Simulate outcomes from an N-state partitioned survival model.

An R6::R6Class object.

Incerti and Jansen (2021). See Section 2.3 for a mathematical description of a PSM and Section 4.2 for an example in oncology. The mathematical approach used to simulate costs and QALYs from state probabilities is described in Section 2.1.

The `PsmCurves`

documentation
describes the class for the survival models and the `StateVals`

documentation
describes the class for the cost and utility models. A `PsmCurves`

object is typically created using `create_PsmCurves()`

.
The `PsmCurves`

documentation provides an example in which the model
is parameterized from parameter objects (i.e., without having the patient-level
data required to fit a model with `R`

). A longer example is provided in
`vignette("psm")`

.

`survival_models`

The survival models used to predict survival curves. Must be an object of class

`PsmCurves`

.`utility_model`

The model for health state utility. Must be an object of class

`StateVals`

.`cost_models`

The models used to predict costs by health state. Must be a list of objects of class

`StateVals`

, where each element of the list represents a different cost category.`n_states`

Number of states in the partitioned survival model.

`t_`

A numeric vector of times at which survival curves were predicted. Determined by the argument

`t`

in`$sim_curves()`

.`survival_`

An object of class survival simulated using

`sim_survival()`

.`stateprobs_`

An object of class stateprobs simulated using

`$sim_stateprobs()`

.`qalys_`

An object of class qalys simulated using

`$sim_qalys()`

.`costs_`

An object of class costs simulated using

`$sim_costs()`

.

`new()`

Create a new `Psm`

object.

`Psm$new(survival_models = NULL, utility_model = NULL, cost_models = NULL)`

`sim_stateprobs()`

Simulate health state probabilities from `survival_`

using a partitioned
survival analysis.

An instance of `self`

with simulated output of class stateprobs
stored in `stateprobs_`

.

`sim_qalys()`

Simulate quality-adjusted life-years (QALYs) as a function of `stateprobs_`

and
`utility_model`

. See `sim_qalys()`

for details.

```
Psm$sim_qalys(
dr = 0.03,
integrate_method = c("trapz", "riemann_left", "riemann_right"),
lys = TRUE
)
```

`dr`

Discount rate.

`integrate_method`

Method used to integrate state values when computing costs or QALYs. Options are

`trapz`

for the trapezoid rule,`riemann_left`

for a left Riemann sum, and`riemann_right`

for a right Riemann sum.`lys`

If

`TRUE`

, then life-years are simulated in addition to QALYs.

An instance of `self`

with simulated output of class qalys stored
in `qalys_`

.

`sim_costs()`

Simulate costs as a function of `stateprobs_`

and `cost_models`

.
See `sim_costs()`

for details.

```
Psm$sim_costs(
dr = 0.03,
integrate_method = c("trapz", "riemann_left", "riemann_right")
)
```

`dr`

Discount rate.

`integrate_method`

Method used to integrate state values when computing costs or QALYs. Options are

`trapz`

for the trapezoid rule,`riemann_left`

for a left Riemann sum, and`riemann_right`

for a right Riemann sum.

An instance of `self`

with simulated output of class costs stored
in `costs_`

.

`summarize()`

Summarize costs and QALYs so that cost-effectiveness analysis can be performed.
See `summarize_ce()`

.

```
library("flexsurv")
library("ggplot2")
theme_set(theme_bw())
# Model setup
strategies <- data.frame(strategy_id = c(1, 2, 3),
strategy_name = paste0("Strategy ", 1:3))
patients <- data.frame(patient_id = seq(1, 3),
age = c(45, 50, 60),
female = c(0, 0, 1))
states <- data.frame(state_id = seq(1, 3),
state_name = paste0("State ", seq(1, 3)))
hesim_dat <- hesim_data(strategies = strategies,
patients = patients,
states = states)
labs <- c(
get_labels(hesim_dat),
list(curve = c("Endpoint 1" = 1,
"Endpoint 2" = 2,
"Endpoint 3" = 3))
)
n_samples <- 2
# Survival models
surv_est_data <- psm4_exdata$survival
fit1 <- flexsurvreg(Surv(endpoint1_time, endpoint1_status) ~ factor(strategy_id),
data = surv_est_data, dist = "exp")
fit2 <- flexsurvreg(Surv(endpoint2_time, endpoint2_status) ~ factor(strategy_id),
data = surv_est_data, dist = "exp")
fit3 <- flexsurvreg(Surv(endpoint3_time, endpoint3_status) ~ factor(strategy_id),
data = surv_est_data, dist = "exp")
fits <- flexsurvreg_list(fit1, fit2, fit3)
surv_input_data <- expand(hesim_dat, by = c("strategies", "patients"))
psm_curves <- create_PsmCurves(fits, input_data = surv_input_data,
uncertainty = "bootstrap", est_data = surv_est_data,
n = n_samples)
# Cost model(s)
cost_input_data <- expand(hesim_dat, by = c("strategies", "patients", "states"))
fit_costs_medical <- lm(costs ~ female + state_name,
data = psm4_exdata$costs$medical)
psm_costs_medical <- create_StateVals(fit_costs_medical,
input_data = cost_input_data,
n = n_samples)
# Utility model
utility_tbl <- stateval_tbl(tbl = data.frame(state_id = states$state_id,
min = psm4_exdata$utility$lower,
max = psm4_exdata$utility$upper),
dist = "unif")
psm_utility <- create_StateVals(utility_tbl, n = n_samples,
hesim_data = hesim_dat)
# Partitioned survival decision model
psm <- Psm$new(survival_models = psm_curves,
utility_model = psm_utility,
cost_models = list(medical = psm_costs_medical))
psm$sim_survival(t = seq(0, 5, 1/12))
autoplot(psm$survival_, labels = labs, ci = FALSE, ci_style = "ribbon")
psm$sim_stateprobs()
autoplot(psm$stateprobs_, labels = labs)
psm$sim_costs(dr = .03)
head(psm$costs_)
#> sample strategy_id patient_id grp_id state_id dr category costs
#> <num> <int> <int> <int> <int> <num> <char> <num>
#> 1: 1 1 1 1 1 0.03 medical 30348.34
#> 2: 1 1 1 1 2 0.03 medical 15339.41
#> 3: 1 1 1 1 3 0.03 medical 15682.50
#> 4: 1 1 2 1 1 0.03 medical 30348.34
#> 5: 1 1 2 1 2 0.03 medical 15339.41
#> 6: 1 1 2 1 3 0.03 medical 15682.50
head(psm$sim_qalys(dr = .03)$qalys_)
#> sample strategy_id patient_id grp_id state_id dr qalys lys
#> <num> <int> <int> <int> <int> <num> <num> <num>
#> 1: 1 1 1 1 1 0.03 0.8759927 1.0170828
#> 2: 1 1 1 1 2 0.03 0.4895583 0.6482033
#> 3: 1 1 1 1 3 0.03 0.3468770 0.5055821
#> 4: 1 1 2 1 1 0.03 0.8759927 1.0170828
#> 5: 1 1 2 1 2 0.03 0.4895583 0.6482033
#> 6: 1 1 2 1 3 0.03 0.3468770 0.5055821
```