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Calculate Productivity Anomalies from Survey Data

Source: R/productivity_anomaly.R
create_productivity_anomaly.Rd

Processes survey and species data to calculate recruitment-spawner ratios (r/s) and their anomalies (z-scores) across species and EPUs. Outputs data formatted for State of the Ecosystem (SOE) reporting.

Usage

create_productivity_anomaly(
  input_survey_bio,
  input_survey_bio_epu,
  input_static_lw_table,
  inputPathSpecies,
  input_static_length_convert,
  species2include = c("SPINY DOGFISH", "BARNDOOR SKATE", "WINTER SKATE",
    "CLEARNOSE SKATE", "ROSETTE SKATE", "LITTLE SKATE", "SMOOTH SKATE", "THORNY SKATE",
    "OFFSHORE HAKE", "SILVER HAKE", "ATLANTIC COD", "HADDOCK", "POLLOCK", "WHITE HAKE",
    "RED HAKE", "ATLANTIC HALIBUT", "AMERICAN PLAICE", "SUMMER FLOUNDER",
    "YELLOWTAIL FLOUNDER", "WINTER FLOUNDER", "WITCH FLOUNDER", "WINDOWPANE",
    "BUTTERFISH", "BLUEFISH", "BLACK SEA BASS", "SCUP", "TILEFISH", "ACADIAN REDFISH",
    "ATLANTIC WOLFFISH", "OCEAN POUT", "GOOSEFISH", "BLUELINE TILEFISH", 
    
    "ATLANTIC SALMON")
)

Arguments

input_survey_bio

Character string. Full path to the survey data with bio rds file

input_survey_bio_epu

File path to survey data with bio data and epu (.rds format)

input_static_lw_table

File path to length weight table from Miller 2013 (.rda format)

inputPathSpecies

File path to species lookup table (.rds format)

input_static_length_convert

File path to length conversion table (.rda format)

species2include

Character vector of species to include (default: commonly surveyed species)

Value

a combined productivity anomaly data set

Examples

if (FALSE) { # \dontrun{
create_productivity_anomaly(
  input_survey_bio = "survey_bio.rds",
  input_survey_bio_epu = "survey_bio_epu.rds",
  input_static_lw_table = "lw_table.rda",
  input_static_length_convert = "df_lconv.rda",
  inputPathSpecies = "species_lookup.rds"
)
} # }