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Annotate metier

Source: R/metierAnnotation.R
appendMetier.Rd

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'

Value

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

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'.

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)
#> 
#>  FPO   GN  GNS  HAR  LHM   LL  LLD  LTL  MIS  OTB  OTM  OTT   PS  PTB  PTM  SSC 
#>   12 1690  252    4    6  812   10    2   27 2069  282  144  855  324  239 2023 
#>   SX  TBN  TBS   TX 
#>    6   50  922 1508 

 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)
#>          
#>           MIS_MIS OTB_CRU OTB_DEF PTB_DEF
#>   OTB/PRA       0       0      21       0
#>   PTB/PRA       0       0       0       1
#>   TB/PRA        1       0       0       0
#>   TBN/PAN       0       1       0       0
#>   TBS/PAN       0       2       0       0
#>   TBS/PRA       0      22       0       0
#>   TM/PRA        1       0       0       0
#>   TMS/PRA       0       1       0       0

 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)
#>          
#>           OTB_CRU_16-31_0_0_all OTB_CRU_32-69_0_0_all OTB_DEF_>=120_0_0_all
#>   MIS_MIS                     0                     2                     0
#>   OTB_CRU                     2                    22                     1
#>   OTB_DEF                     0                    16                     5
#>   PTB_DEF                     0                     1                     0
#>          
#>           OTB_SPF_32-69_0_0_all
#>   MIS_MIS                     0
#>   OTB_CRU                     1
#>   OTB_DEF                     0
#>   PTB_DEF                     0