# Generated by vignette example_diabetes.Rmd: do not edit by hand # Instead edit example_diabetes.Rmd and then run precompile.R skip_on_cran() params <- list(run_tests = FALSE) ## ----code=readLines("children/knitr_setup.R"), include=FALSE-------------------------------------- ## ----eval = FALSE--------------------------------------------------------------------------------- ## library(multinma) ## options(mc.cores = parallel::detectCores()) ## ----setup, echo = FALSE-------------------------------------------------------------------------- library(multinma) nc <- switch(tolower(Sys.getenv("_R_CHECK_LIMIT_CORES_")), "true" =, "warn" = 2, parallel::detectCores()) options(mc.cores = nc) ## ------------------------------------------------------------------------------------------------- head(diabetes) ## ------------------------------------------------------------------------------------------------- db_net <- set_agd_arm(diabetes, study = studyc, trt = trtc, r = r, n = n) db_net ## ----eval=FALSE----------------------------------------------------------------------------------- ## plot(db_net, weight_edges = TRUE, weight_nodes = TRUE) ## ----diabetes_network_plot, echo=FALSE------------------------------------------------------------ plot(db_net, weight_edges = TRUE, weight_nodes = TRUE) + ggplot2::theme(legend.box.margin = ggplot2::unit(c(0, 0, 0, 4), "lines")) ## ------------------------------------------------------------------------------------------------- summary(normal(scale = 100)) ## ------------------------------------------------------------------------------------------------- db_fit_FE <- nma(db_net, trt_effects = "fixed", link = "cloglog", regression = ~offset(log(time)), prior_intercept = normal(scale = 100), prior_trt = normal(scale = 100)) ## ------------------------------------------------------------------------------------------------- db_fit_FE ## ----eval=FALSE----------------------------------------------------------------------------------- ## # Not run ## print(db_fit_FE, pars = c("d", "mu")) ## ----db_FE_pp_plot, fig.width=8, fig.height=6, out.width="100%"----------------------------------- plot_prior_posterior(db_fit_FE) ## ------------------------------------------------------------------------------------------------- summary(normal(scale = 100)) summary(half_normal(scale = 5)) ## ------------------------------------------------------------------------------------------------- db_fit_RE <- nma(db_net, trt_effects = "random", link = "cloglog", regression = ~offset(log(time)), prior_intercept = normal(scale = 10), prior_trt = normal(scale = 10), prior_het = half_normal(scale = 5), init_r = 0.5) ## ------------------------------------------------------------------------------------------------- db_fit_RE ## ----eval=FALSE----------------------------------------------------------------------------------- ## # Not run ## print(db_fit_RE, pars = c("d", "mu", "delta")) ## ----db_RE_pp_plot-------------------------------------------------------------------------------- plot_prior_posterior(db_fit_RE, prior = c("trt", "het")) ## ------------------------------------------------------------------------------------------------- (dic_FE <- dic(db_fit_FE)) ## ------------------------------------------------------------------------------------------------- (dic_RE <- dic(db_fit_RE)) ## ----db_FE_resdev_plot---------------------------------------------------------------------------- plot(dic_FE) ## ----db_RE_resdev_plot---------------------------------------------------------------------------- plot(dic_RE) ## ----diabetes_releff_FE, fig.height=3------------------------------------------------------------- (db_releff_FE <- relative_effects(db_fit_FE, trt_ref = "Diuretic")) plot(db_releff_FE, ref_line = 0) ## ----diabetes_releff_RE, fig.height=3------------------------------------------------------------- (db_releff_RE <- relative_effects(db_fit_RE, trt_ref = "Diuretic")) plot(db_releff_RE, ref_line = 0) ## ----db_pred_FE, fig.height = 2------------------------------------------------------------------- db_pred_FE <- predict(db_fit_FE, newdata = data.frame(time = 3), baseline = distr(qnorm, mean = -4.2, sd = 1.11^-0.5), trt_ref = "Diuretic", type = "response") db_pred_FE plot(db_pred_FE) ## ----db_pred_RE, fig.height = 2------------------------------------------------------------------- db_pred_RE <- predict(db_fit_RE, newdata = data.frame(time = 3), baseline = distr(qnorm, mean = -4.2, sd = 1.11^-0.5), trt_ref = "Diuretic", type = "response") db_pred_RE plot(db_pred_RE) ## ----db_pred_RE_all, fig.height=16---------------------------------------------------------------- db_pred_RE_studies <- predict(db_fit_RE, type = "response") db_pred_RE_studies plot(db_pred_RE_studies) ## ----diabetes_ranks------------------------------------------------------------------------------- (db_ranks <- posterior_ranks(db_fit_RE)) plot(db_ranks) ## ----diabetes_rankprobs--------------------------------------------------------------------------- (db_rankprobs <- posterior_rank_probs(db_fit_RE)) plot(db_rankprobs) ## ----diabetes_cumrankprobs------------------------------------------------------------------------ (db_cumrankprobs <- posterior_rank_probs(db_fit_RE, cumulative = TRUE)) plot(db_cumrankprobs) ## ----diabetes_tests, include=FALSE, eval=params$run_tests----------------------------------------- #--- Test against TSD 2 results --- library(testthat) library(dplyr) tol <- 0.05 tol_dic <- 0.1 # TSD treatment codes # trt_codes <- c(1 = "Diuretic", # 2 = "Placebo", # 3 = "Beta Blocker", # 4 = "CCB", # 5 = "ACE Inhibitor", # 6 = "ARB") # FE Relative effects tsd_FE <- tribble( ~trt , ~mean, ~sd , ~median, ~lower, ~upper, "Placebo" , -0.25, 0.06, -0.25 , -0.36 , -0.14 , "Beta Blocker" , -0.06, 0.06, -0.06 , -0.17 , 0.05 , "CCB" , -0.25, 0.05, -0.25 , -0.36 , -0.15 , "ACE Inhibitor", -0.36, 0.05, -0.36 , -0.46 , -0.25 , "ARB" , -0.45, 0.06, -0.45 , -0.58 , -0.33 , ) %>% mutate(trt = ordered(trt, levels = levels(db_net$treatments))) %>% arrange(trt) db_releff_FE <- as.data.frame(db_releff_FE) test_that("FE relative effects", { expect_equivalent(db_releff_FE$mean, tsd_FE$mean, tolerance = tol) expect_equivalent(db_releff_FE$sd, tsd_FE$sd, tolerance = tol) expect_equivalent(db_releff_FE$`50%`, tsd_FE$median, tolerance = tol) expect_equivalent(db_releff_FE$`2.5%`, tsd_FE$lower, tolerance = tol) expect_equivalent(db_releff_FE$`97.5%`, tsd_FE$upper, tolerance = tol) }) # RE Relative effects tsd_RE <- tribble( ~trt , ~mean, ~sd , ~median, ~lower, ~upper, "Placebo" , -0.29, 0.09, -0.29 , -0.47 , -0.12 , "Beta Blocker" , -0.07, 0.09, -0.07 , -0.25 , 0.10 , "CCB" , -0.24, 0.08, -0.24 , -0.41 , -0.08 , "ACE Inhibitor", -0.40, 0.09, -0.40 , -0.58 , -0.24 , "ARB" , -0.47, 0.11, -0.47 , -0.70 , -0.27 , ) %>% mutate(trt = ordered(trt, levels = levels(db_net$treatments))) %>% arrange(trt) db_releff_RE <- as.data.frame(db_releff_RE) test_that("RE relative effects", { expect_equivalent(db_releff_RE$mean, tsd_RE$mean, tolerance = tol) expect_equivalent(db_releff_RE$sd, tsd_RE$sd, tolerance = tol) expect_equivalent(db_releff_RE$`50%`, tsd_RE$median, tolerance = tol) expect_equivalent(db_releff_RE$`2.5%`, tsd_RE$lower, tolerance = tol) expect_equivalent(db_releff_RE$`97.5%`, tsd_RE$upper, tolerance = tol) }) # Heterogeneity SD db_tau <- as.data.frame(summary(db_fit_RE, pars = "tau")) test_that("RE heterogeneity SD", { expect_equivalent(db_tau$mean, 0.13, tolerance = tol) expect_equivalent(db_tau$sd, 0.04, tolerance = tol) expect_equivalent(db_tau$`50%`, 0.12, tolerance = tol) expect_equivalent(db_tau$`2.5%`, 0.05, tolerance = tol) expect_equivalent(db_tau$`97.5%`, 0.23, tolerance = tol) }) # FE probabilities tsd_pred_FE <- tribble( ~trt , ~mean, ~sd , ~median, ~lower, ~upper, "Diuretic" , 0.065, 0.067, 0.044 , 0.01 ,0.25 , "Placebo" , 0.052, 0.055, 0.034 , 0.01 ,0.20 , "Beta Blocker" , 0.062, 0.064, 0.042 , 0.01 ,0.24 , "CCB" , 0.051, 0.055, 0.034 , 0.01 ,0.20 , "ACE Inhibitor", 0.047, 0.050, 0.031 , 0.00 ,0.18 , "ARB" , 0.043, 0.046, 0.028 , 0.00 ,0.17 , ) %>% mutate(trt = ordered(trt, levels = levels(db_net$treatments))) %>% arrange(trt) db_pred_FE <- as.data.frame(db_pred_FE) test_that("FE predicted probabilities at 3 years", { expect_equivalent(db_pred_FE$mean, tsd_pred_FE$mean, tolerance = tol) expect_equivalent(db_pred_FE$sd, tsd_pred_FE$sd, tolerance = tol) expect_equivalent(db_pred_FE$`50%`, tsd_pred_FE$median, tolerance = tol) expect_equivalent(db_pred_FE$`2.5%`, tsd_pred_FE$lower, tolerance = tol) expect_equivalent(db_pred_FE$`97.5%`, tsd_pred_FE$upper, tolerance = tol) }) # RE probabilities tsd_pred_RE <- tribble( ~trt , ~mean, ~sd , ~median, ~lower, ~upper, "Diuretic" , 0.065, 0.067, 0.044 , 0.01 ,0.25 , "Placebo" , 0.050, 0.053, 0.033 , 0.01 ,0.20 , "Beta Blocker" , 0.061, 0.064, 0.041 , 0.01 ,0.24 , "CCB" , 0.052, 0.056, 0.035 , 0.01 ,0.20 , "ACE Inhibitor", 0.045, 0.048, 0.030 , 0.00 ,0.18 , "ARB" , 0.042, 0.046, 0.028 , 0.00 ,0.17 , ) %>% mutate(trt = ordered(trt, levels = levels(db_net$treatments))) %>% arrange(trt) db_pred_RE <- as.data.frame(db_pred_RE) test_that("RE predicted probabilities at 3 years", { expect_equivalent(db_pred_RE$mean, tsd_pred_RE$mean, tolerance = tol) expect_equivalent(db_pred_RE$sd, tsd_pred_RE$sd, tolerance = tol) expect_equivalent(db_pred_RE$`50%`, tsd_pred_RE$median, tolerance = tol) expect_equivalent(db_pred_RE$`2.5%`, tsd_pred_RE$lower, tolerance = tol) expect_equivalent(db_pred_RE$`97.5%`, tsd_pred_RE$upper, tolerance = tol) }) # RE DIC test_that("RE DIC", { expect_equivalent(dic_RE$resdev, 53.7, tolerance = tol_dic) expect_equivalent(dic_RE$pd, 38.0, tolerance = tol_dic) expect_equivalent(dic_RE$dic, 91.7, tolerance = tol_dic) }) # FE DIC test_that("FE DIC", { expect_equivalent(dic_FE$resdev, 78.25, tolerance = tol_dic) expect_equivalent(dic_FE$pd, 27.0, tolerance = tol_dic) expect_equivalent(dic_FE$dic, 105.2, tolerance = tol_dic) }) # Check that predictions for multiple studies works in any order times <- 1:3 # Baselines named by time bls <- list("1" = distr(qnorm, mean = -4.2, sd = 1.11^-0.5), "2" = distr(qnorm, mean = -4.2, sd = 1.11^-0.5), "3" = distr(qnorm, mean = -4.2, sd = 1.11^-0.5)) db_pred_FE_multi1 <- as.data.frame(predict(db_fit_FE, newdata = data.frame(time = times), baseline = unname(bls), study = time, trt_ref = "Diuretic", type = "response")) db_pred_RE_multi1 <- as.data.frame(predict(db_fit_RE, newdata = data.frame(time = times), baseline = unname(bls), study = time, trt_ref = "Diuretic", type = "response")) db_pred_FE_multi2 <- as.data.frame(predict(db_fit_FE, newdata = data.frame(time = times), baseline = bls, study = time, trt_ref = "Diuretic", type = "response")) db_pred_RE_multi2 <- as.data.frame(predict(db_fit_RE, newdata = data.frame(time = times), baseline = bls, study = time, trt_ref = "Diuretic", type = "response")) db_pred_FE_multi3 <- as.data.frame(predict(db_fit_FE, newdata = data.frame(time = rev(times)), baseline = bls, study = time, trt_ref = "Diuretic", type = "response")) %>% arrange(.study) db_pred_RE_multi3 <- as.data.frame(predict(db_fit_RE, newdata = data.frame(time = rev(times)), baseline = bls, study = time, trt_ref = "Diuretic", type = "response")) %>% arrange(.study) db_pred_FE_multi4 <- as.data.frame(predict(db_fit_FE, newdata = data.frame(time = times), baseline = rev(bls), study = time, trt_ref = "Diuretic", type = "response")) db_pred_RE_multi4 <- as.data.frame(predict(db_fit_RE, newdata = data.frame(time = times), baseline = rev(bls), study = time, trt_ref = "Diuretic", type = "response")) test_that("Predictions for reordered newdata/baselines works", { expect_equivalent(db_pred_FE_multi1$mean, db_pred_FE_multi2$mean, tolerance = tol) expect_equivalent(db_pred_FE_multi1$sd, db_pred_FE_multi2$sd, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`50%`, db_pred_FE_multi2$`50%`, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`2.5%`, db_pred_FE_multi2$`2.5%`, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`97.5%`, db_pred_FE_multi2$`97.5%`, tolerance = tol) expect_equivalent(db_pred_FE_multi1$mean, db_pred_FE_multi3$mean, tolerance = tol) expect_equivalent(db_pred_FE_multi1$sd, db_pred_FE_multi3$sd, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`50%`, db_pred_FE_multi3$`50%`, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`2.5%`, db_pred_FE_multi3$`2.5%`, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`97.5%`, db_pred_FE_multi3$`97.5%`, tolerance = tol) expect_equivalent(db_pred_FE_multi1$mean, db_pred_FE_multi4$mean, tolerance = tol) expect_equivalent(db_pred_FE_multi1$sd, db_pred_FE_multi4$sd, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`50%`, db_pred_FE_multi4$`50%`, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`2.5%`, db_pred_FE_multi4$`2.5%`, tolerance = tol) expect_equivalent(db_pred_FE_multi1$`97.5%`, db_pred_FE_multi4$`97.5%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$mean, db_pred_RE_multi2$mean, tolerance = tol) expect_equivalent(db_pred_RE_multi1$sd, db_pred_RE_multi2$sd, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`50%`, db_pred_RE_multi2$`50%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`2.5%`, db_pred_RE_multi2$`2.5%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`97.5%`, db_pred_RE_multi2$`97.5%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$mean, db_pred_RE_multi3$mean, tolerance = tol) expect_equivalent(db_pred_RE_multi1$sd, db_pred_RE_multi3$sd, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`50%`, db_pred_RE_multi3$`50%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`2.5%`, db_pred_RE_multi3$`2.5%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`97.5%`, db_pred_RE_multi3$`97.5%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$mean, db_pred_RE_multi4$mean, tolerance = tol) expect_equivalent(db_pred_RE_multi1$sd, db_pred_RE_multi4$sd, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`50%`, db_pred_RE_multi4$`50%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`2.5%`, db_pred_RE_multi4$`2.5%`, tolerance = tol) expect_equivalent(db_pred_RE_multi1$`97.5%`, db_pred_RE_multi4$`97.5%`, tolerance = tol) }) # Force clean up rm(list = ls()) gc()