The config's species catalog names the taxa a run was set up for. A formatted export carries every taxon the survey counted, which is most of a hundred, and any of them can be modelled. This reads the candidates off the file.
Usage
available_species(
zoop_file,
stage_pattern = stage_suffix_pattern(),
exclude = measurement_columns()
)Arguments
- zoop_file
path to a formatted database, or its column names
- stage_pattern
regular expression matching a life stage
- exclude
columns to leave out. The default drops the in-situ measurements the ECOMON export carries, which are numeric columns that are not taxa; pass
character()to see them.
Value
a data frame of species (the column header name), shorthand,
form ("total" or "stages"), and stages, one row per candidate
Details
A taxon with stage columns is reported once, as a prefix, since that is how a config selects it and how its stages are summed. Everything else is reported as a total.
What it cannot tell you
A formatted database has had the units cut off its taxon columns, so nothing
in the name distinguishes a taxon from the in-situ measurements the export
also carries. STATION_DEPTH and BTM_TEMP are candidates here in exactly
the way CALANUS_FINMARCHICUS is. The list is what could be an abundance
column, not what is one. Run zoop_taxa() against the raw export for the
answer the raw column names still hold.
Examples
available_species(c("station", "year", "month", "day", "lon", "lat",
"CALANUS_FINMARCHICUS", "PSEUDOCALANUS_SPP_CIV",
"PSEUDOCALANUS_SPP_CV"))
#> species shorthand form stages
#> 1 CALANUS_FINMARCHICUS cfin total
#> 2 PSEUDOCALANUS_SPP pcal stages CIV, CV