Showing content from http://cran.rstudio.com/web/packages/Rcpp/../RcppArray/../Rcpp/../trtswitch/vignettes/msm.R below:
## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(trtswitch) library(dplyr, warn.conflicts = FALSE) library(ggplot2) ## ----data example 1----------------------------------------------------------- sim1 <- tssim( tdxo = 0, coxo = 0, p_R = 0.5, p_X_1 = 0.3, p_X_0 = 0.3, rate_T = 0.002, beta1 = -0.5, beta2 = 0.3, gamma0 = 0.3, gamma1 = -0.9, gamma2 = 0.7, gamma3 = 1.1, gamma4 = -0.8, zeta0 = -3.5, zeta1 = 0.5, zeta2 = 0.2, zeta3 = -0.4, alpha0 = 0.5, alpha1 = 0.5, alpha2 = 0.4, theta1_1 = -0.4, theta1_0 = -0.4, theta2 = 0.2, rate_C = 0.0000855, followup = 20, days = 30, n = 500, NSim = 100, seed = 314159) ## ----analysis example 1------------------------------------------------------- fit1 <- msm( sim1[[1]], id = "id", tstart = "tstart", tstop = "tstop", event = "Y", treat = "trtrand", swtrt = "xo", swtrt_time = "xotime", base_cov = "bprog", numerator = "bprog", denominator = c("bprog", "L"), ns_df = 3, swtrt_control_only = TRUE, boot = FALSE) ## ----switching models example 1----------------------------------------------- # denominator switching model fit fit1$fit_switch[[1]]$fit_den$parest[, c("param", "beta", "sebeta", "z")] # numerator switching model fit fit1$fit_switch[[1]]$fit_num$parest[, c("param", "beta", "sebeta", "z")] ## ----weights example 1-------------------------------------------------------- # unstabilized weights ggplot(fit1$data_outcome %>% filter(trtrand == 0), aes(x = unstabilized_weight)) + geom_density(fill="#77bd89", color="#1f6e34", alpha=0.8) + scale_x_continuous("unstabilized weights") # stabilized weights ggplot(fit1$data_outcome %>% filter(trtrand == 0), aes(x = stabilized_weight)) + geom_density(fill="#77bd89", color="#1f6e34", alpha=0.8) + scale_x_continuous("stabilized weights") ## ----cox example 1------------------------------------------------------------ fit1$fit_outcome$parest[, c("param", "beta", "sebeta", "z")] exp(fit1$fit_outcome$parest[1, c("beta", "lower", "upper")])
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