{"action":"created","issue":{"url":"https://api.github.com/repos/jhpoelen/fb-osmose-bridge/issues/114","repository_url":"https://api.github.com/repos/jhpoelen/fb-osmose-bridge","labels_url":"https://api.github.com/repos/jhpoelen/fb-osmose-bridge/issues/114/labels{/name}","comments_url":"https://api.github.com/repos/jhpoelen/fb-osmose-bridge/issues/114/comments","events_url":"https://api.github.com/repos/jhpoelen/fb-osmose-bridge/issues/114/events","html_url":"https://github.com/jhpoelen/fb-osmose-bridge/issues/114","id":231462282,"number":114,"title":"Making sure to provide as few NAs as possible for background functional 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September, 10th 2017","description":null,"creator":{"login":"agruss2","id":16559622,"avatar_url":"https://avatars1.githubusercontent.com/u/16559622?v=4","gravatar_id":"","url":"https://api.github.com/users/agruss2","html_url":"https://github.com/agruss2","followers_url":"https://api.github.com/users/agruss2/followers","following_url":"https://api.github.com/users/agruss2/following{/other_user}","gists_url":"https://api.github.com/users/agruss2/gists{/gist_id}","starred_url":"https://api.github.com/users/agruss2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/agruss2/subscriptions","organizations_url":"https://api.github.com/users/agruss2/orgs","repos_url":"https://api.github.com/users/agruss2/repos","events_url":"https://api.github.com/users/agruss2/events{/privacy}","received_events_url":"https://api.github.com/users/agruss2/received_events","type":"User","site_admin":false},"open_issues":7,"closed_issues":2,"state":"open","created_at":"2017-09-01T19:07:13Z","updated_at":"2017-09-04T22:22:54Z","due_on":null,"closed_at":null},"comments":15,"created_at":"2017-05-25T21:16:21Z","updated_at":"2017-09-06T14:36:42Z","closed_at":null,"author_association":"COLLABORATOR","body":"@jhpoelen @Dengaloo \r\nThe “osm_param-ltl.csv” file provides estimates for three parameters: “plankton.size.min.plkX”, “plankton.size.max.plkX” and “plankton.TL.plkX”. \r\nThe default values of these three parameters (which are specified in “fishbase-mapping.csv”) are problematic. \r\nIndeed, it is impossible to specify a default value for these three parameters for all the fish and invertebrates recorded in FishBase and SeaLifeBase. \r\nTo solve this issue, we have two options:\r\n\r\n(Option 1) Setting the default value of the “plankton.size.min.plkX”, “plankton.size.max.plkX” and “plankton.TL.plkX” parameters to “NA” (not available) in the “fishbase-mapping.csv” file. \r\n\r\nOr \r\n\r\n(Option 2) Implementing a rule of thumb in the API such that, if the API is unable to define a value for one parameter (for example “plankton.size.min.plkX”) for a given functional group, it uses information for the other species belonging to the genuses, families and orders considered in the functional group. (These other species can be found anywhere across the globe). \r\nFor instance, let’s say that:\r\n(i) We are dealing with the Iceland Shelf/Sea ecosystem and that the bridge between FishBase/SeaLifeBase and OSMOSE defines a functional group called “demersalmollusc” for us. \r\n(ii) We choose to define “demersalmollusc” as a “background” functional group. \r\n(iii) The “demersalmollusc” functional group includes three species: Falcidens thorensis (Aplacophora), Prochaetoderma clenchi (Aplacophora) and Micropilina minuta (Monoplacophora). \r\n(iv) Estimates are not available for Falcidens thorensis, Prochaetoderma clenchi and Micropilina minuta to define a value for the parameter “plankton.size.min.plkX” for the “demersalmollusc” functional group. \r\n(v) Then, the API: identifies the genuses, families and orders to which Falcidens thorensis, Prochaetoderma clenchi and Micropilina minuta belong; and uses the information available for all the species that belong to the genuses, families and orders to which Falcidens thorensis, Prochaetoderma clenchi and Micropilina minuta belong to define a value for the parameter “plankton.size.min.plkX” for the “demersalmollusc” functional group.\r\n\r\nPersonnally, I prefer Option 2. We do not want to provide a lot of NA’s to the user; this would be frustrating to them. \r\nPlus I am not sure that the API can handle something else than numbers regarding the default values taken from the “Default value” column of the “fishbase-mapping.csv” file.  @jhpoelen Is that correct? \r\n\r\nBut then, if we choose Option 2, how should the estimates be computed? \r\nI was thinking that the best option in the case presented above would be to: (i) consider all the minimum size estimates available for the species that belong to the genuses, families and orders to which Falcidens thorensis, Prochaetoderma clenchi and Micropilina minuta belong; and (ii) produce a mean estimate from all the available estimates.  \r\n\r\nPlease let me know what you think. \r\nAfter I have received your input, I will close the present issue and will create new API issues. \r\nMany thanks. "},"comment":{"url":"https://api.github.com/repos/jhpoelen/fb-osmose-bridge/issues/comments/327503868","html_url":"https://github.com/jhpoelen/fb-osmose-bridge/issues/114#issuecomment-327503868","issue_url":"https://api.github.com/repos/jhpoelen/fb-osmose-bridge/issues/114","id":327503868,"user":{"login":"jhpoelen","id":1084872,"avatar_url":"https://avatars2.githubusercontent.com/u/1084872?v=4","gravatar_id":"","url":"https://api.github.com/users/jhpoelen","html_url":"https://github.com/jhpoelen","followers_url":"https://api.github.com/users/jhpoelen/followers","following_url":"https://api.github.com/users/jhpoelen/following{/other_user}","gists_url":"https://api.github.com/users/jhpoelen/gists{/gist_id}","starred_url":"https://api.github.com/users/jhpoelen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jhpoelen/subscriptions","organizations_url":"https://api.github.com/users/jhpoelen/orgs","repos_url":"https://api.github.com/users/jhpoelen/repos","events_url":"https://api.github.com/users/jhpoelen/events{/privacy}","received_events_url":"https://api.github.com/users/jhpoelen/received_events","type":"User","site_admin":false},"created_at":"2017-09-06T14:36:42Z","updated_at":"2017-09-06T14:36:42Z","author_association":"OWNER","body":"I haven't done any performance tests to check how long a species list can be. I do imagine the performance depends on the data richness of the species in the list: the more data, the faster the creation of the generation of related osmose configuration will be.\r\n\r\nI'd like to suggest two things:\r\n\r\n1. close issues #115 and #114 (this issue) - the issues are the same, as seen in the duplication of comments.\r\n2. open a new, specific issue for the NAs - the issue describes specifically step-by-step instructions on how to reproduce what @agruss2 is seeing . Also, the issue would include an expected behavior with specific description (e.g., silly example: I expect a value for ear size of fish of functional group with species mickey, donald and minni.). "}}
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