fixed error in df3

jinseob2kim · Oct 22, 2024 · 0ad7167 · 0ad7167
1 parent 0a59f2c
commit 0ad7167
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Showing 3 changed files with 20 additions and 12 deletions.
diff --git a/R/jskm.R b/R/jskm.R
@@ -129,7 +129,7 @@ jskm <- function(sfit,
   n.risk <- n.censor <- surv <- strata <- lower <- upper <- NULL
 
   times <- seq(0, max(sfit$time), by = timeby)
-  if (!is.null(theme) && theme == "nejm") legendposition <- c(1, 0.5)
+  if (!is.null(theme) && theme == "nejm") legendposition <- legendposition
   if (is.null(subs)) {
     if (length(levels(summary(sfit)$strata)) == 0) {
       subs1 <- 1
@@ -190,7 +190,7 @@ jskm <- function(sfit,
       L <- summary(sfit)$table["0.95LCL"][[1]]
       U <- summary(sfit)$table["0.95UCL"][[1]]
       median_time <- summary(sfit)$table["median"][[1]]
-      ystratalabs2 <- paste0(ystratalabs, " (median : ", median_time, ", 0.95 CI : ",L, "-", U, ")")
+      ystratalabs2 <- paste0(ystratalabs, " (median : ", median_time, ", 95%CI : ",L, "-", U, ")")
     } else {
       # [subs1]
       if (is.null(ystratalabs)) 
@@ -200,7 +200,7 @@ jskm <- function(sfit,
         L <- summary(sfit)$table[,"0.95LCL"][[i]]
         U <- summary(sfit)$table[,"0.95UCL"][[i]]
         median_time <- summary(sfit)$table[,"median"][[i]]
-        ystratalabs2 <- c(ystratalabs2, paste0(ystratalabs[[i]], " (median : ", median_time, ", 0.95 CI : ",L, "-", U, ")"))
+        ystratalabs2 <- c(ystratalabs2, paste0(ystratalabs[[i]], " (median : ", median_time, ", 95%CI : ",L, "-", U, ")"))
       }
     }
   }
@@ -377,6 +377,10 @@ jskm <- function(sfit,
     scale_x_continuous(xlabs, breaks = times, limits = xlims) +
     scale_y_continuous(ylabs, limits = ylims, labels = scale_labels)
 
+
+
+
+
   if (!is.null(theme) && theme == "jama") {
     p <- p + theme(
       panel.grid.major.x = element_blank()
@@ -467,6 +471,8 @@ jskm <- function(sfit,
   }
 
   # Add median value
+
+
   if (med == TRUE & is.null(cut.landmark) & is.null(status.cmprsk)){
     if (length(levels(summary(sfit)$strata)) == 0) {
       median_time <- summary(sfit)$table["median"][[1]]
@@ -506,7 +512,7 @@ jskm <- function(sfit,
 
   # Add 95% CI to plot
   if (ci == TRUE) {
-    if (med == FALSE | !is.null(status.cmprsk)) {
+    if (med == FALSE | !is.null(status.cmprsk) | (!is.null(theme) && theme == "nejm")) {
       if (all(linecols2 == "black")) {
         p <- p + geom_ribbon(data = df, aes(ymin = lower, ymax = upper), alpha = 0.25, colour = NA)
       } else if (is.null(col.pal)) {
@@ -705,7 +711,8 @@ jskm <- function(sfit,
 
   if (!is.null(theme) && theme == "nejm") {
     p2 <- p1 + coord_cartesian(ylim = nejm.infigure.ylim) + theme(axis.title.x = element_blank(), axis.title.y = element_blank(),
-                                                                  axis.text = element_text(size = 10 * nejm.infigure.ratiow)
+                                                                  axis.text = element_text(size = 10 * nejm.infigure.ratiow), 
+
     ) + guides(colour = "none", linetype = "none")
     p <- p + patchwork::inset_element(p2, 1 - nejm.infigure.ratiow, 1 - nejm.infigure.ratioh, 1, 1, align_to = "panel")
   }
@@ -719,4 +726,5 @@ jskm <- function(sfit,
   } else {
     p
   }
-}
+}
+
diff --git a/R/svyjskm.R b/R/svyjskm.R
@@ -90,7 +90,7 @@ svyjskm <- function(sfit,
                     ...) {
   surv <- strata <- lower <- upper <- NULL
 
-  if (!is.null(theme) && theme == "nejm") legendposition <- c(1, 0.5)
+  if (!is.null(theme) && theme == "nejm") legendposition <- legendposition
   if (is.null(timeby)) {
     if (inherits(sfit, "svykmlist")) {
       timeby <- signif(max(sapply(sfit, function(x) {
@@ -264,7 +264,7 @@ svyjskm <- function(sfit,
     times <- seq(0, max(sfit$time), by = timeby)
     if (is.null(ystratalabs)) {
       ystratalabs <- "All"
-      ystratalabs2 <- paste0(ystratalabs, " (median : ", unique(df3$med), ")")
+      ystratalabs2 <- paste0(ystratalabs, " (median : ", unique(df$med), ")")
     }
     if (is.null(xlims)) {
       xlims <- c(0, max(sfit$time))
@@ -289,14 +289,14 @@ svyjskm <- function(sfit,
 
   # Final changes to data for survival plot
   levels(df$strata) <- ystratalabs
-  zeros <- if (med == T){
+  zeros <- if (med == T & is.null(cut.landmark)){
     data.frame("strata" = factor(ystratalabs, levels = levels(df$strata)), "time" = 0, "surv" = 1, "med" = 0.5)
   } else {
     data.frame("strata" = factor(ystratalabs, levels = levels(df$strata)), "time" = 0, "surv" = 1)
   }
 
   if (ci) {
-    if (med == T){
+    if (med == T & is.null(cut.landmark)){
       zeros$med <- NULL  
       zeros$upper <- 1
       zeros$lower <- 1

diff --git a/tests/testthat/test-km.R b/tests/testthat/test-km.R
@@ -7,7 +7,7 @@ library(ggplot2)
 test_that("Run jskm", {
   fit <- survfit(Surv(time, status) ~ rx, data = colon)
   expect_is(jskm(fit, timeby = 500, table = T, pval = T), "gg")
-  expect_is(jskm(fit,
+  expect_is(jskm(fit, med = T,
     table = T, pval = T, label.nrisk = "No. at risk", timeby = 365, xlabs = "Time(Day)", ylabs = "Survival", marks = F, xlims = c(0, 3500), ylims = c(0.25, 1),
     ystratalabs = c("Obs", "Lev", "Lev + 5FU"), ystrataname = "rx"
   ), "gg")
@@ -37,7 +37,7 @@ test_that("Run svyjskm", {
   s1 <- survey::svykm(Surv(time, status > 0) ~ sex, design = dpbc, se = T)
   expect_is(svyjskm(s1, ci = T), "gg")
   expect_is(svyjskm(s1, ci = F, ylabs = "Suvrival (%)", surv.scale = "percent"), "gg")
-  expect_is(svyjskm(s1, table = T, pval = T, design = dpbc), "gg")
+  expect_is(svyjskm(s1, table = T, pval = T, design = dpbc, med = T), "gg")
   expect_is(svyjskm(s1, ci = T, cumhaz = T), "gg")
   expect_is(svyjskm(s1, ci = F, cumhaz = T), "gg")
   s2 <- survey::svykm(Surv(time, status > 0) ~ sex, design = dpbc, se = F)