FisheryBySpecie: FisheryBySpecie

Description

The FisheryBySpecie class implements the class of SMART to handle species samplings.

Arguments

Value

Object of R6Class with attributes and methods for the fishery data.

Format

R6Class object.

Fields

specie: Name of the specie.

year

Years of the time serie.

rawLFD

data.frame, raw length frequency distribution.

abuAvg

data.frame, average abundances by depth' stratum.

meditsIndex

data.frame, medits index by depth' stratum.

lengClas

numeric, length classes.

nCoho

numeric, number of cohorts.

spreDist

list of DF, lfd by sex.

sprePlot

plots of LFD statistics.

spreSpat

list of DF, spatial distribution by sex.

sampMcmc

list, mcmc output chains.

groMixout

list of DF, aged individuals by sex.

groPars

list of DF, growth parameters by sex.

LWpar

list of DF, length/weight parameters by sex.

#' @section Methods:

initialize(sing_spe): Automatic initialization made by the SmartProject class
setRawData(raw_data): This method is used load the initial raw dataset
setYears(): This method is used to store the years in the provided time-serie
setSpecie(): This method is used to store the name of the specie of the initial raw data
setLClass(): This method is used to store the unique length values of the sampled specie
setDepth(bathyMatrix): This method is used to assign the depth value corresponding to each sampling location
setStratum(vecStrata): This method is used to set the depth strata of each sampling location
setIndSpe(): This method is used to aggregate the abundance data into the medits index
setAbuAvg(): This method is used to standardize the spatial abundances by depth strata
setNCoho(num_coh): This method is used to setup the number of cohorts for the ageing module
setLWpar(alphaVal, betaVal, sex): This method is used to store the alpha and beta values for the length/weight relationship
setWeight(sexVal = "Female"): This method is used to compute the fish weight given their length and the LWrelationship
setSpreDistSing(): This method is used to spread the aggregated LFD abundances into single individuals
setSprePlot(sampSex): This method is used to setup the plots of the LFD statistics
setSpatDistSing(): This method is used to setup the spatial distribution of the single specimens
setSpatPlot(sampSex): This method is used to store the spatial plots of the population
getMCsamps(numSamp, numAdap, numIter, sexDrop, curveSel): This method is used to get a sample of the population to feed the mcmc module
getGrowPar(sexDrop): This method is used to extract the growth parameters from the mcmc results
getMCage(sexDrop): This method is used to assign an age to each fish
setMCplot(sexDrop, selCurve): This method is used to setup the plot of the mcmc results
calcMixDate(nAdap, nSamp, nIter, sexDrop, curveSel): This method is used to estimate the growth parameters of a population
ggplotMcmcOut(selCompo, selSex): This method is used to output the stored plots of mcmc results