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Text from the ECOTOX database to mixed_units

Source: R/process_unit.r
as_unit_ecotox.Rd

[Experimental] Convert text to units after sanitising.

Usage

as_unit_ecotox(
  x,
  type = c("concentration", "duration", "length", "media", "application", "size",
    "weight", "unknown"),
  ...,
  warn = TRUE
)

Arguments

x

A vector of character strings. It expects fields as commonly returned from the ECOTOX database.

type

The type of unit that can help the sanitation process. See the 'usage' section for available options. These options are linked to the different unit tables in the database (see vignette("ecotox-schema")). It can help to interpret ambiguous units correctly. For instance, 'dpm' can both mean 'disintegrations per minute' (type = "concentration") and 'days post-moult' (type = "duration").

...

Ignored.

warn

If set to FALSE warnings while converting text to units are suppressed.

Value

A vector of ?units::unit class objects with the same length as x.

Details

The following steps are performed (in the order as listed) to sanitise text before coercing it to units:

  • The following is removed:

    • Leading/trailing white spaces

    • Square brackets and commas

    • A list of common prefixes

    • Double spaces are replaced by single spaces

    • Brackets around multiply symbol

  • The following is corrected/adjusted:

    • 'for' is interpreted as multiplication

    • Scientific notation of numbers is standardised where possible.

    • A list of ambiguous patterns is replaced with more explicit strings. For instance, 'deg' is replaced with 'degree'.

  • The following miscellaneous corrections are made:

    • A list of 'known' annotations are removed from the units

    • A list of elements kown to represent counts are renamed 'counts'.

    • Percentages are renamed as explicit concentration in mass per volume or volume per volume units where possible

    • 'CI' is renamed 'Curies'.

    • 'M' is renamed 'mol/L'.

    • Units expressed as 'parts per ...' are explicitly renamed to mass over volume, or volum over volume where possible

  • Type specific sanitation steps

    • Concentration units:

      • 'K' is renamed 'Karmen'

      • 'dpm' is renamed 'counts/min' (i.e., disintegrations per minute)

    • Media units:

      • 'K' is renamed 'Kelvin'

      • 'C' is renamed 'Celsius'

  • Some final miscellaneous adjustments:

    • Scientific notation in numbers is not supported by the units package. Numbers are formatted in decimal notation where possible.

    • Spaces are removed if preceded by numeric and followed by alphabetical character

    • All equivalents of ambiguous synonyms for time units are explicitly renamed to their respective unit (e.g., 'dph' (days post hatching) -> 'day')

    • unreported/missing units are renamed 'unit'

It is your own responsibility to check if the sanitising steps are appropriate for your analyses.

See also

Other ecotox-sanitisers: as_date_ecotox(), as_numeric_ecotox(), mixed_to_single_unit(), process_ecotox_dates(), process_ecotox_numerics(), process_ecotox_units()

Author

Pepijn de Vries

Examples

## Try parsing a random set of units from the database:
c("ppm-d", "ml/2.5 cm eu", "fl oz/10 gal/1k sqft", "kg/100 L",
  "mopm", "ng/kg", "ug", "AI ng/g", "PH", "pm", "uM/cm3", "1e-4 mM",
  "degree", "fs", "mg/TI", "RR", "ug/g org/d", "1e+4 IU/TI", "pg/mg TE",
  "pmol/mg", "1e-9/l", "no >15 cm", "umol/mg pro", "cc/org/wk", "PIg/L",
  "ug/100 ul/org", "ae mg/kg diet/d", "umol/mg/h", "cmol/kg d soil",
  "ug/L diet", "kg/100 kg sd", "1e+6 cells", "ul diet", "S", "mmol/h/g TI",
  "g/70 d", "vg", "ng/200 mg diet", "uS/cm2", "AI ml/ha", "AI pt/acre",
  "mg P/h/g TI", "no/m", "kg/ton sd", "ug/g wet wt", "AI mg/2 L diet",
  "nmol/TI", "umol/g wet wt", "PSU", "Wijs number") |>
  as_unit_ecotox(warn = FALSE)
#> Mixed units: d*ppm (1), ml/2.5cm (1), oz/1000ft2/10gal (1), kg/100L (1), month (1), ng/kg (1), ug (1), ng/g (1), unit (13), umol/L/cm3 (1), 0.0001mmol/L (1), ° (1), ug/d/g (1), pg/mg (1), pmol/mg (1), umol/mg (1), counts/counts/week (1), ug/100ul/counts (1), mg/d/kg (1), umol/h/mg (1), cmol/kg (1), ug/L (1), kg/100kg (1), 1000000counts (1), ul (1), S (1), mmol/g/h (1), g/70d (1), ng/200mg (1), uS/cm2 (1), ml/ha (1), pt/acre (1), mg/g/h (1), counts/m (1), kg/ton (1), ug/g (1), mg/2L (1), umol/g (1) 
#> 1 [d*ppm], 1 [ml/2.5cm], 1 [oz/1000ft2/10gal], 1 [kg/100L], 1 [month], 1 [ng/kg], 1 [ug], 1 [ng/g], 1 [unit], 1 [unit], 1 [umol/L/cm3], 1 [0.0001mmol/L], 1 [°], 1 [unit], 1 [unit], 1 [unit], 1 [ug/d/g], 1 [unit], 1 [pg/mg], 1 [pmol/mg], 1 [unit], 1 [unit], 1 [umol/mg], 1 [counts/counts/week], 1 [unit], 1 [ug/100ul/counts], 1 [mg/d/kg], 1 [umol/h/mg], 1 [cmol/kg], 1 [ug/L], 1 [kg/100kg], 1 [1000000counts], 1 [ul], 1 [S], 1 [mmol/g/h], 1 [g/70d], 1 [unit], 1 [ng/200mg], 1 [uS/cm2], 1 [ml/ha], 1 [pt/acre], 1 [mg/g/h], 1 [counts/m], 1 [kg/ton], 1 [ug/g], 1 [mg/2L], 1 [unit], 1 [umol/g], 1 [unit], 1 [unit] 

## Adding the type of measurement can affect interpretation:
as_unit_ecotox(c("C", "K"), type = "concentration")
#> Mixed units: C (1), unit (1) 
#> 1 [C], 1 [unit] 
as_unit_ecotox(c("C", "K"), type = "media")
#> Mixed units: °C (1), K (1) 
#> 1 [°C], 1 [K]