sim_stateprobs.survival {hesim}

Simulate state probabilities from survival curves

Description

Simulate health state probabilities from a survival object using partitioned survival analysis.

Usage

## S3 method for class 'survival'
sim_stateprobs(x, ...)

Arguments

x

An object of class survival.

...

Further arguments passed to or from other methods.

Details

In an N-state partitioned survival model there are N-1 survival curves and S_n(t) is the cumulative survival function denoting the probability of survival to health state n or a lower indexed state beyond time t. The probability that a patient is in health state 1 at time t is simply S_1(t). State membership in health states 2,\ldots, N -1 is calculated as S_n(t) - S_{n-1}(t). Finally, the probability of being in the final health state N (i.e., the death state) is 1-S_{N-1}(t), or one minus the overall survival curve.

In some cases, the survival curves may cross. hesim will issue a warning but the function will still run. Probabilities will be set to 0 in a health state if the prior survival curve lies above the curve for state n; that is, if S_n(t) < S_{n-1}(t), then the probability of being in state n is set to 0 and S_n(t) is adjusted to equal S_{n-1}(t). The probability of being in the final health state is also adjusted if necessary to ensure that probabilities sum to 1.

Value

A stateprobs object.

See Also

survival

Examples

library("data.table")
library("survival")

# This example shows how to simulate a partitioned survival model by
# manually constructing a "survival" object. We will consider a case in which
# Cox proportional hazards models from the survival package---which are not
# integrated with hesim---are used for parameter estimation. We will use 
# point estimates in the example, but bootstrapping, Bayesian modeling,
# or other techniques could be used to draw samples for a probabilistic 
# sensitivity analysis. 

# (0) We first setup our model per usual by defining the treatment strategies,
# target population, and health states
hesim_dat <- hesim_data(
  strategies = data.table(strategy_id = 1:3,
                          strategy_name = c("SOC", "New 1", "New 2")),
  patients = data.table(patient_id = 1:2,
                        female = c(0, 1),
                        grp_id = 1),
  states = data.table(state_id = 1:2,
                      state_name = c("Stable", "Progression"))
)

# (1) Next we will estimate Cox models with survival::coxph(). We illustrate 
# by predicting progression free survival (PFS) and overall survival (OS)
## Fit models
onc3_pfs_os <- as_pfs_os(onc3, patient_vars = c("patient_id", "female",
                                                "strategy_name"))
fit_pfs <- coxph(Surv(pfs_time, pfs_status) ~ strategy_name + female,
                 data = onc3_pfs_os)
fit_os <- coxph(Surv(os_time, pfs_status) ~ strategy_name + female,
                data = onc3_pfs_os)

## Predict survival on input data
surv_input_data <- expand(hesim_dat)
times <- seq(0, 14, 1/12)
predict_survival <- function(object, newdata, times) {
  surv <- summary(survfit(object, newdata = newdata, se.fit = FALSE),
                  t = times)
  pred <- newdata[rep(seq_len(nrow(newdata)), each = length(times)), ]
  pred[, sample := 1] # Point estimates only in this example
  pred[, time := rep(surv$time, times = nrow(newdata))]
  pred[, survival := c(surv$surv)]
  return(pred[, ])
}
pfs <- predict_survival(fit_pfs, newdata = surv_input_data, times = times)
os <- predict_survival(fit_os, newdata = surv_input_data, times = times)
surv <- rbind(
  as.data.table(pfs)[, curve := 1L],
  as.data.table(os)[, curve := 2L]
)

## Convert predictions to a survival object
surv <- survival(surv, t = "time")
## Not run: autoplot(surv)

# (2) We can then compute state probabilities from the survival object
stprobs <- sim_stateprobs(surv)

# (3) Finally, we can use the state probabilities to compute QALYs and costs
## A dummy utility model to illustrate
utility_tbl <- stateval_tbl(
  data.table(state_id = 1:2,
             est = c(1, 1)
  ),
  dist = "fixed"
)
utilitymod <- create_StateVals(utility_tbl, 
                               hesim_data = hesim_dat,
                               n = 1)

## Instantiate Psm class and compute QALYs
psm <- Psm$new(utility_model = utilitymod)
psm$stateprobs_ <- stprobs
psm$sim_qalys()
psm$qalys_