cli_3.1.0 parallel_4.1.0 # [19] curl_4.3.2 fastmap_1.1.0 withr_2.4.2 # [22] duckdb_0.3.1-1 dplyr_1.0.7 httr_1.4.2 # [25] stringr_1.4.0 generics_0.1.1 fs_1.5.0 # [28] vctrs_0.3.8 askpass_1.1 hms_1.1.1 # [31] bit64_4.0.5 tidyselect_1.1.1 glue_1.4.2 # [34] R6_2.5.1 fansi_0.5.0 vroom_1.5.5 # [37] purrr_0.3.4 readr_2.0.2 tzdb_0.2.0 # [40] magrittr_2.0.1 ellipsis_0.3.2 assertthat_0.2.1 # [43] utf8_1.2.2 stringi_1.7.5 openssl_1.4.5 # [46] cachem_1.0.6 crayon_1.4.2 fishbase # Error: object 'fishbase' not found data(package = "rfishbase") ``` Data sets in package ‘rfishbase’: species_fields (fields) A list of the species_fields available
cboettig commented 2 years ago

Apologies, that documentation needs updating!

That information is now available through load_taxa() (duplicate #240 #241)