In qPharmetra/PMDatR: Pharmacometric Data Management in R

README

library(pmunits)
suppressWarnings(library(tidyverse, quietly = T))

Units API

setting units

units are an attribute labeled pmunits (to not clash with udunits or other units labels).

Units are set via set_units

set_units(10, "mg/L")
set_units(1:10, "mg/L")

and can be used to set units to columns in dplyr.

head(Theoph %>% mutate(conc = set_units(conc, "mg/L")))

set_units expects udunits2 parseable units, so will error

set_units(10, "mg/imnotaunit")

#> Error in set_units(10, "mg/imnotaunit") : units not parseable

A list of column-name/units can be provided to set units across a dataframe.

theoph_units <- set_units_from_list(Theoph, list(Wt = "kg", Dose = "mg/kg", Time = "hours", conc = "mg/L"))
lapply(theoph_units, attributes)

arithmetic

the common arithmetic +-*/ functions have been provided, so that unitful columns will be managed.

When adding/subtracting, the resulting units will be those of the left-hand-side of the operator

x mg/L + y ug/L --> z mg/L

set_units(10, "mg/L") + set_units(100, "ug/L")

To add or subtract, the units must be convertible

set_units(10, "mg/L") + set_units(1, "km/hour")

#> Error in `+.pmunits`(set_units(10, "mg/L"), set_units(1, "km/hour")) : units incompatible

However, for multiplication/division, the unit combination is more lazy, passing along until the user requests a conversion

nonsense_unit <- set_units(10, "mg")/set_units(1, "km")
nonsense_unit

When a divisor is present, pmunits will automatically add parenthesis around the original unit sets to distinguish

set_units(10, "mg/kg")*set_units(100, "kg")

This is especially important when dealing with more complex units, for example, with molar conversions the unit set mg/L/g/mol will not parse but (mg/L)/(g/mol) will properly parse and can be converted

Units may also be multiplied against 'constants' however there is no magic here, if the multiplication is actually not a constant or one that would affect the units in any way, the user must reset the units to be safe.

set_units(10, "mg/kg")*10

set_units(10, "mg/kg")/10

conversion via convert

pmunit vectors may ultimately be converted to the final expected result via convert, which takes the form:

convert(<units_col>, "<units/to/convert>")

convert(set_units(10, "mg/L"), "ug/L")

is_mg <- set_units(10, "mg/kg")*set_units(100, "kg")
is_mg

convert can also be used to confirm a combination of units can be properly reduced

convert(is_mg, "mg")

Additional conversions

Specific complex conversion have been pre-baked into the library, namely

• molar conversion - conc_to_molar

conc_to_molar(set_units(10, "mg/L"), set_units(50, "g/mol"))

conc_to_molar(set_units(10, "mg/L"), set_units(50, "g/mol"), "umol/L")

NOT considered

• what about statistical transformation - log(DV)

qPharmetra/PMDatR documentation built on April 7, 2024, 5:42 p.m.