demo/getBiomass.R

In imarpe/path: Pelagic Assessment Tools for Hydroacoustics

require(path)

# Parameters -----------------------------------------------------------------------------

inputFolder       = "inputs/"
boot              = TRUE
n                 = 5
umbralIndividuos  = 150
crucero           = "150810"
sp                = "anchoveta"
method            = "simmonds2010"


# Analysis and results -------------------------------------------------------------------

file.acustica   = "Celdas 120 kHz Olaya-Flores 1508-10.csv"
file.biometrico = "biometricoMF_FULL.csv"
file.biologico  = "biologico_1508_10_FULL.csv"

allData = leerDatos(acustica   = file.acustica, 
                    biometrico = file.biometrico,
                    biologia   = file.biologico,
                    crucero    = crucero, 
                    dir        = inputFolder)

biomasa = estimarBiomasa(data = allData,
                         sp = sp, 
                         boot = boot, 
                         n = n, 
                         umbralIndividuos = umbralIndividuos, 
                         method = method)

# Write outputs
escribirResultados(biomasa)

# Get distribution indices
estimarIndices(object = allData, dir = file.path(inputFolder, "../"))

# Plot distribution of 
plot(biomasa)