Writes the species.catalog block a config needs, one entry per taxon.
Suitable for passing to generate_config() as species.
Usage
species_catalog_from(
header,
suffix = "_10M2",
stage_pattern = stage_suffix_pattern(),
threshold = list(type = "percentile", value = 0.9),
aliases = NULL
)Arguments
- header
column names, a raw export, or a path to one
- suffix
the units suffix marking taxon columns
- stage_pattern
regular expression matching a life stage
- threshold
the threshold every entry gets
- aliases
optional named character vector giving short config keys to taxa, e.g.
c(cfin = "CALANUS_FINMARCHICUS")
Details
Which form an entry takes depends on the file. A taxon whose stages the
dataset resolves gets column_prefix, so a run can select stages or leave
them out to sum every one. A taxon reported only as a total gets
abundance_column, because there is no prefix for anything to match.
A taxon carrying both a total and some stages gets the prefix form, and the
bare total column is then not read: column_prefix matches only
<taxon>_<something>, which is what keeps the total from being summed
alongside the stages that compose it. Worth knowing that summing the resolved
stages need not reproduce the reported total, since a dataset may resolve only
some of them. Use abundance_column explicitly if the total is what you
want.
Examples
header <- c("CALANUS_FINMARCHICUS_CV_10M2", "CALANUS_FINMARCHICUS_CVI_10M2",
"CENTROPAGES_TYPICUS_10M2")
# cfin resolves stages here, so it gets a prefix; ctyp is a total.
species_catalog_from(header, aliases = c(cfin = "CALANUS_FINMARCHICUS"))
#> $cfin
#> $cfin$column_prefix
#> [1] "CALANUS_FINMARCHICUS"
#>
#> $cfin$threshold
#> $cfin$threshold$type
#> [1] "percentile"
#>
#> $cfin$threshold$value
#> [1] 0.9
#>
#>
#>
#> $ctyp
#> $ctyp$abundance_column
#> [1] "CENTROPAGES_TYPICUS"
#>
#> $ctyp$threshold
#> $ctyp$threshold$type
#> [1] "percentile"
#>
#> $ctyp$threshold$value
#> [1] 0.9
#>
#>
#>