{"action":"created","comment":{"url":"https://api.github.com/repos/ropensci/rfishbase/pulls/comments/199646428","pull_request_review_id":133806532,"id":199646428,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5OTY0NjQyOA==","diff_hunk":"@@ -1,50 +1,57 @@\n #' species_list\n #' \n #' Return the a species list given a taxonomic group\n+#' @param SuperClass Request all species of this Superclass\n #' @param Class Request all species in this taxonomic Class\n #' @param Order Request all species in this taxonomic Order\n #' @param Family Request all species in this taxonomic Family\n-#' @param SubFamily Request all species in this taxonomic SubFamily\n+#' @param Subfamily Request all species in this taxonomic SubFamily\n #' @param Genus Request all species in this taxonomic Genus\n #' @param Species Request all species in this taxonomic Species\n #' @param SpecCode Request species name of species matching this SpecCode\n-#' @param SpeciesRefNo Request species name of all species matching this SpeciesRefNo\n-#' @param all_taxa The data.frame of all taxa used for the lookup. By default will be loaded\n-#'  from cache if available, otherwise must be downloaded from the server; about 13 MB, may be \n-#'  slow.\n-#' \n-#' @details The first time the function is called it will download and cache the complete\n-#' @importFrom dplyr select_ %>%\n-#' @importFrom lazyeval interp\n-#' @importFrom tidyr unite_\n+#' @param server fishbase or \n #' @examples\n-#' \\dontrun{\n+#' \\donttest{","path":"R/species_list.R","position":25,"original_position":25,"commit_id":"d76fb1e6504abe501fdce434669e84fc2c20c983","original_commit_id":"d76fb1e6504abe501fdce434669e84fc2c20c983","user":{"login":"cboettig","id":222586,"node_id":"MDQ6VXNlcjIyMjU4Ng==","avatar_url":"https://avatars3.githubusercontent.com/u/222586?v=4","gravatar_id":"","url":"https://api.github.com/users/cboettig","html_url":"https://github.com/cboettig","followers_url":"https://api.github.com/users/cboettig/followers","following_url":"https://api.github.com/users/cboettig/following{/other_user}","gists_url":"https://api.github.com/users/cboettig/gists{/gist_id}","starred_url":"https://api.github.com/users/cboettig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cboettig/subscriptions","organizations_url":"https://api.github.com/users/cboettig/orgs","repos_url":"https://api.github.com/users/cboettig/repos","events_url":"https://api.github.com/users/cboettig/events{/privacy}","received_events_url":"https://api.github.com/users/cboettig/received_events","type":"User","site_admin":false},"body":"yeah, I'm not 100% clear on it but that's basically what I'm going for.  I need some kind of `dont` there because the command can take > 5 s (at least the first time), but otherwise wanted it to run as part of the regular test.  ","created_at":"2018-07-02T23:18:17Z","updated_at":"2018-07-02T23:18:17Z","html_url":"https://github.com/ropensci/rfishbase/pull/142#discussion_r199646428","pull_request_url":"https://api.github.com/repos/ropensci/rfishbase/pulls/142","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/ropensci/rfishbase/pulls/comments/199646428"},"html":{"href":"https://github.com/ropensci/rfishbase/pull/142#discussion_r199646428"},"pull_request":{"href":"https://api.github.com/repos/ropensci/rfishbase/pulls/142"}},"in_reply_to_id":199642648},"pull_request":{"url":"https://api.github.com/repos/ropensci/rfishbase/pulls/142","id":196014873,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk2MDE0ODcz","html_url":"https://github.com/ropensci/rfishbase/pull/142","diff_url":"https://github.com/ropensci/rfishbase/pull/142.diff","patch_url":"https://github.com/ropensci/rfishbase/pull/142.patch","issue_url":"https://api.github.com/repos/ropensci/rfishbase/issues/142","number":142,"state":"open","locked":false,"title":"3.0 -- a static-API version","user":{"login":"cboettig","id":222586,"node_id":"MDQ6VXNlcjIyMjU4Ng==","avatar_url":"https://avatars3.githubusercontent.com/u/222586?v=4","gravatar_id":"","url":"https://api.github.com/users/cboettig","html_url":"https://github.com/cboettig","followers_url":"https://api.github.com/users/cboettig/followers","following_url":"https://api.github.com/users/cboettig/following{/other_user}","gists_url":"https://api.github.com/users/cboettig/gists{/gist_id}","starred_url":"https://api.github.com/users/cboettig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cboettig/subscriptions","organizations_url":"https://api.github.com/users/cboettig/orgs","repos_url":"https://api.github.com/users/cboettig/repos","events_url":"https://api.github.com/users/cboettig/events{/privacy}","received_events_url":"https://api.github.com/users/cboettig/received_events","type":"User","site_admin":false},"body":"@sckott Not to merge right away, but wanted to get your review on this.  This is my go at a static-API version along the lines we discussed.  I've tried to maintain compatibility with the current rfishbase function api as much as possible; there's a few cases where I've revised things that I thought needed revision anyway (e.g. vectorizing some things that weren't vectorized before and adjusting return types to be more consistently data.frames).  \r\n\r\n\r\nIt uses memoise for caching, so the first time you run any function it is a bit slow, mostly since it builds the taxa table on the fly, but there-after should be very fast.  I should probably create a local cache of the taxa table just as we do in the current version, which would eliminate most of the delay.  Probably should also give the user the ability to turn on memoise's disk-based cache option for the memoised functions, but even without any of that this should be much faster for calls involving thousands or tens of thousands of species.  \r\n\r\n\r\nSo far doesn't include sealifebase but should otherwise have just about all the functions of the API-based version.  \r\n","created_at":"2018-06-20T03:47:21Z","updated_at":"2018-07-02T23:18:17Z","closed_at":null,"merged_at":null,"merge_commit_sha":"bb258f47e3e74b690d876798bff8d0a2d369e7d4","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/ropensci/rfishbase/pulls/142/commits","review_comments_url":"https://api.github.com/repos/ropensci/rfishbase/pulls/142/comments","review_comment_url":"https://api.github.com/repos/ropensci/rfishbase/pulls/comments{/number}","comments_url":"https://api.github.com/repos/ropensci/rfishbase/issues/142/comments","statuses_url":"https://api.github.com/repos/ropensci/rfishbase/statuses/d76fb1e6504abe501fdce434669e84fc2c20c983","head":{"label":"ropensci:3.0","ref":"3.0","sha":"d76fb1e6504abe501fdce434669e84fc2c20c983","user":{"login":"ropensci","id":1200269,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEyMDAyNjk=","avatar_url":"https://avatars3.githubusercontent.com/u/1200269?v=4","gravatar_id":"","url":"https://api.github.com/users/ropensci","html_url":"https://github.com/ropensci","followers_url":"https://api.github.com/users/ropensci/followers","following_url":"https://api.github.com/users/ropensci/following{/other_user}","gists_url":"https://api.github.com/users/ropensci/gists{/gist_id}","starred_url":"https://api.github.com/users/ropensci/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ropensci/subscriptions","organizations_url":"https://api.github.com/users/ropensci/orgs","repos_url":"https://api.github.com/users/ropensci/repos","events_url":"https://api.github.com/users/ropensci/events{/privacy}","received_events_url":"https://api.github.com/users/ropensci/received_events","type":"Organization","site_admin":false},"repo":{"id":2799822,"node_id":"MDEwOlJlcG9zaXRvcnkyNzk5ODIy","name":"rfishbase","full_name":"ropensci/rfishbase","owner":{"login":"ropensci","id":1200269,"node_id":"MDEyOk9yZ2FuaXphdGlvbjEyMDAyNjk=","avatar_url":"https://avatars3.githubusercontent.com/u/1200269?v=4","gravatar_id":"","url":"https://api.github.com/users/ropensci","html_url":"https://github.com/ropensci","followers_url":"https://api.github.com/users/ropensci/followers","following_url":"https://api.github.com/users/ropensci/following{/other_user}","gists_url":"https://api.github.com/users/ropensci/gists{/gist_id}","starred_url":"https://api.github.com/users/ropensci/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ropensci/subscriptions","organizations_url":"https://api.github.com/users/ropensci/orgs","repos_url":"https://api.github.com/users/ropensci/repos","events_url":"https://api.github.com/users/ropensci/events{/privacy}","received_events_url":"https://api.github.com/users/ropensci/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/ropensci/rfishbase","description":"R 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