FishFleet: FishFleet

Description

The FishFleet class implements the class of SMART to manage fleet data.

Arguments

Value

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

Format

R6Class object.

Fields

rawRegister: data.frame, raw fleet register data.

vmsRegister

data.frame, raw fleet register data for vms vessels only.

rawEffort

list of DF, raw effort data.

dayEffoMatr

list of DF, daily aggregated effort data.

prodMatr

list of DF, production data.

effoProd

list of DF, merged effort and production data.

effoProdMont

list of DF, monthly aggregated effort and production data.

effoMont

list of DF, monthly aggregated effort data.

effoProdAll

data.frame, monthly aggregated effort and production data.

effoAll

data.frame, monthly aggregated effort data.

regHarbsUni

data.frame, Harbours name, longitude, latitude and distance from the environment grid.

regHarbsBox

data.frame, Harbours name, longitude, latitude, number of registered vessels and distance from the environment grid within the grid box.

rawProduction

list of DF, raw production data.

rawEconomy

data.frame, raw economic data.

registerIds

character, vessel identification from fleet register.

predProd

list of matrix, simulated production.

productionIds

list of int, vessel ids with production data available.

prodSpec

list of character, specie with production data.

specSett

list of DF, logit parameter settings by specie.

specLogit

list, logit results by specie.

effortIds

list of int, vessel ids with effort data available.

idsEffoProd

list of int, merged vessel ids with both effort and production data available.

effoProdAllLoa

data.frame, monthly aggregated effort, production and loa data.

effoAllLoa

data.frame, monthly aggregated effort and loa data.

effortIndex

data.frame, effort index by vessel, year and month with loa data.

daysAtSea

data.frame, days at sea index by vessel, year, month with loa and Kw data.

prodIndex

data.frame, production index by vessel, year and month.

resNNLS

list, lander results by specie.

betaMeltYear

list of DF, melted yearly productivity by specie.

prodMeltYear

list of DF, melted yearly production by specie.

fishPoinPara

data.frame, fishing point parameters.

ecoPrice

list of DF, price/size by specie.

inSpatialReg

data.frame, input for spatial index regression.

inEffortReg

data.frame, input for effort index regression.

inProductionReg

data.frame, input for production index regression.

outSpatialReg

list, output for spatial index regression.

outEffortReg

list, output for effort index regression.

outProductionReg

list, output for production index regression.

plotSpatialReg

ggplot, spatial index regression results.

plotEffortReg

ggplot, effort index regression results.

plotProductionReg

ggplot, production index regression results.

Methods

setVmsRegister(): This method is used to exclude the fleet register records of vessels without vms
setRegHarbs(): This method is used to fetch the harbours coordinates
setEcoPrice(sel_specie, price_df): This method is used to set the price/size attribute by species
saveFleetHarb(harb_path): This method is used to export the rds with the harbours' coordinates
loadFleetHarb(harb_path): This method is used to import the rds with the harbours' coordinates
loadFleetRegis(register_path): This method is used to load the raw fleet register
loadMatEffort(effort_path): This method is used to import the raw effort matrix
loadRawEconomy(economic_path): This method is used to load the raw csv file with economic data
setInSpatial(): This method is used to setup the input for the spatial regression
setInEffort(): This method is used to setup the input for the effprt regression
getRegSpatial(): This method is used to compute the spatial regression
getRegEffort(): This method is used to compute the effort regression
getRegProduction(): This method is used to compute the production regression
getCostOutput(): This method is a wrapper function to get the economic regressions
setCostPlot(): This method is used to setup the plot of the economic regression
loadProduction(production_path): This method is used to load the raw csv of the production data
setFishPoinPara(speed_range, depth_range): This method is used to setup the fishign points parameters
setWeekMonthNum(): This method is used to assign the week and month num to the raw effort data
setFishPoin(): This method is used to filter the fishing points
plotFishPoinStat(): This method is used to show the basic statistics for the fishing points
plotSpeedDepth(which_year, speed_range, depth_range): This method is used to show the speed/depth profile
setEffortIds(): This method is used to set the distinct vessel' ids in the effort dataset
setProdSpec(): This method is used to set the distinct specie in the production dataset
setBetaMeltYear(specie): This method is used to set the melted yearly productivity by specie
setProdMeltYear(specie): This method is used to set the melted yearly production by specie
plotTotProd(specie): This method is used to plot the total production by specie
plotNNLS(specie, thresR2): This method is used to show the NNLS results
setSpecSettItm(specie, thresh, brea, max_xlim): This method is used to set the logit parameters by specie
plotLogitROC(selSpecie): This method is used to show the ROC of the logit results
setSpecLogitConf(selSpecie, cutoff): This method is used to set the confusion matrix of the logit results by specie
setLogitTrain(selSpecie, train, cp_val, cv_val): This method is used to setup the train dataset for the logit model
setLogitTest(selSpecie, test): This method is used to setup the test dataset for the logit model
setLogitPred(selSpecie, test): This method is used to compute the prediction for the logit model
setLogitCut(selSpecie): This method is used to tune the cutoff of the logit model
setLogitRoc(selSpecie): This method is used to set the ROC of the logit model
setLogitConf(selSpecie, test): This method is used to set the confusion matrix of the logit results
setSpecLogit(selSpecie, selModel, cp, cv): This method is a wrapper function to get the logit model
getMatSpeLand(specie): This method is used to get the input data for the logit model
setEffoProdAll(): This method is used to combine the effort/production data from the yearly list into a single data.frame
setEffoAll(): This method is used to combine the effort data from the yearly list into a single data.frame
setEffoProdAllLoa(): This method is used to add the LOA data to the effort/production data
setEffoAllLoa(): This method is used to add the LOA data to the effort data
setProdIds(): This method is used to get the vessel ids with production data available
setIdsEffoProd(): This method is used to get the vessel ids with both effort and production data available
plotCountIDsEffoProd(): This method is used to set the plot of the basic statistics of the effort/production data
plotCountIDsEffo(): This method is used to set the plot of the basic statistics of the effort data
plotCountIDsProd(): This method is used to set the plot of the basic statistics of the production data
setEffoProdMatr(): This method is used to merge the effort and production data
setEffoProdMont(): This method is used to aggregate the effort/production data by month
setEffoMont(): This method is used to aggregate the effort data by month
setProdMatr(): This method is used to create the production matrix from the raw production data
setDayEffoMatrGround(maxFG): This method is used to assign the fishing grounds to the raw effort data
readRegisterEU(reg_path): This method is used to load the raw european fleet register
cleanRegister(): This method is used to clean the raw data in the fleet register
plotRegSum(): This method is used to plot the basic statistics for the fleet register data
setRegIds(): This method is used to get the distinct vessels ids in the fleet register