duration_sim: Generates data-set for Wednesday challenge February

In bonorico/PSI_Wed_Challenge_February: Assessment of total trial duration in planning a survival study for varying key assumptions

Generates data-set for Wednesday challenge February

Description

Simulates various scenarios according to sequence of values for the hazard-rate of the active control and the hazard-ratio.

Usage

duration_sim(
  h_c_seq = seq(0.03, 0.07, 0.005),
  HR_seq = seq(0.75, 0.8, 0.0025),
  uni_dim = TRUE
)

Arguments

h_c_seq	- numeric vector. Sequence of values for the hazard rate in control arm.
HR_seq	- numeric vector. Sequence of values for the hazard ratio.
uni_dim	- logical. Is optimization problem unidimansional ? Default and only current possibility is TRUE and uses 'optimize'. If FALSE the routine will still work using 'optimx' and this alternative allows for development of multidimensinoal optimization (see Discussion of accompanying HTML vignette)

Value

data.frame

Examples

{
## Not run: 
library(gsDesign)
library(optimx)
library(dplyr)
library(ggplot2)
library(gganimate)
library(transformr)
library(gifski)
library(Fallzahlchallenge)
# generate data
system.time(
  dur_dat <- duration_sim()
)

# filter data-set for background reference result (in order to create static layer you have to eliminate the 'transition' variable (here baseline_haz) !!) NOTE: how argument 'size' is transferred from main aes to static layer (also adding legend with no conflict)

ref_dat <- dur_dat %>% filter(baseline_haz == 0.05) %>%
  select(-baseline_haz) %>%
  rename(ref_HR = HR)

# plot data
ggplot(dur_dat, aes(HR, optim_dur, size = required_events)) +
  geom_point(show.legend = FALSE, alpha = 0.8, colour = "pink") +
  geom_point(data = ref_dat, aes(ref_HR, optim_dur),
             alpha = 0.4, colour = "blue", fill = "white") +    #' # reference background
  guides(size = guide_legend("Required\n failures")) +
  ggtitle("Change in total study duration (versus reference in blue)\n by varying of assumed HR and active comparator hazard",
          subtitle = "Active comparator hazard is {round(frame_time, 3)}") +
  ylab("Total study duration (months)") +
  xlab(expression(
    "increasing treatment effect" %<-% HR %->% "decreasing treatment effect" )) +
  geom_vline(xintercept = 0.775, colour = "green", alpha = 0.5) +
  geom_hline(yintercept = 30, colour = "green", alpha = 0.5) +
  transition_time(baseline_haz) +
  ease_aes('linear')

# save gif
anim_save("Wednesday_challenge.gif")

# save data-set
write.table(dur_dat, "dur_dat")

## End(Not run)
}

bonorico/PSI_Wed_Challenge_February documentation built on March 30, 2022, 4 p.m.