A simple discrete event simulation model of a cancer's natural history

In nhppp: Simulating Nonhomogeneous Poisson Point Processes

set.seed(20241017)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
K <- 10^4

The simulation world

We will model a cancer's natural history in a population. We index people by $k \in [K] := {1, \dots, K }$. The following assumptions fix a simulation world.

1. All types of events can be modeleld with nonhomogeneous Poisson point processes (NHPPPs).

2. Persons are alive and cancer free at 40 years of age. No person will live past 110 years. All people can die from causes other than the cancer of interest (hereafter, death from other causes). Write $\rho_k(t)$ for the corresponding intensity function.

3. Some people may be exposed to an environmental toxin, with exposure that varies over time. Write $\xi_k(t) \ge 0$ for the exposure function. Positive values mean that a person is exposed at that particular instance. (The never exposed have zeros throughout their life.) We will assume that the exposure to said toxin is a risk factor only for cancer emergence, and that the toxin has no cumulative effects -- only the instantaneous exposure levels matter. Write $\delta_k$ for the effect of the toxin instantaneous exposure on developing cancer.

4. Some persons will develop a preclinical cancer with a time-varying intensity function $\lambda_{k}(t) = \underbrace{\lambda_{k0}(t)}{\textrm{non-risk factor part}} + \underbrace{\delta_k \ \xi_k(t)}{\textrm{risk factor part}}$.

5. Some preclinical cancers may progress to clinical cancer with an intensity function $\mu_k(t)$, at which point they are considered diagnosed.

6. Once people develop preclinical cancer they can die from cancer with intensity function $\nu_k(t)$. The cancer death rate does not explicitly depend on whether the cancer has been diagnosed or not. Thus, we have two competing causes of death: death due to cancer and due to other causes.

Setup

Load nhppp and data.table. (If you prefer to not use data.table, you should be able to implement this example in base R with little trouble.)

library(data.table)
library(nhppp)

Simulation model

We now fix the mathematical description of the model. We will simulate $K = r K$ males and females (with equal probability) from the 2015 birth cohort.

pop <- data.table(
  id = 1:K,
  birth_cohort = 2015,
  spawn_age = 40,
  max_simulation_age = 110,
  sex = sample(c("male", "female"), K, replace = TRUE)
)

## It would make sense to execute the commented-out code now.
## It generates model parameters used in later stages.
## For expository clarity, we generate each parameter when it is introduced
# pop[, `:=`(
#    param_cancer_emergence_shape = runif(.N, 7, 9),
#    param_cancer_emergence_scale = rnorm(.N, 150, 20),
#    param_toxin_exposure_diff = pmax(0.005, rnorm(.N, 0.01, 0.005)),
#    param_cancer_death_intercept := rnorm(.N, -2, 0.5),
#    param_cancer_death_slope := runif(n= .N, min = 0, max = 0.003),
#    param_clinical_cancer_dx_rate := runif(.N, 0.20, 0.27)
#  )]

Death from other causes

The death from other causes $\rho_k(t)$ depends on the age ($t$, measured in years), sex (male or female), and birth year of person $k$. Function $\rho$ is is a piecewise constant over each year of age. It is a `regular' step function (all steps have the same length of one year).

If the cancer is not a major cause of death, then the intensity function for all cause deaths is a good approximation for the intensity function for death from other causes. The internal dataset annual_mortality_rates_2015 has all cause mortality data for the 2015 birth cohort. It has the values of the piecewise constant $\rho$ per birth cohort, sex, and age. Here is a peek at some columns.

annual_mortality_rates_2015[
  sex %in% c("male", "female"),
  c(1:5, 111:113)
]

When we have a step (piecewise constant) intensity function over regular time intervals (here, all one year long), we can use nhppp's vdraw_sc_step_regular() function. We need to specify the following:

1. Pass the intensities as a matrix (argument lambda_matrix); the number of columns in the matrix are the number of time intervals in the step function.

rhos <- annual_mortality_rates_2015[
  pop,
  on = c("birth_cohort", "sex")
]
setindex(rhos, "id")
rho_matrix <- as.matrix(rhos[, c(paste0("age_", 0:109), "age_110+"),
  with = FALSE
])

rm(list = "rhos") # cleanup

1. Give information about how long each time step is, by specifying the age bounds rate_matrix_t_min and rate_matrix_t_max over which the intensity matrix applies;

2. Optionally, if we want to sample times in a sub-interval of (rate_matrix_t_min, rate_matrix_t_max], we can specify even narrower bounds, t_min and t_max. If you omit t_min or t_max, the software uses rate_matrix_t_min or rate_matrix_t_max, respectively, to specify the sampling interval.

3. Because no person lives beyond the maximum simulation age of 110 years, we need to force the simulation of at least one death event over the simulation interval. This means that we are sampling from a zero-truncated NHPPP. Setting the option atleast1 to TRUE achieves this.

4. We only need to sample the earliest event from this NHPPP. So we set the atmost1 option to TRUE.

pop[
  ,
  age_dead_from_other_causes :=
    nhppp::vdraw_sc_step_regular(
      lambda_matrix = rho_matrix,
      rate_matrix_t_min = 0,
      rate_matrix_t_max = 110,
      t_min = pop$spawn_age, # 40
      t_max = pop$max_simulation_age, # 110
      atmost1 = TRUE,
      atleast1 = TRUE
    )
]

Environmental toxin exposure histories

We will generate environmental exposure histories with a phenomenological model. We will assume that

1. People may be exposed to the environmental toxin with probability $p_{start} = 0.20$.

2. For those who will be exposed, the start age of exposure is $t_{k0} \sim U(12, 35)$, provided that they are still alive.

3. Among those who are exposed, the probability that their exposure will eventually stop is $p_{stop} = 0.60$.

4. In the pertinent subgroup of persons, the duration of the exposure is $d_k \sim U(1, 35)$, if they are still alive.

5. For people with at least some exposure to the toxin, for all times in the exposure window $(t_{k0}, t_{k1}]$ the exposure levels are $\xi_k(t) = \Xi_k \cdot \Big(\frac{1}{2} +\frac{1}{4}\big(\cos(0.5 t) + \cos(0.45 t) \big) \Big)$, where $t$ is a person's age and the amplitude (maximum exposure) $\Xi_k$ has model $\Xi_k \sim U(0.2, 1)$. Otherwise, $\xi_k(t) = 0$.

We now add the per-person parameters for exposure histories in the population data.table. For people who will never be exposed we set $\Xi_k$ to zero, and their exposure start and stop ages at the max_simuation_age. This avoids if ... else statements, and is still pretty fast. If you run a massive model, though, you may want to be smarter about it.

`` {r xi_params} pop[,:=`( exposure_start_age = max_simulation_age, exposure_stop_age = max_simulation_age, maximum_exposure = 0 )][ , will_start_exposure := runif(.N) < 0.20 ][ will_start_exposure == TRUE, will_stop_exposure := runif(.N) < 0.60 ][ will_start_exposure == TRUE, exposure_start_age := pmin(runif(.N, 12, 35), age_dead_from_other_causes) ][ will_stop_exposure == TRUE, exposure_stop_age := pmin( exposure_start_age + runif(.N, 1, 35), age_dead_from_other_causes ) ][ will_start_exposure == TRUE, maximum_exposure := runif(.N, 1 / 5, 1) ]

cleanup

pop[, will_start_exposure := NULL][, will_stop_exposure := NULL]

We implement $\xi_k(t)$ as a function that is vectorized 
over all its arguments. The arguments `start_age`, `stop_age`, `max_exposure` correspond 
to the variables $t_{k0}, t_{k1}, \Xi$ in the equation above.

```r
xi <- toxin_exposure <- function(t, max_exposure, start_age, stop_age) {
  (start_age <= t) * (stop_age >= 1) * max_exposure * (1 / 2 + (cos(t / 2) + cos(0.9 * t / 2)) / 4)
}

Emergence of pre-clinical cancer in unexposed and exposed intervals

Assume that the intensity function for cancer emergence in the absence of toxin exposure is

$\lambda_{k0}(t) = \frac{shape_k}{scale_k} \Big(\frac{t}{scale_k}\Big)^{shape_k -1}$,

where $t$ is age in years.

This intensity function generates a Weibull point process (a special case of an NHPPP). The parameters $shape_k$ and $scale_k$ are assumed to vary across people according to the models $shape_k \sim U(7, 9)$ and $scale_k \sim N(150, 20)$, where $U(\cdot)$ and $N(\cdot)$ stand for uniform and normal distributions. We sample these values for each person in the population.

pop[, `:=`(
  param_cancer_emergence_shape = runif(.N, 7, 9),
  param_cancer_emergence_scale = rnorm(.N, 150, 20)
)]

Generating a Weibull point process is easy in R using the stats::rweibull() function. (This would take care of the cancer emergence times for people without toxin exposure, but not for people with toxin exposures.) Accounting for toxin exposure histories, the intensity function for cancer emergence is $\lambda_{k}(t) = l_{k0}(t) + \delta_k \xi_k(t)$.

We will assume that the toxin exposure effect $\delta_k$ is distributed as $\delta_k \sim N_+\big(2, 0.5\big)$, where $N_+(\cdot)$ is a slab and smear normal distribution.

pop[, param_toxin_exposure_diff := pmax(0, rnorm(.N, 0.01, 0.005))]

We need to sample from an NHPPP with an intensity function that varies over time as per $\lambda_k(t)$. We will use nhppp's vdraw_intensity() function, which needs

1. The intensity function (argument lambda) in a vectorized form, so that age $t$ is the only needed argument and all other arguments are set by default.

2. A majorizer piecewise constant function, which will be specified as a matrix lambda_maj_matrix.

3. The rate_matrix_t_min, rate_matrix_t_max arguments that specify the time bounds for the matrix lambda_maj_matrix.

4. t_min, and t_max arguments, for the subinterval over whchi we will sample times. Here, t_min = 40 -- the spawn age in the simulation, and t_max is the age_dead_from_other_causes.

Let's implement the above.

The intensity function is specified as follows. Observe that it is in vectorized form.

lambda <- function(t, P = pop, ...) {
  # non-risk factor part: shape / scale * (t/scale)^(shape - 1)
  (P$param_cancer_emergence_shape / P$param_cancer_emergence_scale) *
    (t / P$param_cancer_emergence_scale)^(P$param_cancer_emergence_shape - 1) +
    # risk factor (toxin exposure) part: delta_k * xi(t)
    P$param_toxin_exposure_diff *
      xi(
        t = t,
        max_exposure = P$maximum_exposure,
        start_age = P$exposure_start_age,
        stop_age = P$exposure_stop_age
      )
}

We also need a piecewise constant majorizer function $\lambda_(t)$. We say that $\lambda_(t)$ majorizes $\lambda(t)$ if $\lambda_*(t) \ge \lambda(t)$ for all $t$ of interest. The function expects a regular step majorizer function. We will create such a function with $M = 10$ equally-spaced intervals over the whole simulation window. First, generate the endpoints of the $M$ intervals. This will be a matrix where the rows correspond to persons and the columns to the $M + 1 =11$ interval bounds.

# define interval bounds for the step function, one row per person
M <- 10
time_breaks <- matrix(
  data = rep(x = seq(from = 40, to = 110, length.out = M + 1), each = K),
  byrow = FALSE,
  nrow = K
)

time_breaks[1:3, ]

... and now generate the majorizer matrix using nhppp's get_step_majorizer() function. (The paper in the Bibliography explains how this function works.)
``` {r lambda star} lambda_star <- nhppp::get_step_majorizer( fun = lambda, breaks = time_breaks, is_monotone = FALSE, K = 1.9 / 4 # This is the maximum slope of xi() -- which you get with some calculus )

lambda_star[1:3, ]

And now, we can sample the cancer generation times, and create a variable 
to identify patients with cancer.  

```r
pop[
  ,
  age_cancer_emergence := nhppp::vdraw_intensity(
    lambda = lambda,
    lambda_maj_matrix = lambda_star,
    rate_matrix_t_min = 40,
    rate_matrix_t_max = 110,
    t_min = pop$spawn_age,
    t_max = pmin(pop$age_dead_from_other_causes, 110, na.rm = TRUE),
    atmost1 = TRUE
  )
][
  ,
  with_cancer := !is.na(age_cancer_emergence),
]

Dying from cancer

People with preclinical cancer may die from cancer causes. We will assume that the intensity from cancer deaths is loglinear in time, that is

$\nu_k = e^{\alpha_k + \beta_k t}$,

with parameters $\alpha_k \sim N(-3, 0.2)$ and $\beta_k ~ U(0, 0.003)$.

pop[, param_cancer_death_intercept := rnorm(.N, -3, 0.2)]
pop[, param_cancer_death_slope := runif(.N, 0, 0.003)]

We could use the vdraw_intensity() function again, since we already know the intensity $\nu_k$ and we can easily create a majorizer function for it, as we did when we generated cancer emergence times. This would be plenty fast for our small simulation with $K = r K$ and requires no additional mathematics.

We can sample even faster if we can analytically obtain the cumulative intensity function $N_k(t) = \int_0^t{\nu_k(s) \ \textrm{d}s}$, and its inverse $N_k^{-1}(z)$. (The inverse function recovers $t$ from the value of $N_k(t)$: $t = N_k^{-1}\big( N_k(t)\big)$). This sampling is done with nhppp's vdraw_cumulative_intensity() function.

A bit of calculus can yield $N_k(t) = \frac{1}{\beta_k} (e^{\alpha_k + \beta_k t} - e^{\alpha_k})$, which we can implement in vectorized form and with default parameters already set:

Nu <- function(t, Lambda_args = list(population), ...) {
  P <- Lambda_args$population
  (
    exp(P$param_cancer_death_intercept + P$param_cancer_death_slope * t) -
      exp(P$param_cancer_death_intercept)
  ) / P$param_cancer_death_slope
}

The inverse $N_k^{-1}(\cdot)$ is

$N_k^{-1}(z) = \big( \log( \beta_k z + e^\alpha_k ) - \alpha_k \big)/\beta_k $

Nu_inv <- function(z, Lambda_inv_args = list(population), ...) {
  P <- Lambda_inv_args$population
  (
    log(P$param_cancer_death_slope * z +
      exp(P$param_cancer_death_intercept)) -
      P$param_cancer_death_intercept
  ) / P$param_cancer_death_slope
}

Then, we can sample the times to cancer death.

args_list <- list(population = pop[!is.na(age_cancer_emergence), ])
pop[
  !is.na(age_cancer_emergence),
  age_dead_from_cancer_causes := nhppp::vdraw_cumulative_intensity(
    Lambda = Nu,
    Lambda_args = args_list,
    Lambda_inv = Nu_inv,
    Lambda_inv_args = args_list,
    t_min = pop[!is.na(age_cancer_emergence), age_cancer_emergence],
    t_max = pop[!is.na(age_cancer_emergence), age_dead_from_other_causes],
    atmost1 = TRUE
  )
]

rm(list = "args_list") # cleanup

Dying from all causes

The age of death from all causes is the minimum of the ages across both causes of death.

pop[
  ,
  age_dead := pmin(age_dead_from_other_causes,
    age_dead_from_cancer_causes,
    na.rm = TRUE
  )
]

Clinical cancer diagnosis

Cancers first emerge in a pre-clinical stage. Some will be diagnosed as
clinical cancers with intensity function $\mu_k$. We will assume that clinical diagnosis has constant rate which is distributed according to the model

$\mu_k(t) := \mu_k \sim U(0.20, 0.27)$,

where $k$ indexes over people with cancer.

``` {r param_cancer_dx_rates} pop[ !is.na(age_cancer_emergence), param_clinical_cancer_dx_rate := runif(.N, 0.20, 0.27) ]

Constant rates result in exponential
times, which we can easily sample with the `stats::rexp()` function, as per 
the commented out code below.  
``` {r rexp}
### Using rexp()
tictoc::tic()
pop[
  !is.na(age_cancer_emergence),
  age_clinical_cancer_dx :=
    age_cancer_emergence +
    rexp(.N, rate = param_clinical_cancer_dx_rate)
]
pop[
  age_clinical_cancer_dx >= age_dead,
  age_clinical_cancer_dx := NA
]
tictoc::toc()

With nhppp, we can use the vdraw_sc_step_regular() function that samples from piecewise constant intensities. (A constant function over an interval is still a piecewise constant function -- with a single piece.) The nhppp implementation will be only a bit slower -- but it is worth showing.

``` {r cancer_dx_rates} tictoc::tic() mu_mat <- as.matrix(pop[ !is.na(age_cancer_emergence), param_clinical_cancer_dx_rate ])

pop[ !is.na(age_cancer_emergence), age_clinical_cancer_dx := nhppp::vdraw_sc_step_regular( lambda_matrix = mu_mat, rate_matrix_t_min = pop[!is.na(age_cancer_emergence), age_cancer_emergence], rate_matrix_t_max = pop[!is.na(age_cancer_emergence), age_dead], atmost1 = TRUE ) ] tictoc::toc()

## Some descriptives
```r
# pop$age_cancer_emergence |> summary()
summary(pop)

Bibliography

Trikalinos TA, Sereda Y. nhppp: Simulating Nonhomogeneous Poisson Point Processes in R. arXiv preprint arXiv:2402.00358. 2024 Feb 1.

Since the publication of the paper, the syntax and options of the nhppp package have evolved. To reproduce the code in the paper, you have to install the version of nhppp used in the paper. Alternatively, take a look at the vignettes, which are written to work with the current package.

nhppp documentation built on Oct. 30, 2024, 9:28 a.m.