Taxon columns in a raw zooplankton export

The export names every taxon column for the taxon and the units it is reported in: CALANUS_FINMARCHICUS_10M2 is abundance per 10 m². Some datasets also resolve life stages, marked by a C and a Roman numeral — CALANUS_FINMARCHICUS_CV_10M2 is the fifth copepodite stage. A column without one is the total for that taxon.

Usage

zoop_taxa(header, suffix = "_10M2", stage_pattern = stage_suffix_pattern())

Arguments

header: column names, or a path to a CSV to read them from
suffix: the units suffix marking an abundance column
stage_pattern: regular expression matching a stage on the end of a taxon name. The default is a C followed by a Roman numeral one to six.

Value

a data frame with one row per taxon column: column as found, taxon, shorthand, stage (NA when the column is a total), name (the column the formatted database will carry), and the per/unit the counts are reported in

Details

Read off the header rather than kept as a list here. The export carries the better part of a hundred taxa, gains and loses them between versions, and resolves stages for some datasets and not others. A fixed list would be wrong shortly after it was written.

Examples

zoop_taxa(c("CALANUS_FINMARCHICUS_10M2", "CALANUS_FINMARCHICUS_CV_10M2"))
#>                         column                taxon shorthand stage
#> 1    CALANUS_FINMARCHICUS_10M2 CALANUS_FINMARCHICUS      cfin  <NA>
#> 2 CALANUS_FINMARCHICUS_CV_10M2 CALANUS_FINMARCHICUS      cfin    CV
#>                      name per unit
#> 1    CALANUS_FINMARCHICUS  10   M2
#> 2 CALANUS_FINMARCHICUS_CV  10   M2