DataCombo

DataCombo is a class for two-drug combination toxicity data. It inherits from GeneralData and stores patient-level dose combinations.

Usage

DataCombo(
  x = matrix(numeric(), ncol = 2L),
  y = integer(),
  ID = integer(),
  cohort = integer(),
  doseGrid = list(drug1 = numeric(), drug2 = numeric()),
  drugNames = names(doseGrid),
  backfilled = rep(FALSE, nrow(x)),
  response = rep(NA_integer_, nrow(x)),
  ...
)

.DefaultDataCombo()

Arguments

x

(matrix) numeric matrix with 2 columns giving the doses of the two drugs.

y

(integer) the vector of toxicity events (0 or 1).

ID

(integer) unique patient IDs.

cohort

(integer) the cohort (non-negative sorted) indices.

doseGrid

(list) named list of length 2 with all possible doses for each drug.

drugNames

(character) names of the two drugs.

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.

Slots

x

(matrix) numeric matrix with 2 columns giving the doses of the two drugs.

y

(integer) the vector of toxicity events (0 or 1 integers).

doseGrid

(list) named list of length 2 with the possible doses for each drug.

nGrid

(integer) number of grid points for each drug.

xLevel

(matrix) integer matrix with 2 columns giving the dose levels of x with respect to doseGrid.

drugNames

(character) names of the two drugs.

backfilled

(logical) whether this patient was in a backfill cohort.

response

(integer) whether this patient had a positive efficacy response (0/1/NA).

Note

ID and cohort can be missing. Then a message will be issued and the variables will be filled with default IDs and best guess cohort indices.

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

Examples

## Example for DataCombo ----

DataCombo(
  x = cbind(
    drug1 = c(10, 10, 10, 20, 20, 20),
    drug2 = c(20, 20, 20, 20, 20, 20)
  ),
  y = c(0L, 0L, 1L, 0L, 0L, 0L),
  ID = 1L:6L,
  cohort = c(1L, 1L, 1L, 2L, 2L, 2L),
  doseGrid = list(
    drug1 = c(10, 20, 30),
    drug2 = c(20, 40)
  )
)
#> An object of class "DataCombo"
#> Slot "x":
#>      drug1 drug2
#> [1,]    10    20
#> [2,]    10    20
#> [3,]    10    20
#> [4,]    20    20
#> [5,]    20    20
#> [6,]    20    20
#> 
#> Slot "y":
#> [1] 0 0 1 0 0 0
#> 
#> Slot "doseGrid":
#> $drug1
#> [1] 10 20 30
#> 
#> $drug2
#> [1] 20 40
#> 
#> 
#> Slot "nGrid":
#> [1] 3 2
#> 
#> Slot "xLevel":
#>      drug1 drug2
#> [1,]     1     1
#> [2,]     1     1
#> [3,]     1     1
#> [4,]     2     1
#> [5,]     2     1
#> [6,]     2     1
#> 
#> Slot "drugNames":
#> [1] "drug1" "drug2"
#> 
#> Slot "backfilled":
#> [1] FALSE FALSE FALSE FALSE FALSE FALSE
#> 
#> Slot "response":
#> [1] NA NA NA NA NA NA
#> 
#> Slot "ID":
#> [1] 1 2 3 4 5 6
#> 
#> Slot "cohort":
#> [1] 1 1 1 2 2 2
#> 
#> Slot "nObs":
#> [1] 6
#>