appendMetier: Annotate metier

In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

Annotate metier

Description

annotates metier to data table

Usage

appendMetier(
  data,
  metiertable,
  gearColumn,
  targetColumn = NULL,
  meshSizeColumn = NULL,
  selectivityDeviceColumn = NULL,
  selectivityDeviceMeshSizeColumn = NULL,
  metierColName = "metier"
)

Arguments

data	data.table with data to be annotated
metiertable	MetierTable with metier definitions, or object that can be read with readMetierTable
gearColumn	character() identifies the column in 'data' that encodes gear. Gear definition must match metiertable$gearcode
targetColumn	character(), optional, identifies the column in 'data' that encodes target species. Definition must match metiertable$target
meshSizeColumn	integer(), optional, identifies the column in 'data' that encodes the mesh size of the gear.
selectivityDeviceColumn	character(), optional, identifies the column in 'data' that encodes selectivitydevices mounted on gear. Definition must mathc metiertable$selectivityDevice
selectivityDeviceMeshSizeColumn	integer(), optional, identifies the column in 'data' that encodes the mesh size of any mounted selectivity device.
metierColName	character() name of the column that should be appended to 'data'

Details

Annotates data with metier, given a metier definition (MetierTable) and a selection of data-columns that idenitfies metier-defining variables. Metier names are defined by the column 'metier' in 'metiertable', and does not have to reflect the information actually used for annotation. For example, metiers of the type "OTB_DEF", indicating both gear and target assemblage, can be configured based only on gear codes.

For the metier-defining variables 'gearcode', 'target' and 'selectivityDevice' (see MetierTable), missing values are matches with missing values. That is, a metier that is defined with a missing value for 'target' will be annotated to otherwise matching data which has a missing value in the 'targetColumn'.

Value

data.table 'data' with the column 'metierColName' appended (character).

Examples

 data(metier4table)
 data(activityCensus)

 # annotate metier lvl 4 on the cencus based on gear, and compare with finer gear declaration.
 annotated <- appendMetier(activityCensus,
          metier4table,
          "gearNS",
          metierColName = "metier4")
 table(annotated$metier4)

 data(metier5table)
 # annotate metier lvl 5 on COD-catches based on only gear,
 # and compare with declarations for shrimp fisheries
 annotated <- appendMetier(activityCensus[activityCensus$species=="COD"],
          metier5table,
          "gearNS",
          metierColName = "metier5")
 annotatedShrimp <- annotated[annotated$targetFAO %in% c("PAN", "PRA"),]
 table(paste(annotatedShrimp$gearFAO, annotatedShrimp$targetFAO, sep="/"),
      annotatedShrimp$metier5)

 data(metier6table)
 # annotate metier lvl 6 on COD-catches based on gear and mesh size,
 # and compare with lvl 5 annotations from last example
 annotated <- appendMetier(activityCensus[activityCensus$species=="COD"],
          metier6table,
          "gearNS",
          meshSizeColumn = "meshSize",
          metierColName = "metier6")
 annotated <- appendMetier(annotated,
           metier5table,
           "gearNS",
           metierColName = "metier5")
 annotatedShrimp <- annotated[annotated$targetFAO %in% c("PAN", "PRA"),]
 table(annotatedShrimp$metier5, annotatedShrimp$metier6)
 

StoXProject/RstoxFDA documentation built on Jan. 13, 2024, 12:32 a.m.