R/LengthDistribution.R
AssignmentLengthDistribution.RdThe function AssignmentLengthDistribution calculates the average length distribution of the hauls assigned to each AcousticPSU defined by DefineBioticAssignment, and weighted by BioticAssignmentWeighting. The weights are scaled in bootstrapping by the number of times each haul is resampled. See Details.
AssignmentLengthDistribution(LengthDistributionData, BioticAssignment)The LengthDistributionData data.
The BioticAssignment process data.
An object of StoX datatype AssignmentLengthDistributionData.
The length distribution is normalized to percentage per AcousticPSU by dividing by the summed length distribution and scaling by 100.
Bootstrapping of acoustic-trawl models involve resampling the hauls assigned to the AcousticPSUs. For StoX <= 3.6.2 this resampling (with replacement) was from all hauls assigned to at least one AcousticPSU associated to each stratum (using ResampleBioticAssignmentByStratum). If different hauls were assigned to different AcousticPSUs this resampling included the risk that none of the assigned hauls of a particular AcousticPSU are resampled in a bootstrap replicate. This will result in all zeros in the weights (column WeightingFactor) of the BioticAssignment input to the AssignmentLengthDistribution function. When the length distributions are normalized, this involves dividing 0 by sum of 0, which results in NaN. This is intended, as it reflects that there does not exist a length distribution for that AcousticPSU. This will result in missing Abundance for the required species, but for missing IndividualTotalLength. To avoid this problem it is adviced to use the resampling function ResampleBioticAssignmentByAcousticPSU instead of ResampleBioticAssignmentByStratum, which resamples for each AcousticPSU and will never result in missing assignment length distribution.
LengthDistribution to produce the input LengthDistributionData, and DefineBioticAssignment to produce the input BioticAssignment.