ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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rfishbasee::fishbase not exported #274

Closed andybeet closed 10 months ago

andybeet commented 10 months ago

Trying to get a table of species found in fishbase (https://docs.ropensci.org/rfishbase/reference/fishbase.html) In earlier releases of rfishbase this table was present

rfishbase::fishbase
#> Error: 'fishbase' is not an exported object from 'namespace:rfishbase'

Created on 2023-12-01 with reprex v2.0.2

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.0 (2022-04-22 ucrt) #> os Windows 10 x64 (build 19045) #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United States.utf8 #> ctype English_United States.utf8 #> tz America/New_York #> date 2023-12-01 #> pandoc 2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0) #> cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0) #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.1) #> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.2) #> dbplyr 2.2.0 2022-06-05 [1] CRAN (R 4.2.0) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) #> dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.1) #> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.3) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) #> hms 1.1.1 2021-09-26 [1] CRAN (R 4.2.0) #> htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.2.0) #> knitr 1.41 2022-11-18 [1] CRAN (R 4.2.2) #> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.2) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.2.3) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) #> progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> readr 2.1.2 2022-01-30 [1] CRAN (R 4.2.0) #> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.3) #> rfishbase 4.1.2 2023-06-02 [1] CRAN (R 4.2.3) #> rlang 1.1.1 2023-04-28 [1] CRAN (R 4.2.3) #> rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.1) #> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1) #> stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.3) #> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.3) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.3) #> tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0) #> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.3) #> vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.2) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> xfun 0.36 2022-12-21 [1] CRAN (R 4.2.2) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) #> #> [1] C:/Users/andrew.beet/AppData/Local/Programs/R/R-4.2.0/library #> #> ────────────────────────────────────────────────────────────────────────────── ```
cboettig commented 10 months ago

function names are now aligned more directly with table names used in the FishBase database itself. rfishbase::species() will list all the species found in fishbase.

andybeet commented 10 months ago

so this data object is now obsolete? The documentation still references it.