5.3. Background species
Background species have first been introduced in Osmose by [Fu et al., 2017]. They can be viewed as an intermediary between focal species (i.e. species of interest, whose full life cycle is simulated) and lower trophic levels (plankton for instance). They differ from lower trophic levels since they can feed on focal species and be targeted by fisheries (since version 4.3)
They are available on Osmose since version 4.1.0, although their parameterization has changed in version 4.3.0.
5.3.1. Osmose <= 4.1.0
Background parameters in Osmose version 4.1.0 are paremeterized as follows:
biomass.byDt.bySize.file.bkg# |
CSV file containg the background species biomass by size class and by time step. |
species.trophiclevel.bkg# |
Array of trophic level (one for each size class) |
species.name.bkg# |
Name of the background species |
species.length2weight.allometric.power.bkg# |
Allometric factor for weight to length conversion |
species.length2weight.condition.factor.bkg# |
Allometrioc power for weight to length conversion |
predation.accessibility.stage.threshold.bkg# |
Threshold for accessibility matrix |
predation.efficiency.critical.bkg# |
Critical predation success (\(C_{S_R}\)) |
predation.ingestion.rate.max.bkg# |
\(I_{max}\) (grams of food per gram of fish and per year) |
predation.predPrey.stage.threshold.bkg# |
Age or size thresholds for predation/prey size ratios |
predation.predPrey.sizeRatio.max.bkg# |
Array of \(R_{max}\) values |
predation.predPrey.sizeRatio.min.bkg# |
Array of \(R_{min}\) values |
The biomass provided in the CSV file will then be distributed over the domain using distribution maps (similar to the ones defined for focal species).
movement.bkgspecies.species.map# |
Name of the background species to which the map is associated. |
movement.bkgspecies.class.map# |
Size class for which the map is associated. |
movement.bkgspecies.season.map# |
Time steps during which the map will be used |
movement.bkgspecies.year.min.map# |
Initial year when the map will be used |
movement.bkgspecies.year.max.map# |
Final year when the map will be used |
Warning
For background species, the size classes are fixed!
5.3.1.1. Accessibility matrix
When using background species, the accessibility matrix must be changed accordingly. It must always have the following form:
Focal (pred) |
Background (pred) |
|
Focal (prey) |
||
Background (prey) |
||
LTL (prey) |
5.3.1.2. Background biomass
Background species biomass is defined from a biomass time series (one per species and per size class) and by distribution maps. The distribution maps contain defines the distribution of the background species over space. They contain float values, which are normalize, so that the integral over space equals one:
Before each time step, the background species biomass is reset by multiplying the biomass time series by the map distribution factor. Because of the normalisation, the spatially integrated biomass is equal to the biomass provided in the time-series.
5.3.2. Osmose >= 4.3.0
In Osmose version >= 4.3, background species are parameterized as follows:
Species parameters |
|
species.name.sp# |
Name of the background species |
species.type.sp# |
Type of the background species. Must be |
species.length2weight.allometric.power.sp# |
Allometric factor for weight to length conversion |
species.length2weight.condition.factor.sp# |
Allometrioc power for weight to length conversion |
predation.efficiency.critical.sp# |
Critical predation success (\(C_{S_R}\)) |
predation.ingestion.rate.max.sp# |
\(I_{max}\) (grams of food per gram of fish and per year) |
predation.predPrey.stage.threshold.sp# |
Age or size thresholds for predation/prey size ratios |
predation.predPrey.sizeRatio.max.sp# |
Array of \(R_{max}\) values |
predation.predPrey.sizeRatio.min.sp# |
Array of \(R_{min}\) values |
Resource forcing parameters |
|
species.biomass.total.sp# |
Total biomass for the given ressource (will be distributed over the whole domain) |
species.file.sp# |
Regular expression defining the input files. Can be a file name. |
species.file.caching.sp# |
Resource caching method. Must be |
Background species parameters |
|
species.nclass.sp# |
Number of size classes. |
species.trophiclevel.sp# |
Array of trophic level (one value for each size class) |
species.age.sp# |
Array of school ages (one value per each size class) |
species.length.sp# |
Array of school lengths (one value for each size class) |
species.size.proportion.sp# |
Array of size proportion (one value for each size class) |
The spatio-temporal distribution of background is now defined from a NetCDF file (see Section 5.4).
The distribution among size is now controlled by the species.nclass.sp# and species.size.proportion.sp# parameters.
Warning
At this time, the distribution among the size classes is constant over the entire simulation.