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ToxPi Model

Source: R/allClasses.R, R/methods-TxpModel.R
TxpModel-class.Rd

S4 class to store ToxPi models

Usage

TxpModel(txpSlices, txpWeights = NULL, txpTransFuncs = NULL)

# S4 method for TxpModel
txpSlices(x)

# S4 method for TxpModel
txpSlices(x) <- value

# S4 method for TxpModel
txpWeights(x, adjusted = FALSE)

# S4 method for TxpModel
txpWeights(x) <- value

# S4 method for TxpModel
txpTransFuncs(x)

# S4 method for TxpModel
txpTransFuncs(x) <- value

# S4 method for TxpModel
txpValueNames(x, simplify = FALSE)

# S4 method for TxpModel
names(x)

# S4 method for TxpModel
names(x) <- value

# S4 method for TxpModel
length(x)

# S4 method for TxpModel,TxpModel
merge(x, y)

Arguments

txpSlices

Passed to txpSlices slot

txpWeights

Passed to txpWeights slot

txpTransFuncs

Passed to txpTransFuncs slot

x, y

TxpModel object

value

Replacement value

adjusted

Scalar logical, should the returned weights be adjusted such that they sum to 1?

simplify

Scalar logical, when TRUE the returned list is simplified

Functions

  • txpSlices,TxpModel-method: Return txpSlices slot

  • txpWeights,TxpModel-method: Return txpWeights slot

  • txpTransFuncs,TxpModel-method: Return txpTransFuncs slot

  • txpValueNames,TxpModel-method: Return list of txpValueNames slots for the contained TxpSliceList object, or vector when simplify = TRUE

  • names,TxpModel-method: Return slice names; shortcut for names(txpSlices(x))

  • length,TxpModel-method: Return number of slices in model; shortcut for length(txpSlices(x))

  • merge,TxpModel,TxpModel-method: Merge two TxpModel objects into a single model

Slots

txpSlices

TxpSliceList object

txpWeights

numeric vector specifying the relative weight of each slice; when NULL, defaults to 1 (equal weighting) for each slice

txpTransFuncs

TxpTransFuncList object (or list of functions coercible to TxpTransFuncList)

Examples

## Create TxpSliceList & TxpTransFuncList objects
s1 <- list(S1 = TxpSlice("inpt1"), S2 = TxpSlice("inpt2"))
tf <- list(NULL, sqrt = function(x) sqrt(x))

## Create TxpModel object
m1 <- TxpModel(txpSlices = s1, txpWeights = 2:1, txpTransFuncs = tf)
m1
#> TxpModel with 2 slices.
#>   txpSlices(2): S1 S2
#>   txpWeights(2): 2 1
#>   txpTransFuncs(2): NULL sqrt

## Access TxpModel slots
txpSlices(m1)
#> TxpSliceList of length 2
#> names(2): S1 S2
txpWeights(m1)
#> [1] 2 1
txpWeights(m1, adjusted = TRUE)
#> [1] 0.6666667 0.3333333
txpTransFuncs(m1)
#>   TxpTransFuncList of length 2: NULL sqrt

## length
length(m1) ## equal to length(txpSlices(m1))
#> [1] 2
length(m1) == length(txpSlices(m1))
#> [1] TRUE

## names
names(m1) ## equal to names(txpSlices(m1))
#> [1] "S1" "S2"
all(names(m1) == names(txpSlices(m1)))
#> [1] TRUE

## Replacement
m2 <- m1
txpSlices(m2) <- list(S3 = TxpSlice("inpt3"), S4 = TxpSlice("inpt4"))
m2
#> TxpModel with 2 slices.
#>   txpSlices(2): S3 S4
#>   txpWeights(2): 2 1
#>   txpTransFuncs(2): NULL sqrt
names(m2)[2] <- "hello"
names(m2)
#> [1] "S3"    "hello"
txpTransFuncs(m2) <- NULL
m2
#> TxpModel with 2 slices.
#>   txpSlices(2): S3 hello
#>   txpWeights(2): 2 1
#>   txpTransFuncs(2): NULL NULL
txpTransFuncs(m2)[[1]] <- function(x) x^2
names(txpTransFuncs(m2))[1] <- "sq"
m2
#> TxpModel with 2 slices.
#>   txpSlices(2): S3 hello
#>   txpWeights(2): 2 1
#>   txpTransFuncs(2): sq NULL

## merge
m3 <- merge(m1, m2)
m3
#> TxpModel with 4 slices.
#>   txpSlices(4): S1 S2 S3 hello
#>   txpWeights(4): 2 1 2 1
#>   txpTransFuncs(4): NULL sqrt sq NULL