s

Author: jinseob2kim

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: jskm
 Title: Kaplan-Meier Plot with 'ggplot2'
-Version: 0.3.0
-Date: 2019-02-15
+Version: 0.3.1
+Date: 2019-03-12
 Authors@R: c(person("Jinseob", "Kim", email = "[email protected]", role = c("aut", "cre"),  comment = c(ORCID = "0000-0002-9403-605X")),
              person("Zarathu", role = c("cph", "fnd"))
              )

NEWS.md

@@ -1,3 +1,11 @@
+# jskm 0.3.1
+
+## Update
+
+* The p-value is expressed as the value rounded to the 3rd decimal place.
+
+* Add **pval.testname** option, p-value is expressed with **(Log-rank)** text if **pval.testname == T**.
+
 # jskm 0.3.0
 
 ## New feature

R/jskm.R

@@ -15,6 +15,7 @@
 #' @param pval logical: add the pvalue to the plot?
 #' @param pval.size numeric value specifying the p-value text size. Default is 5.
 #' @param pval.coord numeric vector, of length 2, specifying the x and y coordinates of the p-value. Default values are NULL
+#' @param pval.testname logical: add '(Log-rank)' text to p-value. Default = F
 #' @param marks logical: should censoring marks be added?
 #' @param shape what shape should the censoring marks be, default is a vertical line
 #' @param legend logical. should a legend be added to the plot?
@@ -88,6 +89,7 @@ jskm <- function(sfit,
                  pval = FALSE,
                  pval.size = 5, 
                  pval.coord = c(NULL, NULL),
+                 pval.testname = F,
                  marks = TRUE,
                  shape = 3,
                  legend = TRUE,
@@ -292,7 +294,10 @@ jskm <- function(sfit,
       pvalue <- summary(sdiff)$logtest["pvalue"]
     }
 
-    pvaltxt <- ifelse(pvalue < 0.0001,"p < 0.0001",paste("p =", signif(pvalue, 3)))
+    pvaltxt <- ifelse(pvalue < 0.0001,"p < 0.0001",paste("p =", round(pvalue, 3)))
+    
+    if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
+    
     # MOVE P-VALUE LEGEND HERE BELOW [set x and y]
     if (is.null(pval.coord)){
       p <- p + annotate("text",x = (as.integer(max(sfit$time)/5)), y = 0.1 + ylims[1],label = pvaltxt, size  = pval.size)

R/svyjskm.R

@@ -13,6 +13,7 @@
 #' @param pval logical: add the pvalue to the plot?, Default: FALSE
 #' @param pval.size numeric value specifying the p-value text size. Default is 5.
 #' @param pval.coord numeric vector, of length 2, specifying the x and y coordinates of the p-value. Default values are NULL
+#' @param pval.testname logical: add '(Log-rank)' text to p-value. Default = F
 #' @param legend logical. should a legend be added to the plot? Default: TRUE
 #' @param ci logical. Should confidence intervals be plotted. Default = NULL
 #' @param legendposition numeric. x, y position of the legend if plotted. Default: c(0.85, 0.8)
@@ -56,6 +57,7 @@ svyjskm <- function(sfit,
                     pval = FALSE,
                     pval.size = 5, 
                     pval.coord = c(NULL, NULL),
+                    pval.testname = F,
                     legend = TRUE,
                     legendposition=c(0.85,0.8),
                     ci = NULL,
@@ -224,7 +226,9 @@ svyjskm <- function(sfit,
     }
     pvalue <- sdiff$p.value
 
-    pvaltxt <- ifelse(pvalue < 0.0001,"p < 0.0001",paste("p =", signif(pvalue, 3)))
+    pvaltxt <- ifelse(pvalue < 0.0001,"p < 0.0001",paste("p =", round(pvalue, 3)))
+    if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
+    
     # MOVE P-VALUE LEGEND HERE BELOW [set x and y]
     if (is.null(pval.coord)){
       p <- p + annotate("text",x = (as.integer(max(sapply(sfit, function(x){max(x$time)/5})))), y = 0.1 + ylims[1],label = pvaltxt, size  = pval.size)

man/jskm.Rd

@@ -10,7 +10,7 @@ test_that("Run jskm", {
        ystratalabs = c("Obs", "Lev", "Lev + 5FU"), ystrataname = "rx"), "gtable")
   expect_is(jskm(fit, timeby=500), "gg")
   expect_is(jskm(fit, timeby=500, main = "kaplan", xlabs = "time", ylabs = "Suvrival (%)", surv.scale = "percent"), "gg")
-  expect_is(jskm(fit, pval.size = 7, pval.coord = c(100, 0.2)), "gg")
+  expect_is(jskm(fit, pval.size = 7, pval.coord = c(100, 0.2),  pval.testname = T), "gg")
   expect_is(jskm(fit, timeby=500, ci = T), "gg")
   expect_is(jskm(fit, timeby=500, legend = F), "gg")
   expect_is(jskm(fit, timeby=500, cumhaz = T), "gg")
@@ -39,7 +39,7 @@ test_that("Run svyjskm", {
   expect_is(svyjskm(s1, ci = F, cumhaz = T), "gg")
   s2 <- survey::svykm(Surv(time,status>0)~sex, design=dpbc, se = F)
   expect_is(svyjskm(s2, ci = F), "gg")
-  expect_is(svyjskm(s2, design = dpbc, pval = T, pval.size = 7, pval.coord = c(100, 0.2)), "gg")
+  expect_is(svyjskm(s2, design = dpbc, pval = T, pval.size = 7, pval.coord = c(100, 0.2), pval.testname = T), "gg")
   #pv <- svyjskm(s2, pval = T, design = dpbc)
   #expect_is(pv, "gg")
   expect_error(svyjskm(s2, ci = T))