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osmose-model / osmose-web-api

Web service that generates Osmose configuration files from data sources like Fishbase and SeaLifeBase. Used by https://www.config.osmose-model.org .
MIT License
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Populate the "osm_param-species.csv" config file #97

Closed agruss2 closed 7 years ago

agruss2 commented 7 years ago

@jhpoelen Please make sure that the API now provides estimates for the following parameters of the "osm_param-species.csv" config file: (1) species.egg.size.sp (2) species.egg.weight.sp (3) species.relativefecundity.sp (4) species.sexratio.sp

jhpoelen commented 7 years ago

re: species.egg*: In fishbase-mapping.csv, a non-existent table eggs is referenced. Could it be that this table has not yet been published through fishbase api ? @FIN-JBarile @Dengaloo

re: relativefecundity - the mapping in fishbase-mapping.csv includes fecundity,RelFecundityMean and SpawningCycles,species.relativefecundity.sp. The term "and" is not yet supported by the configuration api. What do you mean when you say: fecundity,RelFecundityMean and SpawningCycles ? @agruss2

re: sexratio - according to a recently generated osmose config.zip, the values are being populated:

e.g. for default Gulf of Mexico

species.sexratio.sp0;52.2 species.sexratio.sp1;75 species.sexratio.sp2;0.5 species.sexratio.sp3;70 species.sexratio.sp4;0.5 species.sexratio.sp5;0.5 species.sexratio.sp6;0.5 species.sexratio.sp7;0.5 species.sexratio.sp8;0.5 species.sexratio.sp9;0.5 species.sexratio.sp10;0.5 species.sexratio.sp11;0.5 species.sexratio.sp12;50 species.sexratio.sp13;52.3 species.sexratio.sp14;0.5 species.sexratio.sp15;50 species.sexratio.sp16;50 species.sexratio.sp17;0.5 species.sexratio.sp18;52 species.sexratio.sp19;0.5 species.sexratio.sp20;0.5 species.sexratio.sp21;50

agruss2 commented 7 years ago

@FIN-JBarile @Dengaloo Please address the following comment from Jorrit: "re: species.egg*: In fishbase-mapping.csv, a non-existent table eggs is referenced. Could it be that this table has not yet been published through fishbase api ?" Moreover, please have a look at the estimates of female:male sex ratios copied/pasted by Jorrit above. Those seem to be extremely high to me. But, perhaps, they make sense based on the ecology of the functional groups/species under consideration. Please analyze this issue and let @jhpoelen and me know. Based on your thoughts, I may decide to set the female:male sex ratio of all focal functional groups to the default value of 0.5. Thanks a lot!

agruss2 commented 7 years ago

@jhpoelen re: relativefecundity For a given focal functional group the RelFecundity and SpawningCycles parameters can be extracted from FishBase/SeaLifeBase's FECUNDITY table and multiplied together to get an estimate of annual number of eggs per gram of mature female. Definitions of RelFecundity and SpawningCycles can be found at: ropensci/fishbaseapi/blob/master/docs/docs-sources/fecundity.csv

agruss2 commented 7 years ago

@FIN-JBarile @Dengaloo Please address the following comment from Jorrit: "re: species.egg*: In fishbase-mapping.csv, a non-existent table eggs is referenced. Could it be that this table has not yet been published through fishbase api ?" Moreover, please have a look at the estimates of female:male sex ratios copied/pasted by Jorrit above. Those seem to be extremely high to me. But, perhaps, they make sense based on the ecology of the functional groups/species under consideration. Please analyze this issue and let @jhpoelen and me know. Based on your thoughts, I may decide to set the female:male sex ratio of all focal functional groups to the default value of 0.5. Thanks a lot!

jhpoelen commented 7 years ago

also see #108 .

jhpoelen commented 7 years ago

@agruss2 species.relativefecundity.sp should now be calculated. Please verify.

agruss2 commented 7 years ago

@jhpoelen Indeed, species.relativefecundity.sp is now being calculated; many thanks! However, I will soon alter the default value of this parameter in the "fishbase-mapping.csv" file, because it cannot be 0.0. More generally, I will rework the "fishbase-mapping.csv" file this weekend to make sure that all the default values provided there are coherent.

jhpoelen commented 7 years ago

Glad to hear that the relativefecundity is now calculated. I've opened a separate issue #109 to document the single remaining issue: the missing eggs fishbase table and am closing this issue.