Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 7,
fig.height = 5,
fig.align = "center"
)
## -----------------------------------------------------------------------------
library(dampack)
run_sick_sicker_model <- function(l_params, verbose = FALSE) {
with(as.list(l_params), {
# l_params must include:
# -- disease progression parameters (annual): r_HD, p_S1S2, hr_S1D, hr_S2D,
# -- initial cohort distribution: v_s_init
# -- vector of annual state utilities: v_state_utility = c(u_H, u_S1, u_S2, u_D)
# -- vector of annual state costs: v_state_cost = c(c_H, c_S1, c_S2, c_D)
# -- time horizon (in annual cycles): n_cyles
# -- annual discount rate: r_disc
####### SET INTERNAL PARAMETERS #########################################
# state names
v_names_states <- c("H", "S1", "S2", "D")
n_states <- length(v_names_states)
# vector of discount weights
v_dw <- 1 / ((1 + r_disc) ^ (0:n_cycles))
# state rewards
v_state_cost <- c("H" = c_H, "S1" = c_S1, "S2" = c_S2, "D" = c_D)
v_state_utility <- c("H" = u_H, "S1" = u_S1, "S2" = u_S2, "D" = u_D)
# transition probability values
r_S1D <- hr_S1D * r_HD # rate of death in sick state
r_S2D <- hr_S2D * r_HD # rate of death in sicker state
p_S1D <- 1 - exp(-r_S1D) # probability of dying when sick
p_S2D <- 1 - exp(-r_S2D) # probability of dying when sicker
p_HD <- 1 - exp(-r_HD) # probability of dying when healthy
## Initialize transition probability matrix
# all transitions to a non-death state are assumed to be conditional on survival
m_P <- matrix(0,
nrow = n_states, ncol = n_states,
dimnames = list(v_names_states, v_names_states)) # define row and column names
## Fill in matrix
# From H
m_P["H", "H"] <- (1 - p_HD) * (1 - p_HS1)
m_P["H", "S1"] <- (1 - p_HD) * p_HS1
m_P["H", "D"] <- p_HD
# From S1
m_P["S1", "H"] <- (1 - p_S1D) * p_S1H
m_P["S1", "S1"] <- (1 - p_S1D) * (1 - (p_S1H + p_S1S2))
m_P["S1", "S2"] <- (1 - p_S1D) * p_S1S2
m_P["S1", "D"] <- p_S1D
# From S2
m_P["S2", "S2"] <- 1 - p_S2D
m_P["S2", "D"] <- p_S2D
# From D
m_P["D", "D"] <- 1
# check that all transition matrix entries are between 0 and 1
if(!all(m_P <= 1 & m_P >= 0)){
stop("This is not a valid transition matrix (entries are not between 0 and 1")
} else
# check transition matrix rows add up to 1
if (!all.equal(as.numeric(rowSums(m_P)),rep(1,n_states))){
stop("This is not a valid transition matrix (rows do not sum to 1)")
}
####### INITIALIZATION #########################################
# create the cohort trace
m_Trace <- matrix(NA, nrow = n_cycles + 1 ,
ncol = n_states,
dimnames = list(0:n_cycles, v_names_states)) # create Markov trace
# create vectors of costs and QALYs
v_C <- v_Q <- numeric(length = n_cycles + 1)
############# PROCESS ###########################################
m_Trace[1, ] <- v_s_init # initialize Markov trace
v_C[1] <- 0 # no upfront costs
v_Q[1] <- 0 # no upfront QALYs
for (t in 1:n_cycles){ # throughout the number of cycles
m_Trace[t + 1, ] <- m_Trace[t, ] %*% m_P # calculate trace for cycle (t + 1) based on cycle t
v_C[t + 1] <- m_Trace[t + 1, ] %*% v_state_cost
v_Q[t + 1] <- m_Trace[t + 1, ] %*% v_state_utility
}
############# PRIMARY ECONOMIC OUTPUTS #########################
# Total discounted costs
n_tot_cost <- t(v_C) %*% v_dw
# Total discounted QALYs
n_tot_qaly <- t(v_Q) %*% v_dw
############# OTHER OUTPUTS ###################################
# Total discounted life-years (sometimes used instead of QALYs)
n_tot_ly <- t(m_Trace %*% c(1, 1, 1, 0)) %*% v_dw
####### RETURN OUTPUT ###########################################
out <- list(m_Trace = m_Trace,
m_P = m_P,
l_params,
n_tot_cost = n_tot_cost,
n_tot_qaly = n_tot_qaly,
n_tot_ly = n_tot_ly)
return(out)
}
)
}
## -----------------------------------------------------------------------------
simulate_strategies <- function(l_params, wtp = 100000){
# l_params must include:
# -- *** Model parameters ***
# -- disease progression parameters (annual): r_HD, p_S1S2, hr_S1D, hr_S2D,
# -- initial cohort distribution: v_s_init
# -- vector of annual state utilities: v_state_utility = c(u_H, u_S1, u_S2, u_D)
# -- vector of annual state costs: v_state_cost = c(c_H, c_S1, c_S2, c_D)
# -- time horizon (in annual cycles): n_cyles
# -- annual discount rate: r_disc
# -- *** Strategy specific parameters ***
# -- treartment costs (applied to Sick and Sicker states): c_trtA, c_trtB
# -- utility with Treatment_A (for Sick state only): u_trtA
# -- hazard ratio of progression with Treatment_B: hr_S1S1_trtB
with(as.list(l_params), {
####### SET INTERNAL PARAMETERS #########################################
# Strategy names
v_names_strat <- c("No_Treatment", "Treatment_A", "Treatment_B")
# Number of strategies
n_strat <- length(v_names_strat)
## Treatment_A
# utility impacts
u_S1_trtA <- u_trtA
# include treatment costs
c_S1_trtA <- c_S1 + c_trtA
c_S2_trtA <- c_S2 + c_trtA
## Treatment_B
# progression impacts
r_S1S2_trtB <- -log(1 - p_S1S2) * hr_S1S2_trtB
p_S1S2_trtB <- 1 - exp(-r_S1S2_trtB)
# include treatment costs
c_S1_trtB <- c_S1 + c_trtB
c_S2_trtB <- c_S2 + c_trtB
####### INITIALIZATION #########################################
# Create cost-effectiveness results data frame
df_ce <- data.frame(Strategy = v_names_strat,
Cost = numeric(n_strat),
QALY = numeric(n_strat),
LY = numeric(n_strat),
stringsAsFactors = FALSE)
######### PROCESS ##############################################
for (i in 1:n_strat){
l_params_markov <- list(n_cycles = n_cycles, r_disc = r_disc, v_s_init = v_s_init,
c_H = c_H, c_S1 = c_S2, c_S2 = c_S1, c_D = c_D,
u_H = u_H, u_S1 = u_S2, u_S2 = u_S1, u_D = u_D,
r_HD = r_HD, hr_S1D = hr_S1D, hr_S2D = hr_S2D,
p_HS1 = p_HS1, p_S1H = p_S1H, p_S1S2 = p_S1S2)
if (v_names_strat[i] == "Treatment_A"){
l_params_markov$u_S1 <- u_S1_trtA
l_params_markov$c_S1 <- c_S1_trtA
l_params_markov$c_S2 <- c_S2_trtA
} else if(v_names_strat[i] == "Treatment_B"){
l_params_markov$p_S1S2 <- p_S1S2_trtB
l_params_markov$c_S1 <- c_S1_trtB
l_params_markov$c_S2 <- c_S2_trtB
}
l_result <- run_sick_sicker_model(l_params_markov)
df_ce[i, c("Cost", "QALY", "LY")] <- c(l_result$n_tot_cost,
l_result$n_tot_qaly,
l_result$n_tot_ly)
df_ce[i, "NMB"] <- l_result$n_tot_qaly * wtp - l_result$n_tot_cost
}
return(df_ce)
})
}
## -----------------------------------------------------------------------------
my_params <- c(#Transition probabilities
"p_HS1",
"p_S1H",
"p_S1S2",
#Hazard ratios
"hr_S1",
"hr_S2",
"hr_S1S2_trtB",
#Costs
"c_H",
"c_S1",
"c_S2",
"c_trtA",
"c_trtB",
#Utilities
"u_H",
"u_S1",
"u_S2",
"u_TrtA")
my_dists <- c(#Transition probabilities
"beta",
"beta",
"beta",
#Hazard ratios
"log-normal",
"log-normal",
"log-normal",
#Costs
"gamma",
"gamma",
"gamma",
"gamma",
"gamma",
#Utilities
"truncated-normal",
"truncated-normal",
"truncated-normal",
"truncated-normal")
my_parameterization_types <- c(#Transition Probabilities
"a, b",
"a, b",
"a, b",
#Hazard ratios
"mean, sd",
"mean, sd",
"mean, sd",
#Costs
"shape, scale",
"shape, scale",
"shape, scale",
"shape, scale",
"shape, scale",
#Utilities
"mean, sd, ll, ul",
"mean, sd, ll, ul",
"mean, sd, ll, ul",
"mean, sd, ll, ul")
my_dists_params <- list(#Transition Probabilities
c(7.5, 42.5),
c(12, 12),
c(15, 133),
#Hazard ratios
c(3, 0.5),
c(10, 0.5),
c(0.6, .01),
#Costs
c(44.5, 45),
c(178, 22.5),
c(900, 16.67),
c(576, 21),
c(676, 19),
#Utilities
c(1, 0.01, NA, 1),
c(0.75, 0.02, NA, 1),
c(0.5, 0.03, NA, 1),
c(0.95, 0.02, NA, 1))
my_psa_params <- gen_psa_samp(params = my_params,
dists = my_dists,
parameterization_types = my_parameterization_types,
dists_params = my_dists_params,
n = 100)
## -----------------------------------------------------------------------------
my_params_basecase <- list(p_HS1 = 0.15,
p_S1H = 0.5,
p_S1S2 = 0.105,
r_HD = 0.002,
hr_S1D = 3,
hr_S2D = 10,
hr_S1S2_trtB = 0.6,
c_H = 2000,
c_S1 = 4000,
c_S2 = 15000,
c_D = 0,
c_trtA = 12000,
c_trtB = 13000,
u_H = 1,
u_S1 = 0.75,
u_S2 = 0.5,
u_D = 0,
u_trtA = 0.95,
n_cycles = 75,
v_s_init = c(1, 0, 0, 0),
r_disc = 0.03)
psa_output <- run_psa(psa_samp = my_psa_params,
params_basecase = my_params_basecase,
FUN = simulate_strategies,
outcomes = c("Cost", "QALY", "LY", "NMB"),
strategies = c("No_Treatment", "Treatment_A", "Treatment_B"),
progress = FALSE)
## -----------------------------------------------------------------------------
cea_psa <- make_psa_obj(cost = psa_output$Cost$other_outcome,
effect = psa_output$QALY$other_outcome,
parameters = psa_output$Cost$parameters,
strategies = psa_output$Cost$strategies,
currency = "$")
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