## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.align = "center" ) ## ----setup-------------------------------------------------------------------- # Install and load PERSUADE # devtools::install_github("Bram-R/PERSUADE", quiet = TRUE) # To install the development version of PERSUADE # install.packages("PERSUADE") # To install CRAN version of PERSUADE library(PERSUADE) ## ----data--------------------------------------------------------------------- # Example dataset years <- flexsurv::bc$recyrs # time to event status <- flexsurv::bc$censrec # event indicator group <- flexsurv::bc$group # grouping variable ## ----settings----------------------------------------------------------------- name <- "BC_OS" # project name time_pred_surv_table <- c(0, 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35) # survival table times time_unit <- 1/12 # monthly data in years time_horizon <- 40 # analysis horizon (years) ## ----f_PERSUADE, eval=FALSE--------------------------------------------------- # PERSUADE <- f_PERSUADE( # name = name, # years = years, # status = status, # group = group, # strata = FALSE, # spline_mod = TRUE, # cure_mod = TRUE, # cure_link = "logistic", # options: "logistic", "loglog", "identity", "probit" # time_unit = time_unit, # time_horizon = time_horizon, # time_pred_surv_table = time_pred_surv_table # ) ## ----PERSUADE_res, eval=FALSE------------------------------------------------- # print(PERSUADE) # summary(PERSUADE, type = "km") # summary(PERSUADE, type = "gof") ## ----PERSUADE_plot, eval=FALSE------------------------------------------------ # palette(rainbow(n = 9, s = 1, v = 1, start = 0, end = max(1, 9 - 1)/9, alpha = 1)) # Set colour palette for Figures # plot(PERSUADE, type = "km") # Kaplan-Meier # plot(PERSUADE, type = "ph") # Proportional hazards # plot(PERSUADE, type = "hr") # Hazard functions # plot(PERSUADE, type = "param_models") # Standard parametric fits # plot(PERSUADE, type = "spline_models") # Spline-based fits # plot(PERSUADE, type = "cure_models") # Cure models # palette("default") # Set colour palette to default ## ----PERSUADE_report, eval=FALSE---------------------------------------------- # f_generate_report(PERSUADE) ## ----PERSUADE_export, eval=FALSE---------------------------------------------- # write.csv(PERSUADE$surv_model_excel, # file.path(tempdir(), paste0(name, "_output"), # "PERSUADE_Time-to-event_models_parameters_comma.csv")) # write.csv2(PERSUADE$surv_model_excel, # file.path(tempdir(), paste0(name, "_output"), # "PERSUADE_Time-to-event_models_parameters_semicolon.csv")) ## ----eval=FALSE--------------------------------------------------------------- # f_get_excel_template()