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Feature request: New logslope & c1 impute_start methods #350 #351

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Feature request: New logslope & c1 impute_start methods #350 #351

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Gero1999
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@Gero1999 Gero1999 commented Jan 3, 2025 •
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New PKNCA_method_start functions that could perhaps be default/standard. Feel free to give them a look and merge them if they are useful!

Closes #350

# Imputes a start concentration based on the logslope method for IV bolus
PKNCA_impute_method_start_logslope <- function(conc, time, start, end, ..., options = list()) { # nolint

  ret <- data.frame(conc = conc, time = time)
  mask_start <- time %in% start
  if (!any(mask_start)) {
    all_concs <- conc[time >= start  &  time <= end]
    all_times <- time[time >= start  &  time <= end]
    if (!all(is.na(all_concs))) {
      c0 <- PKNCA::pk.calc.c0(all_concs, all_times, method = "logslope")
      if (!is.na(c0)) {
        ret <- rbind(ret, data.frame(time = start, conc = c0))
        ret <- ret[order(ret$time), ]
      }
    }
  }
  ret
}

# Imputes a start concentration using the first available concentration measure
PKNCA_impute_method_start_c1 <- function(conc, time, start, end, ..., options = list()) { # nolint
  ret <- data.frame(conc = conc, time = time)
  mask_start <- time %in% start
  if (!any(mask_start)) {
    all_concs <- conc[time >= start  &  time <= end]
    all_times <- time[time >= start  &  time <= end]
    if (!all(is.na(all_concs))) {
      c1 <- all_concs[which.min(all_times)]
      ret <- rbind(ret, data.frame(time = start, conc = c1))
      ret <- ret[order(ret$time), ]
    }
  }
  ret
}

@Gero1999 Gero1999 mentioned this pull request Jan 3, 2025
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@Gero1999 Gero1999 marked this pull request as ready for review January 3, 2025 17:03
billdenney
billdenney requested changes Jan 4, 2025
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R/impute.R
all_concs <- conc[time >= start & time <= end]
all_times <- time[time >= start & time <= end]
if (!all(is.na(all_concs))) {
c0 <- PKNCA::pk.calc.c0(all_concs, all_times, method = "logslope")
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Since this is within PKNCA, please switch to the pk.calc.c0.method.logslope function directly rather than using pk.calc.c0.

R/impute.R
@@ -120,6 +120,46 @@ PKNCA_impute_method_start_predose <- function(conc, time, start, end, conc.group
ret
}

#' @describeIn PKNCA_impute_method Imputes based on a logarithmic slope on the
#' first points a time zero concentration (usually in IV bolus at dose time)
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Please add an additional part to the description: "If this imputation is used for NCA calculations, back-extrapolation percent will not be calculated or will be calculated as zero."

R/impute.R
}

#' @describeIn PKNCA_impute_method Shift the following concentration to a start
#' to become the time zero concentration (rarely used; non-monodecay IV bolus)
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Please add an additional part to the description: "If this imputation is used for NCA calculations, back-extrapolation percent will not be calculated or will be calculated as zero."

R/impute.R
all_concs <- conc[time >= start & time <= end]
all_times <- time[time >= start & time <= end]
if (!all(is.na(all_concs))) {
c0 <- PKNCA::pk.calc.c0(all_concs, all_times, method = "logslope")
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Please set time.dose = start in case the intended start time is not 0. Please add a test for this case as well.

R/impute.R
ret <- data.frame(conc = conc, time = time)
mask_start <- time %in% start
if (!any(mask_start)) {
all_concs <- conc[time >= start & time <= end]
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Please use pk.calc.c0.method.c1. That way, you don't need to filter all_concs, all_times, and your is.na() test below can be on c1. That will also ensure that c1 is consistently calculated anywhere it is used within PKNCA.

tests/testthat/test-impute.R
data.frame(conc = c(3, 3, 1), time = 1:3),
ignore_attr = TRUE
)
})
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Please add tests for:

  1. All concentrations are NA
  2. All times are NA
  3. All concentrations are 0

(I see that list of tests is needed for the other imputation methods, too. I just added an issue, #361, to add those after this PR is merged.)

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@billdenney billdenney billdenney requested changes

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Feature request: New logslope & c1 impute_start methods
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@Gero1999 @billdenney