tpmatrix function

Transition probability matrix

tpmatrix() both defines and evaluates a transition probability matrix in which elements are expressions. It can be used within define_tparams() to create a transition probability matrix or directly to create a tparams_transprobs()

object. These are, in turn, ultimately used to create a CohortDtstmTrans object for simulating health state transitions.

tpmatrix(..., complement = NULL, states = NULL, prefix = "", sep = "_")

Arguments

• ...: Named values of expressions defining elements of the matrix. Each element of ... should either be a vector or a 2-dimensional tabular object such as a data frame. See "Details" and the examples below.
• complement: Either a character vector or a numeric vector denoting the transitions (i.e., the columns of the tabular object formed from ...) that are complementary (see "Details" below). If a character vector, each element should be the name of a column in the tabular object; if a numeric vector, each element should be the index of a column in the tabular object.
• states, prefix, sep: Arguments passed to tpmatrix_names() for naming the columns. If states = NULL (the default), then the states are named s1, ..., sh where h is the number of health states.

Returns

Returns a tpmatrix object that inherits from data.table

where each column is an element of the transition probability matrix with elements ordered rowwise.

Details

A tpmatrix is a 2-dimensional tabular object that stores flattened square transition probability matrices in each row. Each transition probability matrix is filled rowwise. The complementary probability (equal to $1$

minus the sum of the probabilities of all other elements in a row of a transition probability matrix) can be conveniently referred to as C or specified with the complement argument. There can only be one complement for each row in a transition probability matrix.

Examples

p_12 <- c(.7, .6)
tpmatrix(
  C, p_12,
  0, 1
)

tpmatrix(
  C, p_12,
  C, 1
)

# Pass matrix
pmat <- matrix(c(.5, .5, .3, .7), byrow = TRUE, ncol = 4)
tpmatrix(pmat)

# Pass vectors and data frames
p1 <- data.frame(
  p_12 = c(.7, .6),
  p_13 = c(.1, .2)
)

p2 <- data.frame(
  p_21 = 0,
  p_22 = c(.4, .45),
  p_23 = c(.6, .55)
)

p3 <- data.frame(
  p_31 = c(0, 0),
  p_32 = c(0, 0),
  p_33 = c(1, 1)
)

tpmatrix(
  C, p1,
  p2,
  p3
)

# Use the 'complement' argument
pmat <- data.frame(s1_s1 = 0, s1_s2 = .5, s2_s1 = .3, s2_s2 = 0)
tpmatrix(pmat, complement = c("s1_s1", "s2_s2"))
tpmatrix(pmat, complement = c(1, 4)) # Can also pass integers

# Can control column names
tpmatrix(pmat, complement = c(1, 4),
         states = c("state1", "state2"), sep = ".")

See Also

A tpmatrix is useful because it provides a convenient way to construct a tparams_transprobs object, which is the object in hesim used to specify the transition probabilities required to simulate Markov chains with the CohortDtstmTrans class. See the tparams_transprobs documentation for more details.

The summary.tpmatrix() method can be used to summarize a tpmatrix

across parameter samples.