Generating survival data in simstudy

To put all of this in context, this is a simple example of how we can generate survival data using simstudy and then take a look at it using the survival and survminer packages:

library(simstudy)
library(data.table)
library(ggplot2)
library(survminer)
library(survival)

def <- defSurv(varname = "time", formula = -13.7, scale = 1, shape = 0.49)

set.seed(1134)
dd <- genData(101)
dd <- genSurv(dd, def, digits = 0)
dd$status <- 1

dd
##       id time status
##   1:   1  604      1
##   2:   2 1012      1
##   3:   3 1338      1
##   4:   4 1009      1
##   5:   5  335      1
##  ---                
##  97:  97  756      1
##  98:  98  971      1
##  99:  99  381      1
## 100: 100  952      1
## 101: 101  697      1
fit <- survfit( Surv(time, status) ~ 1, data = dd )
ggsurvplot(fit, data = dd, palette = "#7D9D33")

So, we have generated survival data, and it all looks great. However, where did those parameters (formula, scale, and shape) in defSurv come from? That’s what we’re focusing on here.

Weibull-Cox proprtional hazard data generation process

This underlying data generating process draws from a Weibull distribution and satisfies the requirements of a Cox proportional hazards model. The approach was drawn directly from this Bender, Augustin, and Blettner paper, so head over there if you really want the details.

The times to survival \(T\) are generated using three parameters, \(\lambda\) (scale), \(\nu\) (shape), and \(f\), which is really \(\mathbf{\beta^\prime x}\) from a Cox proportional hazard model that may include a covariate vector \(\mathbf{x}\). In the examples here, there will only be an intercept.

\[T = \left[ \frac{- \lambda \ \text{log}(u) }{\text{exp}(f)} \right] ^ \nu\]

A single instance \(T\) is “drawn” from the Weibull distribution by generating \(u\) from the uniform \(U(0,1)\) distribution. It will be the case that \((1-u) \%\) of the survival times \(T\) will fall below the values of \(T\) determined by \(u\); this will be helpful later when we need to generate data with specific distributions in mind.

It turns out that we don’t really need the scale parameter \(\lambda\), because it can be absorbed into \(f\), so in all the examples that follow, we’ll set \(\lambda = 1\), which leaves us with

\[T = \left[ \frac{- \text{log}(u) }{\text{exp}(f)} \right] ^ \nu\]

library(data.table)
library(ggplot2)

get_surv <- function(f, shape, n = 100) {
  
  u <- seq(1, 0.001, length = n)
  
  dd <- data.table(
    f = f,
    shape = shape,
    T = (-(log(u)/exp(f)))^(shape),
    p = round(1 - cumsum(rep(1/length(u), length(u))), 3)
  )
  
  return(dd)

}

get_surv(-10, .3, n = 10)
##       f shape        T   p
##  1: -10   0.3  0.00000 0.9
##  2: -10   0.3 10.56988 0.8
##  3: -10   0.3 13.26785 0.7
##  4: -10   0.3 15.31471 0.6
##  5: -10   0.3 17.11875 0.5
##  6: -10   0.3 18.85288 0.4
##  7: -10   0.3 20.64903 0.3
##  8: -10   0.3 22.68619 0.2
##  9: -10   0.3 25.40811 0.1
## 10: -10   0.3 35.86613 0.0

f <- c(-26, -27, -28, -29)
shape <- c(0.16, .18, .20, .22)

eg <- expand.grid(f=f, shape=shape)
eg <- asplit(eg, MARGIN = 1)

l <- lapply(eg, function(x) get_surv(x[1], x[2]))
l <- rbindlist(l)

ggplot(data = l, aes(x = T, y = p)) +
  geom_line(aes(group = f, color = factor(f))) +
  ylim(0,1) +
  xlim(0, 800) +
  facet_grid ( ~ shape) +
  theme(panel.grid = element_blank(),
        axis.text = element_text(size = 7.5)) +
  scale_color_manual(
    values = c("#7D9D33", "#CED38C", "#DCC949", "#BCA888", "#CD8862", "#775B24"),
    name = "  f"
  )

Generating a particular distribution

The interpretation of the parameters is a bit opaque. If we have covariates embedded in \(f\) the coefficients do have pretty clear interpretations as hazard ratios. But the intercept term (remember, I have set \(\lambda = 1\)) really defines the scale. So how do we go about selecting values for \(f\) and \(\nu\) to get the desired distribution?

If we can reasonably characterize the desired distribution by two points on the survival curve, the task actually becomes remarkably easy. By this, I mean we pick two time points and a probability of survival for each time point. For example, we may want a distribution with 80% survival until day 180 and 20% survival at day 365. Or, in a second scenario, we may want to have 90% survival at day 180 and 40% survival at day 365. Here is an animation of how we might find the curves by adjusting \(f\) and \(\nu\) (see addendum for code to generate this):

dsurv <- get_surv(-13.655, 0.486, n = 1000)
dsurv
##             f shape          T     p
##    1: -13.655 0.486    0.00000 0.999
##    2: -13.655 0.486   26.55994 0.998
##    3: -13.655 0.486   37.20774 0.997
##    4: -13.655 0.486   45.32308 0.996
##    5: -13.655 0.486   52.13693 0.995
##   ---                               
##  996: -13.655 0.486 1714.16472 0.004
##  997: -13.655 0.486 1748.87893 0.003
##  998: -13.655 0.486 1792.58585 0.002
##  999: -13.655 0.486 1852.33947 0.001
## 1000: -13.655 0.486 1950.02084 0.000

Addendum

Here is the code that is used to generate the animated plot, which done with the gganimate package:

library(gganimate)

sdd <- list()

sdd[[1]] <- get_surv(-6,  1, n = 1000)
sdd[[2]] <- get_surv(-7.566, 0.783 , n = 1000)
sdd[[3]] <- get_surv(-9.981, 0.587, n = 1000)
sdd[[4]] <- get_surv(-11.137, 0.521, n = 1000)
sdd[[5]] <- get_surv(-13.814, 0.417, n = 1000)
sdd[[6]] <- get_surv(-16.014, 0.358, n = 1000)
sdd[[7]] <- get_surv(-6,  1, n = 1000)
sdd[[8]] <- get_surv(-8.125, 0.777 , n = 1000)
sdd[[9]] <- get_surv(-10.183, 0.619, n = 1000)
sdd[[10]] <- get_surv(-12.481, 0.490, n = 1000)
sdd[[11]] <- get_surv(-14.595, 0.414, n = 1000)
sdd[[12]] <- get_surv(-18.139, 0.327, n = 1000)

k <- length(sdd)

sdds <- lapply(1:k, function(x) sdd[[x]][ , c("iter", "color") := list(x, "black")])
sdds[[k/2]][, color := "green"]
sdds[[k]][, color := "green"]
sdd <- rbindlist(sdds)

targets <- data.table(iter = 1:k, days1 = rep(180, k), days2 = rep(365, k),
  p1 = rep(c(.8, .9), each = k/2), p2 = rep(c(.2, .4), each = k/2))

dt_anot <- sdd[, .SD[1,], keyby = iter]
dt_anot[iter <= (k/2), targets := 1]
dt_anot[iter > (k/2), targets := 2]
dt_anot[, targets := factor(targets, labels = c("Scenario one", "Scenario two"))]
dt_anot[, color := "black"]
dt_anot[iter == (k/2), color := "green"]
dt_anot[iter == k, color := "green"]

a <- ggplot() +
  geom_point(data = targets, aes(x = days1, y=p1), pch = 1, size = 2) +
  geom_point(data = targets, aes(x = days2, y=p2), pch = 1, size = 2) +
  geom_point(data = sdd, aes(x = T, y = p, group = p, color = color), size = .2) +
  geom_vline(xintercept = c(180, 365), lty = 1, size = .3, color = "grey70") +
  geom_text(x = 750, y = .68, size = 5.5, hjust = "left", fontface = "bold",
            aes(label = targets), data = dt_anot) +
  geom_text(x = 750, y = .6, size = 5.5, hjust = "left",
            aes(label = paste("f:", f), color = color), data = dt_anot) +
  geom_text(x = 750, y = .54, size = 5.5, hjust = "left",
            aes(label = paste("shape:", shape), color = color), data = dt_anot) +
  scale_x_continuous(limits = c(0, 1250), 
                     breaks = c(seq(0, 1250, by = 250), 180, 365), name = "time") +
  scale_color_manual(values = c("black","#7D9D33")) +
  scale_y_continuous(limits = c(0.05, 0.995), 
                     breaks = c(0.2, 0.4, 0.6, 0.8), name = "probability of survival") +
  theme(panel.grid = element_blank(),
        legend.position = "none") +
  transition_states(iter, state_length = 1, transition_length = 1) 

animate(a, duration = 24, fps = 10, height = 350, width = 550)

A note on where the parameters for the animation came from

You may be wondering where the parameters used in the animation come from. I really wanted to generate a series of curves that started at a fair distance from the true value and converged to the right spot. My idea was to use a simple loss function that involved the unknown parameters \(f\) and \(\nu\), which would be optimized (in this case minimized) at the correct values (the same as those derived above). If I could recover the interim values of optimization algorithm, those would provide a sequence of parameters and curves the converge on the true values.

The loss function is a simple squared loss, which is the sum of the squared loss for both points that define the curve:

\[\left[ \hat{\nu} \ (\text{log} \left[ -\text{log}(u_1)\right] - \hat{f}) - \text{log}(T_1) \right]^2 + \left[ \hat{\nu} \ (\text{log} \left[ -\text{log}(u_2)\right] - \hat{f}) - \text{log}(T_2) \right]^2\]

This is implemented as function fx, which is to be optimized using function optim. I know this may not be the best optimization option in R, but given that this is quite a simple problem, it should suffice. In the function \(x[1]\) represents \(f\), and \(x[2]\) represents \(\nu\).

fx <- function(x, p, times) {
  (x[2]*(log(-log(p[1])) - x[1]) - log(times[1])) ^ 2 + 
  (x[2]*(log(-log(p[2])) - x[1]) - log(times[2])) ^ 2 
}

The optimization provides starting values for \(f\) and \(\nu\). I chose values of \(f\) and \(\nu\) that would locate the initial curve between the two target points. \(\nu\) is constrained to be non-negative (and \(f\) is unconstrained). The key here is that the trace option is set so that interim values of \(f\) and \(\nu\) are reported. I am not showing the full output here, because it is quite lengthy. I only used four interim values (plus the starting and ending values) to create the animation. The final output includes the values of \(f\) and \(\nu\) that optimize the quadratic loss:

optim(
  par = c(-(log((180+365)/2) - log(-log(.5))), 1), 
  fn = fx, 
  p = c(.8, .2), 
  times = c(180, 365),
  method = "L-BFGS-B", 
  lower = c(-Inf, 0),
  upper = c(Inf, Inf),
  control= list(trace = 5)
)
## $par
## [1] -16.0137061   0.3577952
## 
## $value
## [1] 1.065948e-13
## 
## $counts
## function gradient 
##       33       33 
## 
## $convergence
## [1] 0
## 
## $message
## [1] "CONVERGENCE: REL_REDUCTION_OF_F <= FACTR*EPSMCH"

Incidentally, our analytic formulas give us

\[\nu^* = \frac{\text{log}(365) - \text{log}(180)}{\text{log}(-\text{log}(0.2)) - \text{log}(-\text{log}(0.8))} = 0.3577951\]

\[f^* = \text{log}(-\text{log}(0.8)) - \frac{1}{0.3577951} \text{log}(180) =-16.01371\]