Data — Data-class • crmPack

Data is a class for the data input. It inherits from GeneralData.

Usage

Data(
  x = numeric(),
  y = integer(),
  ID = integer(),
  cohort = integer(),
  doseGrid = numeric(),
  placebo = FALSE,
  backfilled = rep(FALSE, length(x)),
  response = rep(NA_integer_, length(x)),
  ...
)

.DefaultData()

Arguments

x: (numeric)
the doses for the patients.
y: (integer)
the vector of toxicity events (0 or 1). You can also supply numeric vectors, but these will then be converted to integer internally.
ID: (integer)
unique patient IDs. You can also supply numeric vectors, but these will then be converted to integer internally.
cohort: (integer)
the cohort (non-negative sorted) indices. You can also supply numeric vectors, but these will then be converted to integer internally.
doseGrid: (numeric)
all possible doses.
placebo: (flag)
if TRUE the first dose level in the doseGrid is considered as placebo.
backfilled: (logical)
whether each patient was in a backfill cohort.
response: (integer)
whether each patient had a positive efficacy response (1 = yes, 0 = no). May contain NA.
...: not used.

Details

The cohort can be missing if and only if placebo is equal to FALSE.

Slots

x: (numeric)
the doses for the patients.
y: (integer)
the vector of toxicity events (0 or 1 integers).
doseGrid: (numeric)
the vector of all possible doses (sorted), i.e. the dose grid.
nGrid: (integer)
number of gridpoints.
xLevel: (integer)
the levels for the doses the patients have been given, w.r.t doseGrid.
placebo: (logical)
if TRUE the first dose level in the doseGridis considered as PLACEBO.
backfilled: (logical)
whether this patient was in a backfill cohort.
response: (integer)
whether this patient had a positive efficacy response (0 or 1 integers).

Note

ID and cohort can be missing. Then a message will be issued and the variables will be filled with default IDs and best guesses cohort, i.e. a sorted (in ascending order) sequence of values from {1, 2, ...}.

Typically, end users will not use the .DefaultData() function.

Examples

my_data <- Data(
  x = c(0.1, 0.5, 1.5, 3, 6, 10, 10, 10),
  y = c(0, 0, 0, 0, 0, 0, 1, 0),
  ID = as.integer(1:8),
  cohort = as.integer(c(1, 2, 3, 4, 5, 6, 6, 6)),
  doseGrid = c(
    0.1,
    0.5,
    1.5,
    3,
    6,
    seq(from = 10, to = 80, by = 2)
  )
)
my_data
#> An object of class "Data"
#> Slot "x":
#> [1]  0.1  0.5  1.5  3.0  6.0 10.0 10.0 10.0
#> 
#> Slot "y":
#> [1] 0 0 0 0 0 0 1 0
#> 
#> Slot "doseGrid":
#>  [1]  0.1  0.5  1.5  3.0  6.0 10.0 12.0 14.0 16.0 18.0 20.0 22.0 24.0 26.0 28.0
#> [16] 30.0 32.0 34.0 36.0 38.0 40.0 42.0 44.0 46.0 48.0 50.0 52.0 54.0 56.0 58.0
#> [31] 60.0 62.0 64.0 66.0 68.0 70.0 72.0 74.0 76.0 78.0 80.0
#> 
#> Slot "nGrid":
#> [1] 41
#> 
#> Slot "xLevel":
#> [1] 1 2 3 4 5 6 6 6
#> 
#> Slot "placebo":
#> [1] FALSE
#> 
#> Slot "backfilled":
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 
#> Slot "response":
#> [1] NA NA NA NA NA NA NA NA
#> 
#> Slot "ID":
#> [1] 1 2 3 4 5 6 7 8
#> 
#> Slot "cohort":
#> [1] 1 2 3 4 5 6 6 6
#> 
#> Slot "nObs":
#> [1] 8
#>