SurveyBySpecie: SurveyBySpecie

In d-lorenz/smartR: Spatial Management and Assessment of Demersal Resources for Trawl Fisheries

Description

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

Format

R6Class object.

Value

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

Fields

specie

Name of the specie.

year

Years in 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.

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

d-lorenz/smartR documentation built on May 9, 2020, 12:57 p.m.