Nothing
## ----setup, include=FALSE-----------------------------------------------------
library(heemod)
## -----------------------------------------------------------------------------
surv_dist_1 <- define_survival(
distribution = "exp",
rate = .5
)
surv_dist_2 <- define_spline_survival(
scale = "odds",
gamma = c(-11.643, 1.843, 0.208),
knots = c(4.077537, 5.883183, 6.458338)
)
## ----fig.width=6, fig.height=6------------------------------------------------
library(flexsurv)
fit_w <- flexsurvreg(
formula = Surv(futime, fustat) ~ 1,
data = ovarian, dist = "weibull"
)
plot(fit_w)
fit_spl <- flexsurvspline(
formula = Surv(futime, fustat) ~ 1,
data = ovarian,
scale = "odds",
k=1
)
plot(fit_spl)
## ----fig.width=6, fig.height=6------------------------------------------------
fit_cov <- flexsurvreg(
formula = Surv(rectime, censrec) ~ group,
dist = "weibull",
data = bc
)
plot(fit_cov)
fitcov_good <- set_covariates(fit_cov, group = "Good")
fitcov_medium <- set_covariates(fit_cov, group = "Medium")
fitcov_poor <- set_covariates(fit_cov, group = "Poor")
## ----fig.width=6, fig.height=6------------------------------------------------
library(survival)
km_1 <- survfit(
formula = Surv(futime, fustat) ~ 1,
data = ovarian
)
km_cov <- survfit(
formula = Surv(rectime, censrec) ~ group,
data = bc
)
plot(km_cov)
km_good <- set_covariates(km_cov, group = "Good")
km_medium <- set_covariates(km_cov, group = "Medium")
km_poor <- set_covariates(km_cov, group = "Poor")
## -----------------------------------------------------------------------------
km_poor_ph <- apply_hr(km_poor, hr = 0.5)
km_medium_af <- apply_af(km_medium, af = 1.2)
## -----------------------------------------------------------------------------
km_poor_join <- join(
km_poor,
fitcov_poor,
at = 365
)
models_all <- mix(
fitcov_good, fitcov_medium, fitcov_poor,
weights = c(0.25, 0.25, 0.5)
)
combined_risks <- add_hazards(
fit_w, fitcov_good
)
## -----------------------------------------------------------------------------
compute_surv(surv_dist_2, time = 1:5)
## -----------------------------------------------------------------------------
fit_cov %>%
set_covariates(group = "Good") %>%
apply_hr(hr = 2) %>%
join(
fitcov_poor,
at = 3
) %>%
mix(
fitcov_medium,
weights = c(0.25, 0.75)
) %>%
add_hazards(
fit_w
) %>%
compute_surv(time = 1:5)
## ----fig.width=6, fig.height=6------------------------------------------------
param <- define_parameters(
p1 = compute_surv(
surv_dist_1,
time = model_time # can also be state_time
),
p2 = km_1 %>%
join(fit_w, at = 730) %>%
compute_surv(
time = model_time,
cycle_length = 365 # time is in days in km_medium, in years in model_time
)
)
tm <- define_transition(
C, p1 - p2, p2,
0, C, p2,
0, 0, C
)
plot(tm)
sA <- define_state(
cost = 10, ut = 1
)
sB <- define_state(
cost = 20, ut = .5
)
sC <- define_state(
cost = 0, ut = 0
)
stratTM <- define_strategy(
transition = tm,
A = sA, B = sB, C = sC
)
resTM <- run_model(
parameters = param,
stratTM,
cycles = 15,
cost = cost, effect = ut
)
## ----fig.width=6, fig.height=4------------------------------------------------
plot(resTM)
## ----fig.width=6, fig.height=4------------------------------------------------
ps <- define_part_surv(
pfs = surv_dist_1,
os = km_1 %>%
join(fit_w, at = 730),
cycle_length = c(1, 365) # 1 for pfs, 365 for os
)
stratPS <- define_strategy(
transition = ps,
A = sA, B = sB, C = sC
)
resPS <- run_model(
stratPS,
cycles = 15,
cost = cost, effect = ut
)
plot(resPS)
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