<commit_before>FishBase table,FishBase column(s),OSMOSE property,Default value,Notes from Arnaud
species,LongevityWild,species.lifespan.sp,0,Longevity. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
popgrowth,K,species.K.sp,0.0,Instantaneous growth rate at small size. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
popgrowth,Loo,species.lInf.sp,0.0,Maximum size. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
popgrowth,to,species.t0.sp,0.0,Theoretical age of zero length. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
poplw,a,species.length2weight.condition.factor.sp,0.0,Constant of proportionality of the allometric length-weight relationship. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
poplw,b,species.length2weight.allometric.power.sp,0.0,Exponent of the allometric length-weight relationship. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
maturity,Lm,species.maturity.size.sp,0.0,Size at sexual maturity. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
maturity,tm,species.maturity.age.sp,0.0,Age at sexual maturity. This is a parameter that can directly be obtained from FishBase/SeaLifeBase. 
?,?,species.vonbertalanffy.threshold.age.sp,0.0,Threshold age below which a linear growth model is used to calculate mean length increase. This is a parameter that could easily be obtained from FishBase/SeaLifeBase to my mind. The following issue needs to be addressed: jhpoelen/fb-osmose-bridge/issues/23 
poplw,Type,species.length2weight.fl.sp,true,Length-weight relationship estimated for fork lengths (FLs)?: Boolean variable. This is a parameter that I created for the OSMOSE-WFS model but which will undoubtedly be useful for other OSMOSE applications. This parameter can easily be obtained from queries in FishBase/SeaLifeBase. The following issue needs to be addressed: jhpoelen/fb-osmose-bridge/issues/30  
fecundity,RelFecundityMean and SpawningCycles,species.relativefecundity.sp,0.0,Annual number of eggs per gram of mature female. This is a parameter that can easily be obtained from queries in FishBase/SeaLifeBase; for a given focal functional group the RelFecundity and SpawningCycles parameters can be extracted from  FishBase/SeaLifeBase 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 
spawning,SexRatiomid,species.sexratio.sp,0.0,Female:male sex ratio. This is a parameter that can easily be obtained from queries in FishBase/SeaLifeBase. Nota bene: SexRatiomid in FishBase's spawning.csv is the percentage of spawning females in spawning stock; female:male sex ratio in OSMOSE is a quantity lower than 1
popqb,PopQB,predation.ingestion.rate.max.osmose.sp,0.0,Maximum annual ingestion rate expressed in grams of food per gram of individual and per year. This parameter is usually set to 3.5 g of food per g of individual and per year for all focal functional groups in OSMOSE models. It is similar to Ecopath's Q/B parameter. This parameter can be directly obtained from FishBase/SeaLifeBase 
popqb,MaintQB and PopQB,predation.efficiency.critical.sp,0.0,Critical predation efficiency. This is the predation efficiency ensuring body maintenance. This parameter is usually set to 0.57 for all focal functional groups in OSMOSE models. This is a parameter can easily be obtained by extracting the MaintQB and PopQB parameters in FishBase's popqb.csv and dividing the former parameter by the latter.   
?,?,mortality.starvation.rate.max.sp,,Maximum annual starvation mortality. This parameter is usually set to 0.3 year-1 for all focal functional groups in OSMOSE models.I am still unclear whether and how this parameter could be obtained through the bridge between FishBase/SeaLifeBase and OSMOSE. The following issue needs to be addressed: jhpoelen/fb-osmose-bridge/issues/25      
,,predation.predPrey.sizeRatio.min.sp,,Minimum predator/prey size ratios defined for juveniles (immature individuals) and adults (mature individuals) of each focal functional group. NB: the predator/prey size ratios of juveniles and adults of a given focal functional group can be identical if this makes sense from an ecological standpoint. These are parameters that could possibly be obtained from queries in FishBase/SeaLifeBase to my mind. <NAME> once mentioned that Predator/prey size ratios could be estimated by FishBase/SeaLifeBase from a calculation of gape size; gape size can be obtained as a percentage of total length (see morphometrics in FishBase/SeaLifeBase) 
,,predation.predPrey.sizeRatio.max.sp,,Maximum predator/prey size ratios defined for juveniles (immature individuals) and adults (mature individuals) of each focal functional group. NB: the predator/prey size ratios of juveniles and adults of a given focal functional group can be identical if this makes sense from an ecological standpoint. These are parameters that could possibly be obtained from queries in FishBase/SeaLifeBase to my mind. <NAME> once mentioned that Predator/prey size ratios could be estimated by FishBase/SeaLifeBase from a calculation of gape size; gape size can be obtained as a percentage of total length (see morphometrics in FishBase/SeaLifeBase) <commit_msg>Update fishbase-mapping.csv<commit_after>FishBase table,FishBase column(s),OSMOSE property,Default value,Notes from Arnaud
species,LongevityWild,species.lifespan.sp,0,Longevity. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
popgrowth,K,species.K.sp,0.0,Instantaneous growth rate at small size. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
popgrowth,Loo,species.lInf.sp,0.0,Maximum size. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
popgrowth,to,species.t0.sp,0.0,Theoretical age of zero length. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
poplw,a,species.length2weight.condition.factor.sp,0.0,Constant of proportionality of the allometric length-weight relationship. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
poplw,b,species.length2weight.allometric.power.sp,0.0,Exponent of the allometric length-weight relationship. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
maturity,Lm,species.maturity.size.sp,0.0,Size at sexual maturity. This is a parameter that can directly be obtained from FishBase/SeaLifeBase
maturity,tm,species.maturity.age.sp,0.0,Age at sexual maturity. This is a parameter that can directly be obtained from FishBase/SeaLifeBase. 
?,?,species.vonbertalanffy.threshold.age.sp,1.0,Threshold age below which a linear growth model is used to calculate mean length increase. This is a parameter that could easily be obtained from FishBase/SeaLifeBase to my mind. The following issue needs to be addressed: jhpoelen/fb-osmose-bridge/issues/23 
poplw,Type,species.length2weight.fl.sp,true,Length-weight relationship estimated for fork lengths (FLs)?: Boolean variable. This is a parameter that I created for the OSMOSE-WFS model but which will undoubtedly be useful for other OSMOSE applications. This parameter can easily be obtained from queries in FishBase/SeaLifeBase. The following issue needs to be addressed: jhpoelen/fb-osmose-bridge/issues/30  
fecundity,RelFecundityMean and SpawningCycles,species.relativefecundity.sp,0.0,Annual number of eggs per gram of mature female. This is a parameter that can easily be obtained from queries in FishBase/SeaLifeBase; for a given focal functional group the RelFecundity and SpawningCycles parameters can be extracted from  FishBase/SeaLifeBase 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 
spawning,SexRatiomid,species.sexratio.sp,0.0,Female:male sex ratio. This is a parameter that can easily be obtained from queries in FishBase/SeaLifeBase. Nota bene: SexRatiomid in FishBase's spawning.csv is the percentage of spawning females in spawning stock; female:male sex ratio in OSMOSE is a quantity lower than 1
popqb,PopQB,predation.ingestion.rate.max.osmose.sp,0.0,Maximum annual ingestion rate expressed in grams of food per gram of individual and per year. This parameter is usually set to 3.5 g of food per g of individual and per year for all focal functional groups in OSMOSE models. It is similar to Ecopath's Q/B parameter. This parameter can be directly obtained from FishBase/SeaLifeBase 
popqb,MaintQB and PopQB,predation.efficiency.critical.sp,0.0,Critical predation efficiency. This is the predation efficiency ensuring body maintenance. This parameter is usually set to 0.57 for all focal functional groups in OSMOSE models. This is a parameter can easily be obtained by extracting the MaintQB and PopQB parameters in FishBase's popqb.csv and dividing the former parameter by the latter.   
?,?,mortality.starvation.rate.max.sp,0.3,Maximum annual starvation mortality. This parameter is usually set to 0.3 year-1 for all focal functional groups in OSMOSE models.I am still unclear whether and how this parameter could be obtained through the bridge between FishBase/SeaLifeBase and OSMOSE. The following issue needs to be addressed: jhpoelen/fb-osmose-bridge/issues/25      
,,predation.predPrey.sizeRatio.min.sp,,Minimum predator/prey size ratios defined for juveniles (immature individuals) and adults (mature individuals) of each focal functional group. NB: the predator/prey size ratios of juveniles and adults of a given focal functional group can be identical if this makes sense from an ecological standpoint. These are parameters that could possibly be obtained from queries in FishBase/SeaLifeBase to my mind. Deng Palomares once mentioned that Predator/prey size ratios could be estimated by FishBase/SeaLifeBase from a calculation of gape size; gape size can be obtained as a percentage of total length (see morphometrics in FishBase/SeaLifeBase) 
,,predation.predPrey.sizeRatio.max.sp,,Maximum predator/prey size ratios defined for juveniles (immature individuals) and adults (mature individuals) of each focal functional group. NB: the predator/prey size ratios of juveniles and adults of a given focal functional group can be identical if this makes sense from an ecological standpoint. These are parameters that could possibly be obtained from queries in FishBase/SeaLifeBase to my mind. Deng Palomares once mentioned that Predator/prey size ratios could be estimated by FishBase/SeaLifeBase from a calculation of gape size; gape size can be obtained as a percentage of total length (see morphometrics in FishBase/SeaLifeBase) 
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