Spring-Run Yearling Growth — yearling

Generates transition probability matrices for yearling growth

yearling_growth(
  year,
  yearlings,
  mode,
  survival_adjustment,
  yearling_territory_size = springRunDSM::params$yearling_territory_size,
  inchannel_habitat_fry = springRunDSM::params$inchannel_habitat_fry,
  inchannel_habitat_juvenile = springRunDSM::params$inchannel_habitat_juvenile,
  floodplain_habitat = springRunDSM::params$floodplain_habitat,
  avg_temp = springRunDSM::params$avg_temp,
  prob_strand_early = springRunDSM::params$prob_strand_early,
  prob_strand_late = springRunDSM::params$prob_strand_late,
  proportion_diverted = springRunDSM::params$proportion_diverted,
  total_diverted = springRunDSM::params$total_diverted,
  weeks_flooded = springRunDSM::params$weeks_flooded,
  prop_high_predation = springRunDSM::params$prop_high_predation,
  contact_points = springRunDSM::params$contact_points,
  growth_rates = springRunDSM::params$growth_rates,
  growth_rates_floodplain = springRunDSM::params$growth_rates_floodplain,
  ..surv_juv_rear_int = springRunDSM::..surv_juv_rear_int,
  .surv_juv_rear_contact_points = springRunDSM::.surv_juv_rear_contact_points,
  ..surv_juv_rear_contact_points = springRunDSM::..surv_juv_rear_contact_points,
  .surv_juv_rear_prop_diversions = springRunDSM::.surv_juv_rear_prop_diversions,
  ..surv_juv_rear_prop_diversions = springRunDSM::..surv_juv_rear_prop_diversions,
  .surv_juv_rear_total_diversions = springRunDSM::.surv_juv_rear_total_diversions,
  ..surv_juv_rear_total_diversions = springRunDSM::..surv_juv_rear_total_diversions,
  .surv_juv_rear_avg_temp_thresh = springRunDSM::.surv_juv_rear_avg_temp_thresh,
  .surv_juv_rear_high_predation = springRunDSM::.surv_juv_rear_high_predation,
  .surv_juv_rear_stranded = springRunDSM::.surv_juv_rear_stranded,
  .surv_juv_rear_medium = springRunDSM::.surv_juv_rear_medium,
  .surv_juv_rear_large = springRunDSM::.surv_juv_rear_large,
  .surv_juv_rear_floodplain = springRunDSM::.surv_juv_rear_floodplain,
  min_survival_rate = springRunDSM::min_survival_rate,
  stochastic
)

Arguments

year: Current simulation year
yearlings: Yearlings in tributaries
mode: The mode to run model in. Can be "seed", "simulate", "calibrate"
yearling_territory_size: Array of juvenile fish territory requirements
inchannel_habitat_fry: 3 dimensional array [watersheds, months, years] representing fry inchannel habitat in square meters
inchannel_habitat_juvenile: 3 dimensional array [watersheds, months, years] representing juvenile inchannel habitat in square meters
floodplain_habitat: 3 dimensional array [watersheds, months, years] representing floodplain habitat in square meters
avg_temp: More details at stream_tempetature
prob_strand_early: More details at prop_strand_early
prob_strand_late: More details at prop_strand_late
proportion_diverted: More details at proportion_diverted
total_diverted: More details at total_diverted
weeks_flooded: More details at weeks_flooded
prop_high_predation: More details at prop_high_predation
contact_points: More details at contact_points
..surv_juv_rear_int: Intercept for surv_juv_rear
.surv_juv_rear_contact_points: Coefficient for surv_juv_rear contact_points variable
..surv_juv_rear_contact_points: Calibrated coefficient for surv_juv_rear contact_points variable
.surv_juv_rear_prop_diversions: Coefficient for surv_juv_rear prop_diversions variable
..surv_juv_rear_prop_diversions: Calibrated coefficient for surv_juv_rear prop_diversions variable
.surv_juv_rear_total_diversions: Coefficient for surv_juv_rear total_diversions variable
..surv_juv_rear_total_diversions: Calibrated coefficient for surv_juv_rear total_diversions variable
.surv_juv_rear_avg_temp_thresh: Coefficient for surv_juv_rear avg_temp_thresh variable
.surv_juv_rear_high_predation: Coefficient for surv_juv_rear high_predation variable
.surv_juv_rear_stranded: Coefficient for surv_juv_rear stranded variable
.surv_juv_rear_medium: Size related intercept for surv_juv_rear medium sized fish
.surv_juv_rear_large: Size related intercept for surv_juv_rear large sized fish
.surv_juv_rear_floodplain: Additional intercept for surv_juv_rear floodplain rearing benefit
min_survival_rate: estimated survival rate if temperature threshold is exceeded

Details

See params for details on parameter sources