calc_titer_lims: Get titer limits

In shwilks/meantiter: Calculate GMTs using different approaches for handling nd titers

Description

Function for getting upper and lower limits of measured titers on the log scale.

Usage

calc_titer_lims(titers, dilution_stepsize, options = list())

Arguments

titers	A numeric/character vector or matrix of titer measurements.
dilution_stepsize	The dilution stepsize, see details
options	A named list of options to pass to 'titer_fit_options()'

Details

HI titers which typically follow a 2-fold dilution series starting from 1/10, then 1/20, 1/40 etc. This represents a "dilution stepsize" of 1 when converted to the log2 scale. When no inhibition was recorded at the highest dilution, the value is typically recorded as <10 but the optimization regime effectively treats this as a <=5, the rationale being that, had the dilution series been continued to higher concentrations, the next lowest titer would have been a 5. Over time the method has also been applied to other neutralization assays that sometimes have a continuous read out with a lower end, in these cases a <10 really means a <10 since any other values like 9.8 or 7.62 would also be possible. To indicate these continuous cases, you can specify the dilution stepsize as 0. Equally, if the dilution regime followed a different pattern, you can also set that here.

Value

Returns a list of length three with values log_titers, max_titers and min_titers, giving the numeric vectors of the straight log converted, upper and lower bounds of the titers on the log scale.

Examples

# Calculate the titer limits of a set of HI titers
titer_lims <- calc_titer_lims(
  titers = c("20", "320", "<10", ">1280"),
  dilution_stepsize = 1
)

# Calculate the titer limits assuming non-default upper and lower bounds for non-detectable
# and greater-than titers.
titer_lims <- calc_titer_lims(
  titers = c("20", "320", "<10", ">1280"),
  dilution_stepsize = 1,
  options = list(
    min_titer_possible = -Inf,
    max_titer_possible = 14
  )
)

shwilks/meantiter documentation built on Dec. 23, 2021, 1:28 a.m.