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D55: EHR/registry-like world (noisy severity), non-random trial consent, trial analyses at 12/24/60 months

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Co-Authored-By: Claude Opus 5.5 <[email protected]>
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chendun1995
2026-10-28 16:26:01 -04:00
co-authored by Claude Opus 5.5
parent 307f75b63e
commit d369a16208
8 changed files with 72 additions and 25 deletions
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reports/draft-report.Rmd
+5 -3
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@@ -17,9 +17,9 @@ S <- file.path(root, "results", "summary")
perf <- fread(file.path(S, "perf.csv")); nc <- fread(file.path(S, "nc_reps.csv"))
ncs <- fread(file.path(S, "nc_summary.csv")); reps <- fread(file.path(S, "reps.csv"))
WORLDS <- c("W0", "W1", "W1_rho0", "W2", "W3", "W4", "W5", "WR")
WORLDS <- c("W0", "W1", "W1_rho0", "W2", "W3", "W4", "W5", "WE", "WR")
WLAB <- c(W0 = "W0 Clean", W1 = "W1 Skill", W1_rho0 = "W1 Skill (rho 0)", W2 = "W2 Style",
W3 = "W3 Style -> outcome", W4 = "W4 Deferral", W5 = "W5 Unmeasured severity", WR = "WR Realistic")
W3 = "W3 Style -> outcome", W4 = "W4 Deferral", W5 = "W5 Unmeasured severity", WE = "WE EHR/registry-like", WR = "WR Realistic")
VAR <- c(V2_cluster = "Ignore physician (cluster SE)", V3_random = "Random intercept",
V4_within = "Within-physician (FE)", none = "Trial (no adjustment)")
VCOL <- c("Ignore physician (cluster SE)" = "#2a78d6", "Random intercept" = "#eb6834",
@@ -35,7 +35,9 @@ pp <- function(x, k = 1) formatC(100 * x, format = "f", digits = k)
theme_set(theme_minimal(base_size = 11) + theme(panel.grid.minor = element_blank(),
panel.grid.major.y = element_blank(), strip.text = element_text(face = "bold", hjust = 0),
legend.position = "bottom"))
perf <- perf[analysis %in% c("main", "rct")] # NCE analyses are used only in Table 4
perf_h <- perf[analysis == "rct"] # trials at 12, 24 and 60 months (D55)
perf <- perf[analysis %in% c("main", "rct") & horizon == 60L] # NCE analyses are used only in Table 4
reps <- reps[horizon == 60L]
perf[, key := paste(design, contrast, sep = "|")]
perf <- merge(perf, METH, by = "key")
perf[, method := factor(method, levels = rev(METH$method))]