@@ -20488,30 +20488,30 @@
maicplus coverage - 54.75%
-
+
| 52 |
- 1x |
+ ! |
names(tte_ipd) <- toupper(names(tte_ipd))
|
-
+
| 53 |
- 1x |
+ ! |
names(tte_pseudo_ipd) <- toupper(names(tte_pseudo_ipd))
|
-
+
| 54 |
- 1x |
+ ! |
trt_var_ipd <- toupper(trt_var_ipd)
|
-
+
| 55 |
- 1x |
+ ! |
trt_var_agd <- toupper(trt_var_agd)
|
@@ -20530,9 +20530,9 @@ maicplus coverage - 54.75%
# pre check
-
+
| 58 |
- 1x |
+ ! |
if (!"maicplus_estimate_weights" %in% class(weights_object)) {
|
@@ -20551,9 +20551,9 @@ maicplus coverage - 54.75%
}
-
+
| 61 |
- 1x |
+ ! |
if (!all(c("USUBJID", "TIME", "EVENT", trt_var_ipd) %in% names(tte_ipd))) {
|
@@ -20572,9 +20572,9 @@ maicplus coverage - 54.75%
}
-
+
| 64 |
- 1x |
+ ! |
if (!all(c("TIME", "EVENT", trt_var_agd) %in% names(tte_pseudo_ipd))) {
|
@@ -20593,9 +20593,9 @@ maicplus coverage - 54.75%
}
-
+
| 67 |
- 1x |
+ ! |
km_layout <- match.arg(km_layout, choices = c("all", "by_trial", "by_arm"), several.ok = FALSE)
|
@@ -20614,37 +20614,37 @@ maicplus coverage - 54.75%
# preparing data
-
+
| 70 |
- 1x |
+ ! |
is_anchored <- !is.null(trt_common)
|
-
+
| 71 |
- 1x |
+ ! |
tte_ipd <- tte_ipd[tte_ipd[[trt_var_ipd]] %in% c(trt_ipd, trt_common), , drop = FALSE]
|
-
+
| 72 |
- 1x |
+ ! |
tte_pseudo_ipd <- tte_pseudo_ipd[tte_pseudo_ipd[[trt_var_agd]] %in% c(trt_agd, trt_common), , drop = FALSE]
|
-
+
| 73 |
- 1x |
+ ! |
tte_ipd$weights <- weights_object$data$weights[match(weights_object$data$USUBJID, tte_ipd$USUBJID)]
|
-
+
| 74 |
- 1x |
+ ! |
tte_pseudo_ipd$weights <- 1
|
@@ -20656,37 +20656,37 @@ maicplus coverage - 54.75%
-
+
| 76 |
- 1x |
+ ! |
tte_ipd$TIME <- get_time_as(tte_ipd$TIME, as = time_scale)
|
-
+
| 77 |
- 1x |
+ ! |
tte_pseudo_ipd$TIME <- get_time_as(tte_pseudo_ipd$TIME, as = time_scale)
|
-
+
| 78 |
- 1x |
+ ! |
my_survfit <- function(data, weighted = FALSE) {
|
-
+
| 79 |
- 6x |
+ ! |
if (weighted) {
|
-
+
| 80 |
- 2x |
+ ! |
survfit(Surv(TIME, EVENT) ~ 1, data = data, conf.type = km_conf_type, weights = data$weights)
|
@@ -20698,9 +20698,9 @@ maicplus coverage - 54.75%
} else {
-
+
| 82 |
- 4x |
+ ! |
survfit(Surv(TIME, EVENT) ~ 1, data = data, conf.type = km_conf_type)
|
@@ -20726,9 +20726,9 @@ maicplus coverage - 54.75%
-
+
| 86 |
- 1x |
+ ! |
if (!is_anchored) {
|
@@ -20782,58 +20782,58 @@ maicplus coverage - 54.75%
basic_kmplot2(kmlist, kmlist_name, ...)
-
+
| 94 |
- 1x |
+ ! |
} else if (is_anchored) {
|
-
+
| 95 |
- 1x |
+ ! |
all_km <- list(
|
-
+
| 96 |
- 1x |
+ ! |
kmobj_A = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_ipd, ]),
|
-
+
| 97 |
- 1x |
+ ! |
kmobj_B = my_survfit(data = tte_pseudo_ipd[tte_pseudo_ipd[, trt_var_agd] == trt_agd, ]),
|
-
+
| 98 |
- 1x |
+ ! |
kmobj_A_adj = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_ipd, ], weighted = TRUE),
|
-
+
| 99 |
- 1x |
+ ! |
kmobj_C = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_common, ]),
|
-
+
| 100 |
- 1x |
+ ! |
kmobj_C_adj = my_survfit(data = tte_ipd[tte_ipd[, trt_var_ipd] == trt_common, ], weighted = TRUE),
|
-
+
| 101 |
- 1x |
+ ! |
kmobj_C_agd = my_survfit(data = tte_pseudo_ipd[tte_pseudo_ipd[, trt_var_agd] == trt_common, ])
|
@@ -20852,44 +20852,44 @@ maicplus coverage - 54.75%
-
+
| 104 |
- 1x |
+ ! |
kmlist_combined <- list()
|
-
+
| 105 |
- 1x |
+ ! |
if (km_layout %in% c("by_trial", "all")) {
|
-
+
| 106 |
- 1x |
+ ! |
kmlist_1_2 <- list(
|
-
+
| 107 |
- 1x |
+ ! |
setNames(
|
-
+
| 108 |
- 1x |
+ ! |
all_km[c(4, 1, 3, 5)],
|
-
+
| 109 |
- 1x |
+ ! |
c(trt_ipd, trt_common, paste0(trt_ipd, " (weighted)"), paste0(trt_common, " (weighted)"))
|
@@ -20901,9 +20901,9 @@ maicplus coverage - 54.75%
),
-
+
| 111 |
- 1x |
+ ! |
setNames(all_km[c(6, 2)], c(trt_common, trt_agd))
|
@@ -20915,23 +20915,23 @@ maicplus coverage - 54.75%
)
-
+
| 113 |
- 1x |
+ ! |
names(kmlist_1_2) <- c(
|
-
+
| 114 |
- 1x |
+ ! |
paste0("Kaplan-Meier Curves \n(", trt_ipd, " vs ", trt_common, ") in the IPD trial"),
|
-
+
| 115 |
- 1x |
+ ! |
paste0("Kaplan-Meier Curves \n(", trt_agd, " vs ", trt_common, ") in the AgD trial")
|
@@ -20943,9 +20943,9 @@ maicplus coverage - 54.75%
)
-
+
| 117 |
- 1x |
+ ! |
kmlist_combined <- c(kmlist_combined, kmlist_1_2)
|
@@ -20957,9 +20957,9 @@ maicplus coverage - 54.75%
}
-
+
| 119 |
- 1x |
+ ! |
if (km_layout %in% c("by_arm", "all")) {
|
@@ -21034,9 +21034,9 @@ maicplus coverage - 54.75%
}
-
+
| 130 |
- 1x |
+ ! |
if (km_layout == "all") {
|
@@ -21062,51 +21062,51 @@ maicplus coverage - 54.75%
-
+
| 134 |
- 1x |
+ ! |
splots <- mapply(
|
-
+
| 135 |
- 1x |
+ ! |
FUN = basic_kmplot2,
|
-
+
| 136 |
- 1x |
+ ! |
kmlist = kmlist_combined,
|
-
+
| 137 |
- 1x |
+ ! |
kmlist_name = lapply(kmlist_combined, names),
|
-
+
| 138 |
- 1x |
+ ! |
main_title = names(kmlist_combined),
|
-
+
| 139 |
- 1x |
+ ! |
MoreArgs = list(...),
|
-
+
| 140 |
- 1x |
+ ! |
SIMPLIFY = FALSE
|
@@ -21118,9 +21118,9 @@ maicplus coverage - 54.75%
)
-
+
| 142 |
- 1x |
+ ! |
survminer::arrange_ggsurvplots(splots, nrow = 1 + (km_layout == "all"))
|
@@ -21363,16 +21363,16 @@ maicplus coverage - 54.75%
-
+
| 177 |
- 2x |
+ ! |
if (is.null(use_line_types)) {
|
-
+
| 178 |
- 2x |
+ ! |
use_line_types <- c(1, 1, 2, 2)
|
@@ -21391,16 +21391,16 @@ maicplus coverage - 54.75%
-
+
| 181 |
- 2x |
+ ! |
if (is.null(use_colors)) {
|
-
+
| 182 |
- 2x |
+ ! |
use_colors <- c("#5450E4", "#00857C", "#6ECEB2", "#7B68EE")
|
@@ -21426,156 +21426,156 @@ maicplus coverage - 54.75%
# Produce the Kaplan-Meier plot
-
+
| 186 |
- 2x |
+ ! |
survminer_plot <- survminer::ggsurvplot(kmlist,
|
-
+
| 187 |
- 2x |
+ ! |
linetype = use_line_types,
|
-
+
| 188 |
- 2x |
+ ! |
palette = use_colors,
|
-
+
| 189 |
- 2x |
+ ! |
size = 0.2,
|
-
+
| 190 |
- 2x |
+ ! |
combine = TRUE,
|
-
+
| 191 |
- 2x |
+ ! |
risk.table = show_risk_set,
|
-
+
| 192 |
- 2x |
+ ! |
risk.table.y.text.col = TRUE,
|
-
+
| 193 |
- 2x |
+ ! |
risk.table.y.text = FALSE,
|
-
+
| 194 |
- 2x |
+ ! |
break.x.by = break_x_by,
|
-
+
| 195 |
- 2x |
+ ! |
censor = censor,
|
-
+
| 196 |
- 2x |
+ ! |
censor.size = 2,
|
-
+
| 197 |
- 2x |
+ ! |
xlab = "Time",
|
-
+
| 198 |
- 2x |
+ ! |
ylab = endpoint_name,
|
-
+
| 199 |
- 2x |
+ ! |
legend.title = "Treatment",
|
-
+
| 200 |
- 2x |
+ ! |
legend = c(0.85, 0.82),
|
-
+
| 201 |
- 2x |
+ ! |
title = paste0(main_title, "\nEndpoint: ", endpoint_name),
|
-
+
| 202 |
- 2x |
+ ! |
legend.labs = kmlist_name,
|
-
+
| 203 |
- 2x |
+ ! |
tables.theme = survminer::theme_cleantable(),
|
-
+
| 204 |
- 2x |
+ ! |
ggtheme = ggplot2::theme_classic(base_size = 10),
|
-
+
| 205 |
- 2x |
+ ! |
fontsize = 3,
|
-
+
| 206 |
- 2x |
+ ! |
conf.int = FALSE,
|
-
+
| 207 |
- 2x |
+ ! |
xlim = xlim
|
@@ -21587,9 +21587,9 @@ maicplus coverage - 54.75%
)
-
+
| 209 |
- 2x |
+ ! |
survminer_plot
|
@@ -22398,14 +22398,14 @@ maicplus coverage - 54.75%
| 35 |
- 16x |
+ 14x |
factor <- match.arg(factor, several.ok = TRUE)
|
| 36 |
- 16x |
+ 14x |
if (!exists("time_conversion", settings_env)) {
|
@@ -22433,7 +22433,7 @@ maicplus coverage - 54.75%
| 40 |
- 16x |
+ 14x |
settings_env$time_conversion[factor]
|
@@ -22524,14 +22524,14 @@ maicplus coverage - 54.75%
| 53 |
- 16x |
+ 14x |
as <- match.arg(as)
|
| 54 |
- 16x |
+ 14x |
times / get_time_conversion(as)
|