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OUTPUT_README.md

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Output Files

The model is capable of producing three different kinds of output files:

State Snapshots

State snapshots can be saved in two ways:

  • Pressing Ctrl+C to interrupt the headless model, then entering the 'save' command (with the desired filename)
  • In the GUI, selecting File -> Save from the menu

State snapshots can be loaded from the GUI using the File -> Load menu item in order to load the saved state of the model.

Sample data

Sample data files are produced by the headless executable, and consist of a record of statistics of population samples taken at various sampling sites throughout the map. This data is also included in state snapshots. Sample data is saved as output_X.nc, where X is the run ID.

Summaries

Summaries are automatically saved as summary_X.nc by the headless executable when a simulation is finished, where X is the run ID.

Tagged Fish Histories

Tagged fish histories can be saved from the GUI using the File -> Save Tagged History menu item. They can also be loaded in the GUI using File -> Load Tagged History in order to view a replay of the history of the tagged fish.

Formats

All model outputs are saved as netCDF 4 files.

State Snapshots

  • Snapshot files contain the following dimensions:

    • n: Indicates individual, for per-fish variables
    • populationHistoryLength: Indicates timestep for population history entries
    • sampleHistoryLength: Indicates sample number for sample history entries (not equivalent to time)

  • Snapshot files contain the following variables:

    • modelTime: int, the current model timestep
    • recruitTime[n]: ints, each fish's entry timestep
    • exitTime[n]: ints, each fish's exit or death timestep (only valid for a given n if status[n] is not 0, since status 0 is Alive)
    • entryForkLength[n]: floats, fork length of each fish upon entry (mm)
    • entryMass[n]: floats, mass of each fish upon entry (g)
    • forkLength[n]: floats, current/final fork length of each fish (mm)
    • mass[n]: floats, current/final mass of each fish (g)
    • status[n]: ints, current/final status of each fish
      • 0: Alive
      • 1: Dead from mortality risk
      • 2: Dead from stranding
      • 3: Dead from starvation
      • 4: Exited
    • location[n]: ints, current/final map node ID where each fish is located
    • travel[n]: floats, most recent timestep's swim distance for each fish (m)
    • lastGrowth[n]: floats, most recent timestep's growth for each fish (g)
    • lastPmax[n]: floats, most recent timestep's Pmax for each fish (p)
    • lastMortality[n]: floats, most recent timestep's mortality risk for each fish (probability value)
    • populationHistory[populationHistoryLength]: ints, per-timestep counts of living individuals in the model
    • sampleSiteID[sampleHistoryLength]: ints, each sample's site ID
      • Refer to data/sampling_sites.csv for a list of sample site names and coordinates. Site IDs correspond to line numbers (site ID 0 is Grain of Sand, 1 is FWP New Site, etc.)
    • sampleTime[sampleHistoryLength]: ints, the timestep when each sample was taken
    • samplePop[sampleHistoryLength]: ints, the number of individuals in each sample
    • sampleMeanMass[sampleHistoryLength]: floats, each sample's mean individual mass (g)
    • sampleMeanLength[sampleHistoryLength]: floats, each sample's mean individual fork length (mm)
    • sampleMeanSpawnTime[sampleHistoryLength]: floats, each sample's mean individual spawn time (timesteps)

Sample data

  • Snapshot files contain the following dimensions:
    • sampleHistoryLength: Indicates sample number for sample history entries (not equivalent to time)
  • Sample data files contain the following variables:
    • sampleSiteID[sampleHistoryLength]: ints, each sample's site ID
      • Refer to data/sampling_sites.csv for a list of sample site names and coordinates. Site IDs correspond to line numbers (site ID 0 is Grain of Sand, 1 is FWP New Site, etc.)
    • sampleTime[sampleHistoryLength]: ints, the timestep when each sample was taken
    • samplePop[sampleHistoryLength]: ints, the number of individuals in each sample
    • sampleMeanMass[sampleHistoryLength]: floats, each sample's mean individual mass (g)
    • sampleMeanLength[sampleHistoryLength]: floats, each sample's mean individual fork length (mm)
    • sampleMeanSpawnTime[sampleHistoryLength]: floats, each sample's mean individual spawn time (timesteps)

Summaries

  • Summary files contain the following dimensions:
    • n: Indicates individual
  • Summary files contain the following variables:
    • recruitTime[n]: ints, each fish's entry timestep
    • exitTime[n]: ints, each fish's exit or death timestep (only valid for a given n if finalStatus[n] is not 0, since status 0 is Alive)
    • entryForkLength[n]: floats, fork length of each fish upon entry (mm)
    • entryMass[n]: floats, mass of each fish upon entry (g)
    • finalForkLength[n]: floats, current/final fork length of each fish (mm)
    • finalMass[n]: floats, current/final mass of each fish (g)
    • finalStatus[n]: ints, current/final status of each fish

Tagged Fish Histories

  • Tagged fish histories contain the following dimensions:
    • n: Indicates individual
    • t: Indicates timestep
  • Tagged fish histories contain the following variables:
    • recruitTime[n]: ints, each fish's entry timestep
    • taggedTime[n]: ints, the timestep when each fish was tagged
    • exitTime[n]: ints, each fish's exit or death timestep (only valid for a given n if finalStatus[n] is not 0, since status 0 is Alive)
    • entryForkLength[n]: floats, fork length of each fish upon entry (mm)
    • entryMass[n]: floats, mass of each fish upon entry (g)
    • finalForkLength[n]: floats, current/final fork length of each fish (mm)
    • finalMass[n]: floats, current/final mass of each fish (g)
    • finalStatus[n]: ints, current/final status of each fish
    • locationHistory[n, t]: ints, the map node ID where each fish was on each timestep (or -1 if a fish wasn't in the model on the timestep in question)
    • growthHistory[n, t]: floats, the growth (g) on each timestep for each fish, or 0 if the fish wasn't in the model on the timestep in question
    • pmaxHistory[n, t]: floats, the pmax (p) on each timestep for each fish, or 0 if the fish wasn't in the model on the timestep in question
    • mortalityHistory[n, t]: floats, the mortality risk (probability) on each timestep for each fish, or 0 if the fish wasn't in the model on the timestep in question
    • tempHistory[n, t]: floats, the temperature in the current location at the end of each timestep for each fish, or 0 if the fish wasn't in the model on the timestep in question
    • depthHistory[n, t]: floats, the water depth in the location at the end of each timestep for each fish, or 0 if the fish wasn't in the model on the timestep in question
    • flowSpeedHistory[n, t]: floats, the flow speed in the location at the end of each timestep for each fish, or 0 if the fish wasn't in the model on the timestep in question