please include your R session info, thanks

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

It seems to work when I include 2 families, but anything more than 3 and it blows up.

@cboettig it's not clear to me if this https://github.com/ropensci/rfishbase/blob/master/R/species_list.R#L69-L82 is supposed to handle more than 1 name as input, or only 1 at a time? It's looking to me like it is supposed to only handle 1 at a time. if so should we document and stop on names > length == 1 ?

Okay, so essentially I will need to do a separate species_list for each of the 290 families I need species lists from?

you might have to, but i'm trying to figure out from my colleague (@cboettig ) what a function does that he wrote

@fishkey yeah, looks like that function isn't gracefully handling the fact that it's not finding any species in your third family.

You can see this by doing the vectorization 'manually', i.e.

out <- sapply(c("Chlamydoselachidae", "Hexanchidae", "Heptranchidae"), function(x) species_list(Family=x))

out
$Chlamydoselachidae
[1] "Chlamydoselachus africana"  "Chlamydoselachus anguineus"

$Hexanchidae
[1] "Heptranchias perlo"     "Hexanchus griseus"      "Hexanchus nakamurai"    "Notorynchus cepedianus"

$Heptranchidae
character(0)

Meanwhile, it's easy enough to work around using the fill taxa table and a bit of standard dplyr:

library(dplyr)
library(rfishbase)
fish <- rfishbase::load_taxa()
myfish <- fish %>%
   filter(Family %in%  c("Chlamydoselachidae", "Hexanchidae", "Heptranchidae"))

@sckott @cboettig thanks very much for your help!! the dplyr, etc. method worked very well. i dug more into why fishbase wasn't returning species for some families and there seem to be four things going on here, one of which you might want to hear about.

(1) spelling changes between fossil record entries and fishbase (generally, changing from 'didae' to 'dae')
(2) species from family from fossil record now included in a different family
(3) a page for that family exists on fishbase, but is empty (no genus, no species; e.g., https://goo.gl/nNRsti & https://goo.gl/TLVaj5)
(4) complete page exits on fishbase w/ genus and species, but returned character(0) (e.g., https://goo.gl/vn8yqi)

The 4th issue is the only one that puzzles me, and its not a big deal because it only occurred for ~1% of the families in my list. Anyway, thanks again for your help on this!

@fishkey thanks for the feedback! Re (4), it's possible that's a recent update to FishBase.org that we don't yet have in our database. @sckott thoughts?

(i assume you didn't mean to close @cboettig )

well, I think we've resolved the title issue(?) but we should let Matt close it out to confirm.

database syncing is probably a separate issue, yes?

RE 4: our last Fishbase database update is from December 2017 https://fishbase.ropensci.org/versions/ - so entirely possible that it's a problem of newer data that we don't have yet.

we've done 1 year apart between most updates. although in an ideal world, we'd have updates much more often 😏

thanks for the update @Dengaloo - Is it possible to get the March 2018 update? Or wait until June?

Okay, sounds good.