Updating DataOrdinal Objects

A method that updates existing DataOrdinal object with new data.

Usage

# S4 method for class 'DataOrdinal'
update(
  object,
  x,
  y,
  ID = length(object@ID) + seq_along(y),
  new_cohort = TRUE,
  check = TRUE,
  ...
)

Arguments

object

(DataOrdinal)
object you want to update.

x

(number)
the dose level (one level only!).

y

(integer)
the vector of toxicity grades (0, 1, 2, ...) for all patients in this cohort. You can also supply numeric vectors, but these will then be converted to integer internally.

ID

(integer)
the patient IDs. You can also supply numeric vectors, but these will then be converted to integer internally.

new_cohort

(flag)
if TRUE (default) the new data are assigned to a new cohort.

check

(flag)
whether the validation of the updated object should be conducted. See Details below.

...

not used.

Value

The new, updated DataOrdinal object.

Details

The current implementation of this update method allows for updating the DataOrdinal class object by adding a single dose level x only. However, there might be some use cases where the new cohort to be added contains a placebo and active dose. Hence, such update would need to be performed iteratively by calling the update method twice. For example, in the first call a user can add a placebo, and then in the second call, an active dose. Since having a cohort with placebo only is not allowed, the update method would normally throw the error when attempting to add a placebo in the first call. To allow for such updates, the check parameter should be then set to FALSE for that first call.

Examples

data <- DataOrdinal(
  x = c(10, 20, 30, 40, 50, 50, 50, 60, 60, 60),
  y = as.integer(c(0, 0, 0, 0, 0, 1, 0, 0, 1, 2)),
  ID = 1L:10L,
  cohort = as.integer(c(1:4, 5, 5, 5, 6, 6, 6)),
  doseGrid = c(seq(from = 10, to = 100, by = 10)),
  yCategories = c("No tox" = 0L, "Sub-tox AE" = 1L, "DLT" = 2L),
  placebo = FALSE
)

update(data, x = 70, y = c(1L, 2L, 1L))
#> An object of class "DataOrdinal"
#> Slot "x":
#>  [1] 10 20 30 40 50 50 50 60 60 60 70 70 70
#> 
#> Slot "y":
#>  [1] 0 0 0 0 0 1 0 0 1 2 1 2 1
#> 
#> Slot "doseGrid":
#>  [1]  10  20  30  40  50  60  70  80  90 100
#> 
#> Slot "nGrid":
#> [1] 10
#> 
#> Slot "xLevel":
#>  [1] 1 2 3 4 5 5 5 6 6 6 7 7 7
#> 
#> Slot "yCategories":
#>     No tox Sub-tox AE        DLT 
#>          0          1          2 
#> 
#> Slot "placebo":
#> [1] FALSE
#> 
#> Slot "ID":
#>  [1]  1  2  3  4  5  6  7  8  9 10 11 12 13
#> 
#> Slot "cohort":
#>  [1] 1 2 3 4 5 5 5 6 6 6 7 7 7
#> 
#> Slot "nObs":
#> [1] 13
#>