Feature request: New logslope & c1 impute_start methods #350

[Gero1999]

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
}

[billdenney]

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.

[Gero1999]

I added an assert before all_concs <- because if any time=NA all_concs will contain NA, let me know what you think of it!

[billdenney]

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.)

[Gero1999]

Hey sorry for the delay on this @billdenney! Some questions regarding the cases and their expected outputs:

1. All concentrations are NA

Initially I developed the functions using the same strucuture as PKNCA_impute_method_start_cmin:

PKNCA_impute_method_start_cmin <- function(conc, time, start, end, ..., options = list()) {
  ret <- data.frame(conc = conc, time = time)
  mask_start <- time %in% start
  if (!any(mask_start)) {
    all_concs <- conc[start <= time & time <= end]
    if (!all(is.na(all_concs))) {
      cmin <- min(all_concs, na.rm = TRUE)
      ret <- rbind(ret, data.frame(time = start, conc = cmin))
      ret <- ret[order(ret$time), ]
    }
  }
  ret
}

In this case, all conc = NA will return the same dataset for PKNCA_impute_method_start_cmin

But if for PKNCA_impute_method_start_c1 we want directly the original pk.calc.c0.method.c1 handling the NA case like in the original function, when all conc = NA then start = NA with a warning message

Is this the desired behavior we would like to have for PKNCA_impute_method_start_c1 even if it is different to PKNCA_impute_method_start_cmin? The same with PKNCA_impute_method_start_logslope?

2. All times are NA

Returns same dataset for PKNCA_impute_method_start_cmin
Returns error for PKNCA_impute_method_start_c1 with default pk.calc.c0.method.c1 behaviour

3. All concs are 0

Should PKNCA_impute_method_start_logslope return same dataset or NA?

[Gero1999]

I kept their original behaviours of these testing cases as on my initial pr. Let me know if you think I need to standardize them. This is probably something we need to consider on the other PKNCA_impute_method_start when doing #361

PKNCA_impute_method_start_logslope

1. All concentrations are NA:

   • The function does not change the input data. The output will have the same NA concentrations as the input.

2. All times are NA:

   • The function does not change the input data. The output will have the same NA times as the input.

3. All concentrations are 0:

   • The function does not change the input data. The output will have the same 0 concentrations as the input.

PKNCA_impute_method_start_c1

1. All concentrations are NA:

   • The function adds the start time with an NA concentration to the data. The output will have NA concentrations, including the imputed start time.

2. All times are NA:

   • The function raises an error indicating that the time vector contains missing values.

3. All concentrations are 0:

   • The function adds the start time with a 0 concentration to the data. The output will have 0 concentrations, including the imputed start time.

[Gero1999]

In order to keep working in other issues I will reframe the branch strategy in my fork. Unfortunately, I have no permissions to simply modify the development branch on this pr, so I duplicated it with the correct branch (#383) and close this one.