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06B_analyze_scenarios.Rmd
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06B_analyze_scenarios.Rmd
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---
title: "Analysis of HB CE model scenarios"
author: "Niklaus Meier"
date: "`r format(Sys.Date(), '%B %d, %Y')`"
output:
word_document:
fig_caption: yes
fig_height: 6
fig_width: 8
highlight: null
reference_docx: word_template.docx
toc: no
toc_depth: 4
# html_document:
# toc: true
# toc_float: true
# number_sections: true
editor_options:
chunk_output_type: console
---
<!-- Setup -->
```{r setup, include = FALSE}
knitr::opts_chunk$set(echo = TRUE)
#===============================================================================
# Load data
#===============================================================================
load(file = paste0(directories$dir_dat_deriv, "/scenarios_inputs_results.Rdata"))
load(file = paste0(directories$dir_dat_deriv, "/scenarios_model.Rdata"))
load(file = paste0(directories$dir_dat_deriv, "/scenarios_patients.Rdata"))
```
```{r Comparison, echo=FALSE}
color_brew <- colorRampPalette(brewer.pal(4, "Set1") )(4)
#===============================================================================
# ETRANACOGENE
#===============================================================================
#-------------------------------------------------------------------------------
# Costs and QALYs
#-------------------------------------------------------------------------------
print("Outcomes depending on ED relative bleed reduction parameter")
ggplot(scen_analysis$ETRANACOGENE_relative_bleed_reduction$model_results, aes(x = ETRANACOGENE_QALYs_disc , y = ETRANACOGENE_cost_disc/1000000)) +
geom_point()+
geom_text(aes(label=ETRANACOGENE_relative_bleed_reduction), nudge_x = 0.02, nudge_y = 0.02, check_overlap = TRUE, col = "red") +
ylab("Costs [Mio. EUR]") + xlab("QALYs") +
settings$ggplot_theme
print("Outcomes depending on ED maximum bleed reduction period parameter")
ggplot(scen_analysis$ETRANACOGENE_max_bleed_reduction_duration$model_results, aes(x = ETRANACOGENE_QALYs_disc , y = ETRANACOGENE_cost_disc/1000000)) +
geom_point()+
geom_text(aes(label=ETRANACOGENE_max_bleed_reduction_duration), nudge_x = 0.01, nudge_y = 0.01, check_overlap = TRUE, col = "red") +
ylab("Costs [Mio. EUR]") + xlab("QALYs") +
settings$ggplot_theme
print("Outcomes depending on ED bleed rate increase per year parameter")
ggplot(scen_analysis$ETRANACOGENE_bleed_increase_per_year$model_results, aes(x = ETRANACOGENE_QALYs_disc , y = ETRANACOGENE_cost_disc/1000000)) +
geom_point()+
geom_text(aes(label=ETRANACOGENE_bleed_increase_per_year), nudge_x = 0.01, nudge_y = 0.01, check_overlap = TRUE, col = "red") +
ylab("Costs [Mio. EUR]") + xlab("QALYs") +
settings$ggplot_theme
print("Outcomes depending on ED success probability parameter")
ggplot(scen_analysis$ETRANACOGENE_success_prob$model_results, aes(x = ETRANACOGENE_QALYs_disc , y = ETRANACOGENE_cost_disc/1000000)) +
geom_point()+
geom_text(aes(label=ETRANACOGENE_success_prob), nudge_x = 0, nudge_y = 0, check_overlap = TRUE, col = "red") +
ylab("Costs [Mio. EUR]") + xlab("QALYs") +
settings$ggplot_theme
#-------------------------------------------------------------------------------
# Comparisons with Prophylaxis
#-------------------------------------------------------------------------------
print("Incremental Outcomes depending on ED relative bleed reduction parameter")
ggplot(scen_analysis$ETRANACOGENE_relative_bleed_reduction$model_results, aes(x = ETRANACOGENE_PROPHYLAXIS_inc_QALY , y = ETRANACOGENE_PROPHYLAXIS_inc_Costs/1000000)) +
geom_point()+
geom_text(aes(label=ETRANACOGENE_relative_bleed_reduction, size = 12), nudge_x = 0.1, nudge_y = 0.1, check_overlap = TRUE, col = color_brew[3]) +
geom_hline(yintercept = 0) +
geom_vline(xintercept = 0) +
scale_y_continuous(limits=c(-2,2),breaks=seq(-2,2,1)) +
scale_x_continuous(limits=c(-2,2),breaks=seq(-2,2,1)) +
ylab("Cost Difference [Mio. EUR]") + xlab("QALY Difference") +
settings$ggplot_theme +
theme(legend.position = "none")
print("Incremental Outcomes depending on ED maximum bleed reduction period parameter")
ggplot(scen_analysis$ETRANACOGENE_max_bleed_reduction_duration$model_results, aes(x = ETRANACOGENE_PROPHYLAXIS_inc_QALY , y = ETRANACOGENE_PROPHYLAXIS_inc_Costs/1000000)) +
geom_point()+
geom_text(aes(label=ETRANACOGENE_max_bleed_reduction_duration, size = 10), nudge_x = 0.2, nudge_y = 0.1, col = color_brew[3]) +
scale_y_continuous(limits=c(-8,1),breaks=seq(-8,1,1)) +
scale_x_continuous(limits=c(-3,3),breaks=seq(-3,3,0.5)) +
geom_hline(yintercept = 0) +
geom_vline(xintercept = 0) +
ylab("Cost Difference [Mio. EUR]") + xlab("QALY Difference") +
settings$ggplot_theme +
theme(legend.position = "none")
print("Incremental Outcomes depending on ED bleed rate increase per year parameter")
ggplot(scen_analysis$ETRANACOGENE_bleed_increase_per_year$model_results, aes(x = ETRANACOGENE_PROPHYLAXIS_inc_QALY , y = ETRANACOGENE_PROPHYLAXIS_inc_Costs/1000000)) +
geom_point()+
geom_text(aes(label=ETRANACOGENE_bleed_increase_per_year, size = 10), nudge_x = 0.3, nudge_y = 0.05, check_overlap = TRUE, col = color_brew[3]) +
scale_y_continuous(limits=c(-2,-1),breaks=seq(-2,-1,1)) +
scale_x_continuous(limits=c(-3,3),breaks=seq(-3,3,0.5)) +
geom_hline(yintercept = 0) +
geom_vline(xintercept = 0) +
ylab("Cost Difference [Mio. EUR]") + xlab("QALY Difference") +
settings$ggplot_theme +
theme(legend.position = "none")
print("Incremental Outcomes depending on ED success probability parameter")
ggplot(scen_analysis$ETRANACOGENE_success_prob$model_results, aes(x = ETRANACOGENE_PROPHYLAXIS_inc_QALY , y = ETRANACOGENE_PROPHYLAXIS_inc_Costs/1000000)) +
geom_point()+
geom_text(aes(label=ETRANACOGENE_success_prob, size = 12), nudge_x = 0.2, nudge_y = 0.1, col = color_brew[3]) +
scale_y_continuous(limits=c(-8,1),breaks=seq(-8,1,1)) +
scale_x_continuous(limits=c(-3,3),breaks=seq(-3,3,0.5)) +
geom_hline(yintercept = 0) +
geom_vline(xintercept = 0) +
ylab("Cost Difference [Mio. EUR]") + xlab("QALY Difference") +
settings$ggplot_theme +
theme(legend.position = "none")
#===============================================================================
# Prices
#==============================================================================
ggplot(scen_analysis$price_ETRANACOGENE$model_results, aes(y = ETRANACOGENE_PROPHYLAXIS_INMB/1000000 , x = scen_analysis$price_ETRANACOGENE$range/1000000)) +
geom_vline(xintercept = scen_analysis$base_case$model_results$price_ETRANACOGENE/1000000,
color = "grey", linetype="dashed") +
annotate("text",
x= scen_analysis$base_case$model_results$price_ETRANACOGENE/1000000 + 0.05,
y= -2.3,
label= "Base case price",
angle= 90, size = 5, color = "grey") +
geom_point()+
geom_line()+
geom_text(aes(label=format(price_ETRANACOGENE/1000000, big.mark = ",", scientific = FALSE), size = 12), nudge_x = 0.1, nudge_y = 0.85, check_overlap = TRUE, col = color_brew[2]) +
scale_y_continuous(limits=c(-4,4),breaks=seq(-4,4,1)) +
scale_x_continuous(limits=c(0,3.5),breaks=seq(0,3.5,0.5)) +
geom_hline(yintercept = 0) +
geom_vline(xintercept = 0) +
ylab("Incremental NMB [Mio. EUR]") + xlab("Price etranacogene dezaparvovec [Mio. EUR]") +
settings$ggplot_theme +
theme(legend.position = "none")
# price of coagulation factor
ggplot(scen_analysis$price_coagulation_factor_IU$model_results, aes(y = ETRANACOGENE_PROPHYLAXIS_INMB/1000000 , x = scen_analysis$price_coagulation_factor_IU$range)) +
geom_vline(xintercept = scen_analysis$base_case$model_results$price_coagulation_factor_IU,
color = "grey", linetype="dashed") +
annotate("text",
x= scen_analysis$base_case$model_results$price_coagulation_factor_IU + 0.05,
y= -2.3,
label= "Base case price",
angle= 90, size = 5, color = "grey") +
geom_point()+
geom_line()+
geom_text(aes(label=format(price_coagulation_factor_IU, big.mark = ",", scientific = FALSE), size = 12), nudge_x = -0.2, nudge_y = 0, check_overlap = TRUE, col = color_brew[2]) +
scale_y_continuous(limits=c(-4,4),breaks=seq(-4,4,1)) +
scale_x_continuous(limits=c(-0.5,3),breaks=seq(-0.5,3,0.5)) +
geom_hline(yintercept = 0) +
geom_vline(xintercept = 0) +
ylab("Incremental NMB [Mio. EUR]") + xlab("Price per IU of coagulation factor [EUR]") +
settings$ggplot_theme +
theme(legend.position = "none")
# Scenario 7 days bleed disutility
columns <- c("Treatment",
"Baseline QALYs", "Baseline total costs", "Baseline INMB",
"Scenario QALYs", "Scenario total costs", "Scenario INMB")
scenario_table_bleed_disutility <- setNames(data.frame(matrix(data = 0,
nrow = 2,
ncol = length(columns))),
columns)
scenario_table_bleed_disutility[,"Treatment"] <- c("ETRANACOGENE", "Prophylaxis")
scenario_table_bleed_disutility[1,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_bleed_disutility[2,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_bleed_disutility[1,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_bleed_disutility[2,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_bleed_disutility[2,"Baseline INMB"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
scenario_table_bleed_disutility[1,"Scenario QALYs"] <- scen_analysis[["scen_bleed_disutility"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_bleed_disutility[2,"Scenario QALYs"] <- scen_analysis[["scen_bleed_disutility"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_bleed_disutility[1,"Scenario total costs"] <- scen_analysis[["scen_bleed_disutility"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_bleed_disutility[2,"Scenario total costs"] <- scen_analysis[["scen_bleed_disutility"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_bleed_disutility[2,"Scenario INMB"] <- scen_analysis[["scen_bleed_disutility"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
kbl(scenario_table_bleed_disutility, format = "simple", digits = 2, caption = "Comparison 1 day vs 7 day bleed disutility")
# Scenario higher price per hospitalization
columns <- c("Treatment",
"Baseline QALYs", "Baseline total costs", "Baseline costs hosp per bleed", "Baseline INMB",
"Scenario QALYs", "Scenario total costs", "Scenario costs hosp per bleed", "Scenario INMB")
scenario_table_high_price_hosp <- setNames(data.frame(matrix(data = 0,
nrow = 2,
ncol = length(columns))),
columns)
scenario_table_high_price_hosp[,"Treatment"] <- c("ETRANACOGENE", "Prophylaxis")
scenario_table_high_price_hosp[1,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_high_price_hosp[2,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_high_price_hosp[1,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_high_price_hosp[2,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_high_price_hosp[1,"Baseline costs hosp per bleed"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_cost_hospitalization_disc"]][1]
scenario_table_high_price_hosp[2,"Baseline costs hosp per bleed"] <- scen_analysis[["base_case"]][["model_results"]][["PROPHYLAXIS_cost_hospitalization_disc"]][1]
scenario_table_high_price_hosp[2,"Baseline INMB"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
scenario_table_high_price_hosp[1,"Scenario QALYs"] <- scen_analysis[["price_hosp_ICU_days"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1]
scenario_table_high_price_hosp[2,"Scenario QALYs"] <- scen_analysis[["price_hosp_ICU_days"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1]
scenario_table_high_price_hosp[1,"Scenario total costs"] <- scen_analysis[["price_hosp_ICU_days"]][["model_results"]]["ETRANACOGENE_cost_disc"][1]
scenario_table_high_price_hosp[2,"Scenario total costs"] <- scen_analysis[["price_hosp_ICU_days"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1]
scenario_table_high_price_hosp[1,"Scenario costs hosp per bleed"] <- scen_analysis[["price_hosp_ICU_days"]][["model_results"]][["ETRANACOGENE_cost_hospitalization_disc"]][1]
scenario_table_high_price_hosp[2,"Scenario costs hosp per bleed"] <- scen_analysis[["price_hosp_ICU_days"]][["model_results"]][["PROPHYLAXIS_cost_hospitalization_disc"]][1]
scenario_table_high_price_hosp[2,"Scenario INMB"] <- scen_analysis[["price_hosp_ICU_days"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
kbl(scenario_table_high_price_hosp, format = "simple", digits = 2, caption = "Comparison base case vs 5x costs per day ICU")
# Scenario no treatment switching Etranacogene Dezaparvovec
columns <- c("Treatment",
"Baseline QALYs", "Baseline total costs", "Baseline costs FIX prophylaxis", "Baseline INMB",
"Scenario QALYs", "Scenario total costs", "Scenario costs FIX prophylaxis", "Scenario INMB")
scenario_table_ETRANACOGENE_no_switch <- setNames(data.frame(matrix(data = 0,
nrow = 2,
ncol = length(columns))),
columns)
scenario_table_ETRANACOGENE_no_switch[,"Treatment"] <- c("ETRANACOGENE", "Prophylaxis")
scenario_table_ETRANACOGENE_no_switch[1,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_ETRANACOGENE_no_switch[2,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_ETRANACOGENE_no_switch[1,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_ETRANACOGENE_no_switch[2,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_ETRANACOGENE_no_switch[1,"Baseline costs FIX prophylaxis"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_cost_PROPHYLAXIS_disc"]][1]
scenario_table_ETRANACOGENE_no_switch[2,"Baseline costs FIX prophylaxis"] <- scen_analysis[["base_case"]][["model_results"]][["PROPHYLAXIS_cost_PROPHYLAXIS_disc"]][1]
scenario_table_ETRANACOGENE_no_switch[2,"Baseline INMB"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
scenario_table_ETRANACOGENE_no_switch[1,"Scenario QALYs"] <- scen_analysis[["scen_ETRANACOGENE_no_switch"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_ETRANACOGENE_no_switch[2,"Scenario QALYs"] <- scen_analysis[["scen_ETRANACOGENE_no_switch"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_ETRANACOGENE_no_switch[1,"Scenario total costs"] <- scen_analysis[["scen_ETRANACOGENE_no_switch"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_ETRANACOGENE_no_switch[2,"Scenario total costs"] <- scen_analysis[["scen_ETRANACOGENE_no_switch"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_ETRANACOGENE_no_switch[1,"Scenario costs FIX prophylaxis"] <- scen_analysis[["scen_ETRANACOGENE_no_switch"]][["model_results"]][["ETRANACOGENE_cost_PROPHYLAXIS_disc"]][1]
scenario_table_ETRANACOGENE_no_switch[2,"Scenario costs FIX prophylaxis"] <- scen_analysis[["scen_ETRANACOGENE_no_switch"]][["model_results"]][["PROPHYLAXIS_cost_PROPHYLAXIS_disc"]][1]
scenario_table_ETRANACOGENE_no_switch[2,"Scenario INMB"] <- scen_analysis[["scen_ETRANACOGENE_no_switch"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
kbl(scenario_table_ETRANACOGENE_no_switch, format = "simple", digits = 2, caption = "Comparison base case no treatment switching for Etranacogene Dezaparvovec")
# Scenario no vial sharing
columns <- c("Treatment",
"Baseline QALYs", "Baseline total costs", "Baseline costs FIX prophylaxis", "Baseline INMB",
"Scenario QALYs", "Scenario total costs", "Scenario costs FIX prophylaxis", "Scenario INMB")
scenario_table_no_vial_sharing <- setNames(data.frame(matrix(data = 0,
nrow = 2,
ncol = length(columns))),
columns)
scenario_table_no_vial_sharing[,"Treatment"] <- c("ETRANACOGENE", "Prophylaxis")
scenario_table_no_vial_sharing[1,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_no_vial_sharing[2,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_no_vial_sharing[1,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_no_vial_sharing[2,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_no_vial_sharing[1,"Baseline costs FIX prophylaxis"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_cost_PROPHYLAXIS_disc"]][1]
scenario_table_no_vial_sharing[2,"Baseline costs FIX prophylaxis"] <- scen_analysis[["base_case"]][["model_results"]][["PROPHYLAXIS_cost_PROPHYLAXIS_disc"]][1]
scenario_table_no_vial_sharing[2,"Baseline INMB"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
scenario_table_no_vial_sharing[1,"Scenario QALYs"] <- scen_analysis[["scen_no_vial_sharing"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_no_vial_sharing[2,"Scenario QALYs"] <- scen_analysis[["scen_no_vial_sharing"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_no_vial_sharing[1,"Scenario total costs"] <- scen_analysis[["scen_no_vial_sharing"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_no_vial_sharing[2,"Scenario total costs"] <- scen_analysis[["scen_no_vial_sharing"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_no_vial_sharing[1,"Scenario costs FIX prophylaxis"] <- scen_analysis[["scen_no_vial_sharing"]][["model_results"]][["ETRANACOGENE_cost_PROPHYLAXIS_disc"]][1]
scenario_table_no_vial_sharing[2,"Scenario costs FIX prophylaxis"] <- scen_analysis[["scen_no_vial_sharing"]][["model_results"]][["PROPHYLAXIS_cost_PROPHYLAXIS_disc"]][1]
scenario_table_no_vial_sharing[2,"Scenario INMB"] <- scen_analysis[["scen_no_vial_sharing"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
kbl(scenario_table_no_vial_sharing, format = "simple", digits = 2, caption = "Comparison base case no vial sharing")
# Scenario age 18
columns <- c("Treatment",
"Baseline QALYs", "Baseline total costs", "Baseline INMB",
"Scenario QALYs", "Scenario total costs", "Scenario INMB")
scenario_table_age_18 <- setNames(data.frame(matrix(data = 0,
nrow = 2,
ncol = length(columns))),
columns)
scenario_table_age_18[,"Treatment"] <- c("ETRANACOGENE", "Prophylaxis")
scenario_table_age_18[1,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_age_18[2,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_age_18[1,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_age_18[2,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_age_18[1,"Baseline costs FIX prophylaxis"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_cost_PROPHYLAXIS_disc"]][1]
scenario_table_age_18[2,"Baseline costs FIX prophylaxis"] <- scen_analysis[["base_case"]][["model_results"]][["PROPHYLAXIS_cost_PROPHYLAXIS_disc"]][1]
scenario_table_age_18[2,"Baseline INMB"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
scenario_table_age_18[1,"Scenario QALYs"] <- scen_analysis[["age_18"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_age_18[2,"Scenario QALYs"] <- scen_analysis[["age_18"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_age_18[1,"Scenario total costs"] <- scen_analysis[["age_18"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_age_18[2,"Scenario total costs"] <- scen_analysis[["age_18"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_age_18[1,"Scenario costs FIX prophylaxis"] <- scen_analysis[["age_18"]][["model_results"]][["ETRANACOGENE_cost_PROPHYLAXIS_disc"]][1]
scenario_table_age_18[2,"Scenario costs FIX prophylaxis"] <- scen_analysis[["age_18"]][["model_results"]][["PROPHYLAXIS_cost_PROPHYLAXIS_disc"]][1]
scenario_table_age_18[2,"Scenario INMB"] <- scen_analysis[["age_18"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
kbl(scenario_table_age_18, format = "simple", digits = 2, caption = "Comparison base case no vial sharing")
# Scenario age 60
columns <- c("Treatment",
"Baseline QALYs", "Baseline total costs", "Baseline INMB",
"Scenario QALYs", "Scenario total costs", "Scenario INMB")
scenario_table_age_60 <- setNames(data.frame(matrix(data = 0,
nrow = 2,
ncol = length(columns))),
columns)
scenario_table_age_60[,"Treatment"] <- c("ETRANACOGENE", "Prophylaxis")
scenario_table_age_60[1,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_age_60[2,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_age_60[1,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_age_60[2,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_age_60[1,"Baseline costs FIX prophylaxis"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_cost_PROPHYLAXIS_disc"]][1]
scenario_table_age_60[2,"Baseline costs FIX prophylaxis"] <- scen_analysis[["base_case"]][["model_results"]][["PROPHYLAXIS_cost_PROPHYLAXIS_disc"]][1]
scenario_table_age_60[2,"Baseline INMB"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
scenario_table_age_60[1,"Scenario QALYs"] <- scen_analysis[["age_60"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_age_60[2,"Scenario QALYs"] <- scen_analysis[["age_60"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_age_60[1,"Scenario total costs"] <- scen_analysis[["age_60"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_age_60[2,"Scenario total costs"] <- scen_analysis[["age_60"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_age_60[1,"Scenario costs FIX prophylaxis"] <- scen_analysis[["age_60"]][["model_results"]][["ETRANACOGENE_cost_PROPHYLAXIS_disc"]][1]
scenario_table_age_60[2,"Scenario costs FIX prophylaxis"] <- scen_analysis[["age_60"]][["model_results"]][["PROPHYLAXIS_cost_PROPHYLAXIS_disc"]][1]
scenario_table_age_60[2,"Scenario INMB"] <- scen_analysis[["age_60"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
kbl(scenario_table_age_60, format = "simple", digits = 2, caption = "Comparison base case no vial sharing")
# Scenario German utilities from Grochtendreis et al. (2019)
columns <- c("Treatment",
"Baseline QALYs", "Baseline total costs", "Baseline INMB",
"Scenario QALYs", "Scenario total costs", "Scenario INMB")
scenario_table_util_german <- setNames(data.frame(matrix(data = 0,
nrow = 2,
ncol = length(columns))),
columns)
scenario_table_util_german[,"Treatment"] <- c("ETRANACOGENE", "Prophylaxis")
scenario_table_util_german[1,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_util_german[2,"Baseline QALYs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_util_german[1,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_util_german[2,"Baseline total costs"] <- scen_analysis[["base_case"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_util_german[2,"Baseline INMB"] <- scen_analysis[["base_case"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
scenario_table_util_german[1,"Scenario QALYs"] <- scen_analysis[["scen_util_german"]][["model_results"]]["ETRANACOGENE_QALYs_disc"][1,]
scenario_table_util_german[2,"Scenario QALYs"] <- scen_analysis[["scen_util_german"]][["model_results"]]["PROPHYLAXIS_QALYs_disc"][1,]
scenario_table_util_german[1,"Scenario total costs"] <- scen_analysis[["scen_util_german"]][["model_results"]]["ETRANACOGENE_cost_disc"][1,]
scenario_table_util_german[2,"Scenario total costs"] <- scen_analysis[["scen_util_german"]][["model_results"]]["PROPHYLAXIS_cost_disc"][1,]
scenario_table_util_german[2,"Scenario INMB"] <- scen_analysis[["scen_util_german"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][1]
kbl(scenario_table_util_german, format = "simple", digits = 2, caption = "Comparison base case vs. German utilities")
# Comparison Table
# In addition to the previous scenarios, we also add scenarios for the values of two ED properties
# 1. The duration of the maximum bleed reduction (20/30 years)
# 2. The bleed rate increase per year (20/30%)
columns <- c("Scenario",
"Incremental QALYs", "Incremental Costs [EUR]", "INMB [EUR]")
scenario_table_comparison <- setNames(data.frame(matrix(data = 0,
nrow = 12,
ncol = length(columns))),
columns)
scenario_table_comparison[,"Scenario"] <- c("Scenario 1: 7 day bleed disutility",
"Scenario 2: 5x costs per day in ICU",
"Scenario 3: No treatment switching",
"Scenario 4: No vial sharing",
"Scenario 5: Cost-minimization",
"Scenario 6: Age 18",
"Scenario 7: Age 60",
"Scenario 8: German utilities",
"Scenario 9: Duration of maximum bleed reduction 20 years",
"Scenario 10: Duration of maximum bleed reduction 30 years",
"Scenario 11: Bleed rate increase 20% per year",
"Scenario 12: Bleed rate increase 30% per year")
scenario_table_comparison[1,"Incremental QALYs"] <- scenario_table_bleed_disutility[1,"Scenario QALYs"] - scenario_table_bleed_disutility[2,"Scenario QALYs"]
scenario_table_comparison[2,"Incremental QALYs"] <- scenario_table_high_price_hosp[1,"Scenario QALYs"] - scenario_table_high_price_hosp[2,"Scenario QALYs"]
scenario_table_comparison[3,"Incremental QALYs"] <- scenario_table_ETRANACOGENE_no_switch[1,"Scenario QALYs"] - scenario_table_ETRANACOGENE_no_switch[2,"Scenario QALYs"]
scenario_table_comparison[4,"Incremental QALYs"] <- scenario_table_no_vial_sharing[1,"Scenario QALYs"] - scenario_table_no_vial_sharing[2,"Scenario QALYs"]
# For the cost-minimization scenario we simply use baseline values
scenario_table_comparison[5,"Incremental QALYs"] <- scenario_table_bleed_disutility[1,"Baseline QALYs"] - scenario_table_bleed_disutility[2,"Baseline QALYs"]
scenario_table_comparison[6,"Incremental QALYs"] <- scenario_table_age_18[1,"Scenario QALYs"] - scenario_table_age_18[2,"Scenario QALYs"]
scenario_table_comparison[7,"Incremental QALYs"] <- scenario_table_age_60[1,"Scenario QALYs"] - scenario_table_age_60[2,"Scenario QALYs"]
scenario_table_comparison[8,"Incremental QALYs"] <- scenario_table_util_german[1,"Scenario QALYs"] - scenario_table_util_german[2,"Scenario QALYs"]
# Additional scenarios
scenario_table_comparison[9,"Incremental QALYs"] <- scen_analysis[["ETRANACOGENE_max_bleed_reduction_duration"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_inc_QALY"]][5]
scenario_table_comparison[10,"Incremental QALYs"] <- scen_analysis[["ETRANACOGENE_max_bleed_reduction_duration"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_inc_QALY"]][7]
scenario_table_comparison[11,"Incremental QALYs"] <- scen_analysis[["ETRANACOGENE_bleed_increase_per_year"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_inc_QALY"]][5]
scenario_table_comparison[12,"Incremental QALYs"] <- scen_analysis[["ETRANACOGENE_bleed_increase_per_year"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_inc_QALY"]][7]
###
scenario_table_comparison[1,"Incremental Costs [EUR]"] <- scenario_table_bleed_disutility[1,"Scenario total costs"] - scenario_table_bleed_disutility[2,"Scenario total costs"]
scenario_table_comparison[2,"Incremental Costs [EUR]"] <- scenario_table_high_price_hosp[1,"Scenario total costs"] - scenario_table_high_price_hosp[2,"Scenario total costs"]
scenario_table_comparison[3,"Incremental Costs [EUR]"] <- scenario_table_ETRANACOGENE_no_switch[1,"Scenario total costs"] - scenario_table_ETRANACOGENE_no_switch[2,"Scenario total costs"]
scenario_table_comparison[4,"Incremental Costs [EUR]"] <- scenario_table_no_vial_sharing[1,"Scenario total costs"] - scenario_table_no_vial_sharing[2,"Scenario total costs"]
# For the cost-minimization scenario we simply use baseline values
scenario_table_comparison[5,"Incremental Costs [EUR]"] <- scenario_table_bleed_disutility[1,"Baseline total costs"] - scenario_table_bleed_disutility[2,"Baseline total costs"]
scenario_table_comparison[6,"Incremental Costs [EUR]"] <- scenario_table_age_18[1,"Scenario total costs"] - scenario_table_age_18[2,"Scenario total costs"]
scenario_table_comparison[7,"Incremental Costs [EUR]"] <- scenario_table_age_60[1,"Scenario total costs"] - scenario_table_age_60[2,"Scenario total costs"]
scenario_table_comparison[8,"Incremental Costs [EUR]"] <- scenario_table_util_german[1,"Scenario total costs"] - scenario_table_util_german[2,"Scenario total costs"]
# Additional scenarios
scenario_table_comparison[9,"Incremental Costs [EUR]"] <- scen_analysis[["ETRANACOGENE_max_bleed_reduction_duration"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_inc_Costs"]][5]
scenario_table_comparison[10,"Incremental Costs [EUR]"] <- scen_analysis[["ETRANACOGENE_max_bleed_reduction_duration"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_inc_Costs"]][7]
scenario_table_comparison[11,"Incremental Costs [EUR]"] <- scen_analysis[["ETRANACOGENE_bleed_increase_per_year"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_inc_Costs"]][5]
scenario_table_comparison[12,"Incremental Costs [EUR]"] <- scen_analysis[["ETRANACOGENE_bleed_increase_per_year"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_inc_Costs"]][7]
###
scenario_table_comparison[1,"INMB [EUR]"] <- scenario_table_bleed_disutility[2,"Scenario INMB"]
scenario_table_comparison[2,"INMB [EUR]"] <- scenario_table_high_price_hosp[2,"Scenario INMB"]
scenario_table_comparison[3,"INMB [EUR]"] <- scenario_table_ETRANACOGENE_no_switch[2,"Scenario INMB"]
scenario_table_comparison[4,"INMB [EUR]"] <- scenario_table_no_vial_sharing[2,"Scenario INMB"]
# For the cost-minimization scenario, negative incremental costs are equal to INMB
scenario_table_comparison[5,"INMB [EUR]"] <- -scenario_table_comparison[6,"Incremental Costs [EUR]"]
scenario_table_comparison[6,"INMB [EUR]"] <- scenario_table_age_18[2,"Scenario INMB"]
scenario_table_comparison[7,"INMB [EUR]"] <- scenario_table_age_60[2,"Scenario INMB"]
scenario_table_comparison[8,"INMB [EUR]"] <- scenario_table_util_german[2,"Scenario INMB"]
# Additional scenarios
scenario_table_comparison[9,"INMB [EUR]"] <- scen_analysis[["ETRANACOGENE_max_bleed_reduction_duration"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][5]
scenario_table_comparison[10,"INMB [EUR]"] <- scen_analysis[["ETRANACOGENE_max_bleed_reduction_duration"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][7]
scenario_table_comparison[11,"INMB [EUR]"] <- scen_analysis[["ETRANACOGENE_bleed_increase_per_year"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][5]
scenario_table_comparison[12,"INMB [EUR]"] <- scen_analysis[["ETRANACOGENE_bleed_increase_per_year"]][["model_results"]][["ETRANACOGENE_PROPHYLAXIS_INMB"]][7]
kbl(scenario_table_comparison, format = "simple", digits = 2, caption = "Comparison Table all scenarios")
```
# System information
```{r sysinfo, echo = TRUE, results = 'asis'}
Sys.info()
sessionInfo(package = NULL)
```
```{r remove, include = FALSE}
rm(color_brew, columns, ETRA, i, summary_costs,
patient_results_combined, model_results_combined,
scen_analysis,
scenario_table_age_18,
scenario_table_age_60,
scenario_table_bleed_disutility,
scenario_table_ETRANACOGENE_no_switch,
scenario_table_high_price_hosp,
scenario_table_no_vial_sharing,
scenario_table_util_german,
scenario_table_comparison)
gc()
```