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Find required fields in a SHARK delivery template

Source: R/read_delivery_template.R
find_required_fields.Rd

Identifies which columns are mandatory in the SHARK delivery template based on rows starting with "*" (one or more). You can specify how many levels of asterisks to include.

Usage

find_required_fields(
  datatype,
  stars = 1,
  bacterioplankton_subtype = "abundance"
)

Arguments

datatype

Character. The datatype name. Available options include:

  • "Bacterioplankton" (subtypes: "abundance", "production")

  • "Chlorophyll"

  • "Epibenthos" (dive transect)

  • "Dropvideo" (epibenthos drop video)

  • "Grey seal"

  • "Harbour seal"

  • "Ringed seal"

  • "Harbour Porpoise"

  • "Physical and Chemical"

  • "Primary production"

  • "Phytoplankton"

  • "Picoplankton"

  • "Sedimentation"

  • "Seal pathology"

  • "Profile"

  • "Zooplankton"

  • "Zoobenthos"

stars

Integer. Maximum number of "" levels to include. Default = 1 (only single ""). For example, stars = 2 includes "" and "**", stars = 3 includes "", "", and "*".

bacterioplankton_subtype

Character. For "Bacterioplankton" only: either "abundance" (default) or "production". Ignored for other datatypes.

Value

A character vector of column names that are required in the template.

Details

Note: A single "*" marks required fields in the standard SHARK template. A double "**" is often used to specify columns required for national monitoring only. For more information, see: https://www.smhi.se/data/hav-och-havsmiljo/datavardskap-oceanografi-och-marinbiologi/leverera-data

Examples

# \donttest{
# Only single "*" required columns
find_required_fields("Bacterioplankton")
#>  [1] "MYEAR"    "STATN"    "PROJ"     "ORDERER"  "SHIPC"    "SDATE"   
#>  [7] "LATIT"    "LONGI"    "POSYS"    "WADEP"    "SMPDEP"   "SLABO"   
#> [13] "ACKR_SMP" "SMTYP"    "SMVOL"    "SPVOL"    "COEFF"    "SUBNO"   
#> [19] "METFP"    "BCTCNT"   "BCTABU"   "BABUFLG"  "BACTBIOM" "ALABO"   
#> [25] "ACKR_ANA" "ANADATE"  "METDC"   

# Include both "*" and "**" required columns (national monitoring too)
find_required_fields("Bacterioplankton", stars = 2)
#>  [1] "MYEAR"    "STATN"    "PROJ"     "ORDERER"  "SHIPC"    "SDATE"   
#>  [7] "LATIT"    "LONGI"    "POSYS"    "WADEP"    "MPROG"    "SMPDEP"  
#> [13] "SLABO"    "ACKR_SMP" "SMTYP"    "SMVOL"    "SPVOL"    "COEFF"   
#> [19] "SUBNO"    "METFP"    "BCTCNT"   "BCTABU"   "BABUFLG"  "BACTBIOM"
#> [25] "ALABO"    "ACKR_ANA" "ANADATE"  "METDC"   

# Include up to three levels of "*"
find_required_fields("Phytoplankton", stars = 3)
#>  [1] "MYEAR"    "STATN"    "PROJ"     "ORDERER"  "SHIPC"    "SDATE"   
#>  [7] "LATIT"    "LONGI"    "POSYS"    "WADEP"    "MSTAT"    "MNDEP"   
#> [13] "MXDEP"    "SLABO"    "ACKR_SMP" "SMTYP"    "SMVOL"    "LATNM"   
#> [19] "SFLAG"    "TRPHY"    "COUNT"    "COEFF"    "SIZCL"    "SIZRF"   
#> [25] "SDVOL"    "QFLAG"    "TAXNM"    "METOA"    "ALABO"    "ACKR_ANA"
#> [31] "ANADATE"  "METDC"   
# }