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ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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Differences between rfishbase query and Fishbase website #161

Closed jflowernet closed 5 years ago

jflowernet commented 5 years ago

Hi, I'm accessing maximum length information for some species and noticed one of the values did not seem right. Running this species("Chaetodon capistratus", fields = c("Species", "Length")) gives a (maximum) length of 7.5, but looking at the Fishbase website I can see it is 15 (https://www.fishbase.de/summary/Chaetodon-capistratus.html).

Also, querying species("Lactophrys triqueter") returns nothing, but species("Rhinesomus triqueter") returns the species information even thought that species name is a non-valid synonym (according to Fishbase).

I understand this is likely due to differences between the Fishbase website and the tables that rfishbase uses for queries, but wanted to check if there is any way of getting the information updated if this is the case.

Thanks for your help and the excellent rfishbase package!

sessionInfo()

R version 3.5.3 (2019-03-11) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 18.3 Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] bindrcpp_0.2.2 rfishbase_3.0.3 loaded via a namespace (and not attached): [1] Rcpp_1.0.0 rstudioapi_0.8 bindr_0.1.1 magrittr_1.5 [5] hms_0.4.2 tidyselect_0.2.5 R6_2.3.0 rlang_0.3.1 [9] fansi_0.4.0 stringr_1.3.1 dplyr_0.7.8 tools_3.5.3 [13] utf8_1.1.4 cli_1.0.1 yaml_2.2.0 assertthat_0.2.0 [17] digest_0.6.18 tibble_2.0.1 crayon_1.3.4 purrr_0.2.5 [21] readr_1.2.1 memoise_1.1.0 glue_1.3.0 stringi_1.2.4 [25] compiler_3.5.3 pillar_1.3.1 pkgconfig_2.0.2
cboettig commented 5 years ago

Thanks, this should be fixed by PR #165 once it is merged, which will make sure rfishbase accesses the latest cache by default. Note that the version can still be set to a fixed timestamp if needed for reproducibility, but will no longer be the default.