SampleMap: SampleMap

Description

The SampleMap class implements the class of SMART to control geographical data.

Arguments

Value

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

Format

R6Class object.

Fields

gridPath: Stores the file path to the selected Environment grid shapefile.

gridName

Stores the file name of the Environment grid shapefile.

gridShp

Stores the SpatialPoligon object of the Environment grid shapefile.

gridBbox

Stores the bounding box coordinates of the Environment grid shapefile.

gridBboxExt

Stores the extended bounding box coordinates of the Environment grid shapefile.

gridBboxSP

Stores the bounding box of the Environment grid as a SpatialPoligon.

areaGrid

Stores the total area covered by the Environment grid.

areaStrata

Stores the area covered by depth strata.

weightStrata

Stores the area covered by depth strata relative to the total area.

harbDbf

Stores coordinates and names of the harbours.

bioPath

Stores the file path of the Substrate map.

bioName

Stores the file name of the Substrate map.

bioShp

Stores the SpatialPoligon object of the Substrate map.

bioDF

Stores the data.frame representation of the Substrate map.

gridPolySet

Stores the PolySet object of the Environment grid.

gridFortify

Stores the fortified SpatialPoligon object of the Environment grid.

nCells

Stores the number of cells in the Environment grid.

griCent

Stores the coordinates of the cells' centroids.

gridBathy

Stores the bathymetric matrix.

centDept

Stores the depth of the cells' centroids.

clusInpu

Stores the input data for the spatial clustering.

clusMat

Stores the results of the spatial clustering.

indSil

Stores the silhouette index of the spatial clustering result.

indCH

Stores the Calinski-Harabasz index of the spatial clustering result.

cutFG

Stores the number of cuts for the spatial clustering.

availData

Stores the names of the variables for the spatial clustering.

rawInpu

Stores the raw input for the spatial clustering.

cutResult

Stores the summary data of the spatial clustering result.

cutResEffo

Stores the average effort data from the spatial clustering result.

cutResShp

Stores the SpatialPoligon object of the spatial clustering result.

cutResShpCent

Stores the coordinates of the clusters' centroids.

cutResShpFort

Stores the fortified SpatialPoligon object of the spatial clustering result.

fgWeigDist

Stores the weighted distance between harbours and fishing grounds.

ggBioDF

Stores the plot of the Substrate map.

ggDepth

Stores the plot of the Bathymetric map.

ggDepthFGbox

Stores the boxplot of the depth values of each fishing ground.

ggEffoFGbox

Stores the boxplot of the effort values of each fishing ground.

ggEffoFGmap

Stores the plot of the Effort map.

ggBioFGmat

Stores the tilemap of the substrate values of each fishing ground.

ggCutFGmap

Stores the plot of the Fishing ground configuration.

ggIchFGlin

Stores the plot of the Calinski-Harabasz index.

ggSilFGlin

Stores the plot of the silhouette index.

ggBetaFGmap

Stores the plot of the Productivity map.

ggBetaFGbox

Stores the boxplot of the Productivity values of each fishing ground.

ggProdFGmap

Stores the plot of the Production map.

ggProdFGbox

Stores the boxplot of the Production values of each fishing ground.

ggMapFgFishery

Stores the plot of the Fishery data coordinates.

ggMapFgSurvey

Stores the plot of the Survey data coordinates.

gooMap

Stores the satellite view of the area of study.

gooMapPlot

Stores the satellite plot of the area of study.

gooGrid

Stores the plot of the Environment Grid.

gooBbox

Stores the plot of the Bounding Box of the Environment Grid.

sampColScale

Stores the color scale for the species plots.

plotRange

Stores the plot ranges for the Environmental Grid.

Methods

setAreaGrid(): This method is used to compute the total area covered by the environmental grid.
setAreaStrata(vectorStrata): This method is used to compute the area covered by each depth strata.
setWeightStrata(): This method is used to compute the area covered by each depth strata relative to the total area of the grid.
loadHarbDbf(dbf_path): This method is used to load a dbf file of coordinates and harbours names.
set_ggMapFgSurvey(rawSampCoo): This method is used to setup the plot of the spatial distribution of survey data.
set_ggMapFgFishery(rawSampCoo): This method is used to setup the plot of the spatial distribution of fishery data.
createGridBbox(): This method is used to setup the bounding box of the environment grid.
getGooMap(): This method is used to retrieve the satellite view of the area of study.
setGooPlot(): This method is used to setup the base plot of the area of study.
setPlotRange(): This method is used to setup the ranges of the base plot.
setGooGrid(): This method is used to setup the plot of the environment grid.
plotGooGrid(): This method is used to plot the environment grid.
plotGooGridData(grid_data): This method is used to plot the environment grid.
setSampColScale(fac_col): This method is used to setup the color scale for the species' plots.
plotGooSpeSur(poi_data): This method is used to plot the spatial distribution of the survey data
plotGooSpeFis(poi_data): This method is used to plot the spatial distribution of the fishery data
setGooBbox(): This method is used to setup the bounding box of the environment grid.
plotGooBbox(): This method is used to plot the bounding box of the environment grid.
setGridPath(path2grid): This method is used to store the path to the grid file.
setGridName(): This method is used to store the name of the grid file.
loadGridShp(): This method is used to load the grid file.
setBioPath(): This method is used to store the path of the seabed substrates file.
setBioName(): This method is used to store the name of the seabed substrates file.
loadBioShp(): This method is used to load the seabed substrates file.
addBioShp(bio_path): This method is used store the path and name of the seabed file and then load the SpatialPoligon object.
loadBioDF(bio_path): This method is used to load a Data.Frame of seabed substrates.
plotBioDF(): This method is used to plot the map of substrates.
setGgBioDF(): This method is used to setup the plot of substrates.
ggplotBioDF(): This method is used to plot the map of substrates.
createPolySet(): This method is used to store the PolySet object of the Environment grid.
fortifyGridShp(): This method is used to fortify the SpatialPolygon od the Environment grid.
setNumCell(): This method is used to setup the number of cells in the grid.
setGridCenter(): This method is used to store the coordinates of cells centroids.
getGridBath(): This method is used to retrieve the bathymetric matrix.
saveGridBath(bathy_path): This method is used to save the bathymetric matrix to file.
loadGridBath(bathy_path): This method is used to load the bathymetric matrix from file.
getCentDept(): This method is used to assign the depth to each cell centroids.
setGgDepth(isoLine): This method is used to setup the bathymetric plot.
ggplotGridBathy(): This method is used to plot the bathymetric map.
plotSamMap(title, celCol): This method is used to plot the Environment map.
plotCoho(abbs): This method is used to plot the spatial distribution of the species.
setClusInpu(whiData, howData): This method is used to setup the input for the spatial clustering
calcFishGrou(numCuts, minsize, maxsize, modeska, skater_method, nei_queen): This method is used to run the spatial clustering routine
plotFishGrou(ind_clu): This method is used to plot the fishing ground configuration
setCutResult(ind_clu): This method is used to choose a fishing ground configuration
setDepthFGbox(): This method is used to setup the boxplot of depth by fishing ground
setEffoFGbox(): This method is used to setup the boxplot of effort by fishing ground
setEffoFGmap(): This method is used to setup the map of effort by fishing ground
setBioFGmat(): This method is used to setup the tileplot of substrate by fishing ground
setCutFGmap(): This method is used to plot the fishing ground map
setIchFGlin(numCut): This method is used to setup the plot of the Calinski-Harabasz index
setSilFGlin(numCut): This method is used to setup the plot of the Silhouette index