Commit ⋅ jinseob2kim/jskm

      }
  }
  
  if (class(sfit) == "svykmlist"){
    if(is.null(ystrataname)) ystrataname <- as.character(formula(sfit)[[3]])
    if (is.null(ci)){
  if (is.null(ci)){
    if (class(sfit) == "svykmlist"){
      ci <- "varlog" %in% names(sfit[[1]])
    } else if (class(sfit) == "svykm"){
      ci <- "varlog" %in% names(sfit)
    }
  }
  
  
  if (ci & !is.null(cut.landmark)){
    if (is.null(design)){
      design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
      if ("error" %in% class(design)){
        stop("'pval' option requires design object. please input 'design' option") 
      }
    }
    var.time <- as.character(formula(sfit)[[2]][[2]])
    var.event <- as.character(formula(sfit)[[2]][[3]])
    if (length(var.event) > 1){
      var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
      var.event <- var.event[sapply(var.event, function(x) {"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))})]
    }
    design1 <- design
    design1$variables[[var.event]][design1$variables[[var.time]] >= cut.landmark] <- 0
    design1$variables[[var.time]][design1$variables[[var.time]] >= cut.landmark] <- cut.landmark
    
    sfit2 <- survey::svykm(formula(sfit), design = subset(design, get(var.time) >= cut.landmark), se = T)
  }
  
  
  
  
  if (class(sfit) == "svykmlist"){
    if(is.null(ystrataname)) ystrataname <- as.character(formula(sfit)[[3]])

    if (ci){
      if ("varlog" %in% names(sfit[[1]])){
        df <- Reduce(rbind, lapply(names(sfit), function(x){data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv, "lower" = pmax(0, exp(log(sfit[[x]]$surv) - 1.96 * sqrt(sfit[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit[[x]]$surv) + 1.96 * sqrt(sfit[[x]]$varlog))))}))
        df <- do.call(rbind, lapply(names(sfit), function(x){data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv, "lower" = pmax(0, exp(log(sfit[[x]]$surv) - 1.96 * sqrt(sfit[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit[[x]]$surv) + 1.96 * sqrt(sfit[[x]]$varlog))))}))
        if (!is.null(cut.landmark)){
          df2 <- do.call(rbind, lapply(names(sfit2), function(x){data.frame("strata" = x, "time" = sfit2[[x]]$time, "surv" = sfit2[[x]]$surv, "lower" = pmax(0, exp(log(sfit2[[x]]$surv) - 1.96 * sqrt(sfit2[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit2[[x]]$surv) + 1.96 * sqrt(sfit2[[x]]$varlog))))}))
          df <- rbind(df[df$time < cut.landmark, ], data.frame("strata" = unique(df$strata), "time" = cut.landmark, "surv" = 1, "lower" = 1, "upper" = 1), df2)
        }
        
      } else{
        stop("No CI information in svykmlist object. please run svykm with se = T option.")
      }
    } else{
      df <- Reduce(rbind, lapply(names(sfit), function(x){data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv)}))
      df <- do.call(rbind, lapply(names(sfit), function(x){data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv)}))
      if (!is.null(cut.landmark)){
        for (v in unique(df$strata)){
          if (nrow(subset(df, time == cut.landmark & strata == v)) == 0){
            df <- rbind(df, data.frame(strata = v, time = cut.landmark, surv = 1))
          } else{
            df[df$time == cut.landmark & df$strata == v, "surv"] <- 1
          }
          
          df[df$time > cut.landmark & df$strata == v, "surv"] <- df[df$time > cut.landmark & df$strata == v, "surv"]/min(df[df$time < cut.landmark & df$strata == v, "surv"])
        }
      }
    }
    
    df$strata <- as.factor(df$strata)

@@ -111,17 +157,28 @@

    
  } else if(class(sfit) == "svykm"){
    if(is.null(ystrataname)) ystrataname <- "Strata"
    if (is.null(ci)){
      ci <- "varlog" %in% names(sfit)
    }

    if (ci){
      if ("varlog" %in% names(sfit)){
        df <- data.frame("strata" = "All", "time" = sfit$time, "surv" = sfit$surv,  "lower" = pmax(0, exp(log(sfit$surv) - 1.96 * sqrt(sfit$varlog))), "upper" = pmax(0, exp(log(sfit$surv) + 1.96 * sqrt(sfit$varlog))))
        if (!is.null(cut.landmark)){
          df2 <- data.frame("strata" = "All", "time" = sfit2$time, "surv" = sfit2$surv,  "lower" = pmax(0, exp(log(sfit2$surv) - 1.96 * sqrt(sfit2$varlog))), "upper" = pmax(0, exp(log(sfit2$surv) + 1.96 * sqrt(sfit2$varlog))))
          df <- rbind(df[df$time < cut.landmark, ], data.frame("strata" = "All", "time" = cut.landmark, "surv" = 1, "lower" = 1, "upper" = 1), df2)
        }
      } else{
        stop("No CI information in svykm object. please run svykm with se = T option.")
      }
    } else{
      df <- data.frame("strata" = "All", "time" = sfit$time, "surv" = sfit$surv)
      if (!is.null(cut.landmark)){
        if (nrow(subset(df, time == cut.landmark)) == 0){
          df <- rbind(df, data.frame(strata = "All", time = cut.landmark, surv = 1))
        } else{
          df[df$time == cut.landmark, "surv"] <- 1
        }
        
        df[df$time > cut.landmark, "surv"] <- df[df$time > cut.landmark, "surv"]/min(df[df$time < cut.landmark, "surv"])
      }
    }
    
    times <- seq(0, max(sfit$time), by = timeby)

@@ -220,7 +277,7 @@

    scale_colour_brewer(name = ystrataname, palette=linecols)
  
  #Add 95% CI to plot
  if(ci == TRUE){
  if(ci){
    if (linecols2 == "black"){
      p <- p +  geom_ribbon(data=df, aes(ymin = lower, ymax = upper), alpha=0.25, colour=NA) 
    } else{

@@ -228,27 +285,67 @@

    } 
  }
  
  if (!is.null(cut.landmark)){
    p <- p + geom_vline(xintercept = cut.landmark, lty = 2)
  }
  
  ## p-value
  if(class(sfit) == "svykm") pval <- FALSE
  #if(is.null(design)) pval <- FALSE
  
  if(pval == TRUE) {
    if(is.null(design)){
      sdiff <- survey::svylogrank(formula(sfit), design = get(as.character(attr(sfit, "call")$design)))
    } else{
      sdiff <- survey::svylogrank(formula(sfit), design = design)
  if(pval) {
    if (is.null(design)){
      design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
      if ("error" %in% class(design)){
        stop("'pval' option requires design object. please input 'design' option") 
      }
    }
    pvalue <- sdiff[[2]][2]
    
    pvaltxt <- ifelse(pvalue < 0.001,"p < 0.001",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)
    if (is.null(cut.landmark)){
      sdiff <- survey::svylogrank(formula(sfit), design = design)
      pvalue <- sdiff[[2]][2]
      
      pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", 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$time)/10}))), y = 0.1 + ylims[1],label = pvaltxt, size  = pval.size)
      } else{
        p <- p + annotate("text",x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size  = pval.size)
      } 
    } else{
      p <- p + annotate("text",x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size  = pval.size)
      if (is.null(design)){
        design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
        if ("error" %in% class(design)){
          stop("'pval' option requires design object. please input 'design' option") 
        }
      }
      var.time <- as.character(formula(sfit)[[2]][[2]])
      var.event <- as.character(formula(sfit)[[2]][[3]])
      if (length(var.event) > 1){
        var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
        var.event <- var.event[sapply(var.event, function(x) {"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))})]
      }
      design1 <- design
      design1$variables[[var.event]][design1$variables[[var.time]] >= cut.landmark] <- 0
      design1$variables[[var.time]][design1$variables[[var.time]] >= cut.landmark] <- cut.landmark
      
      sdiff1 <- survey::svylogrank(formula(sfit), design = design1)
      sdiff2 <- survey::svylogrank(formula(sfit), design = subset(design, get(var.time) >= cut.landmark))
      pvalue <- sapply(list(sdiff1, sdiff2), function(x){x[[2]][2]})
      
      pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
      if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
      
      if (is.null(pval.coord)){
        p <- p + annotate("text",x = c(as.integer(max(sapply(sfit, function(x){max(x$time)/10}))), as.integer(max(sapply(sfit, function(x){max(x$time)/10}))) + cut.landmark), y = 0.1 + ylims[1],label = pvaltxt, size  = pval.size)
      } else{
        p <- p + annotate("text",x = c(pval.coord[1], pval.coord[1] + cut.landmark), y = pval.coord[2], label = pvaltxt, size  = pval.size)
      }
      
    }
    
  }
  
  ## Create a blank plot for place-holding

@@ -185,22 +185,31 @@

    upper = sfit$upper[subs2],
    lower = sfit$lower[subs2]
  )
  
  form <- sfit$call$formula

  if (!is.null(cut.landmark)){
    if (is.null(data)){
      stop("Landmark analysis requires data object. please check 'data' option")
      data <- tryCatch(eval(sfit$call$data), error = function(e) e)
      if ("error" %in% class(data)){
        stop("Landmark analysis requires data object. please input 'data' option") 
      }
    }
    
    var.time <- as.character(sfit$call$formula[[2]][[2]])
    var.event <- as.character(sfit$call$formula[[2]][[3]])
    var.time <- as.character(form[[2]][[2]])
    var.event <- as.character(form[[2]][[3]])
    if (length(var.event) > 1){
      var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
      var.event <- var.event[sapply(var.event, function(x) {"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))})]
    }
    data1 <- data
    data1[[var.event]][data1[[var.time]] >= cut.landmark] <- 0
    data1[[var.time]][data1[[var.time]] >= cut.landmark] <- cut.landmark
  
    sfit1 <- survfit(as.formula(sfit$call$formula), data1)
    sfit2 <- survfit(as.formula(sfit$call$formula), data[data[[var.time]] >= cut.landmark, ])
    sfit1 <- survfit(as.formula(form), data1)
    sfit2 <- survfit(as.formula(form), data[data[[var.time]] >= cut.landmark, ])
    
    if (levels(Factor) == "All"){
    if (length(levels(Factor)) == 1){
      df2 <- merge(subset(df, time >= cut.landmark)[, c("time", "n.risk", "n.event", "n.censor", "strata")], 
                   data.frame(time = sfit2$time, surv = sfit2$surv, strata = "All", upper = sfit2$upper, lower = sfit2$lower), 
                   by = c("time", "strata"))

@@ -228,7 +237,7 @@

  
  #Final changes to data for survival plot
  levels(df$strata) <- ystratalabs
  zeros <- data.frame(time = 0, surv = 1,
  zeros <- data.frame(time = 0, n.risk = NA, n.event = NA, n.censor = NA, surv = 1,
                      strata = factor(ystratalabs, levels=levels(df$strata)),
                      upper = 1, lower = 1)
  if (cumhaz){

@@ -237,7 +246,7 @@

237	246		zeros$upper = 0
238	247		}
239	248
240		-	df <- plyr::rbind.fill(zeros, df)
	249	+	df <- rbind(zeros, df)
241	250		d <- length(levels(df$strata))
242	251
243	252		###################################

@@ -322,40 +331,73 @@

  #####################a
  
  if(length(levels(summary(sfit)$strata)) == 0) pval <- F
  if(!is.null(cut.landmark)) pval <- F
  #if(!is.null(cut.landmark)) pval <- F
  
  if(pval == TRUE) {
    if (is.null(data)){
      data = eval(sfit$call$data)
    }
  
    sdiff <- survival::survdiff(as.formula(sfit$call$formula), data = data)
    pvalue <- pchisq(sdiff$chisq,length(sdiff$n) - 1,lower.tail = FALSE)
    
    ## cluster option
    if (cluster.option == "cluster" & !is.null(cluster.var)){
      form.old <- as.character(sfit$call$formula)
      form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + cluster(", cluster.var, ")", sep="")
      sdiff <- survival::coxph(as.formula(form.new), data = data, model = T, robust = T)
      pvalue <- summary(sdiff)$robscore["pvalue"]
    } else if (cluster.option == "frailty" & !is.null(cluster.var)){
      form.old <- as.character(sfit$call$formula)
      form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + frailty(", cluster.var, ")", sep="")
      sdiff <- survival::coxph(as.formula(form.new), data =data, model = T)
      pvalue <- summary(sdiff)$logtest["pvalue"]
      data <- tryCatch(eval(sfit$call$data), error = function(e) e)
      if ("error" %in% class(data)){
        stop("'pval' option requires data object. please input 'data' option") 
      }
    }
    
    pvaltxt <- ifelse(pvalue < 0.001,"p < 0.001",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$time)/5)), y = 0.1 + ylims[1],label = pvaltxt, size  = pval.size)
    } else{
      p <- p + annotate("text",x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size  = pval.size)
    if (is.null(cut.landmark)){
      sdiff <- survival::survdiff(as.formula(form), data = data)
      pvalue <- pchisq(sdiff$chisq,length(sdiff$n) - 1,lower.tail = FALSE)
      
      ## cluster option
      if (cluster.option == "cluster" & !is.null(cluster.var)){
        form.old <- as.character(form)
        form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + cluster(", cluster.var, ")", sep="")
        sdiff <- survival::coxph(as.formula(form.new), data = data, model = T, robust = T)
        pvalue <- summary(sdiff)$robscore["pvalue"]
      } else if (cluster.option == "frailty" & !is.null(cluster.var)){
        form.old <- as.character(form)
        form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + frailty(", cluster.var, ")", sep="")
        sdiff <- survival::coxph(as.formula(form.new), data =data, model = T)
        pvalue <- summary(sdiff)$logtest["pvalue"]
      }
      
      pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", 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$time)/5)), y = 0.1 + ylims[1],label = pvaltxt, size  = pval.size)
      } else{
        p <- p + annotate("text",x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size  = pval.size)
      }
    } else {
      sdiff1 <- survival::survdiff(as.formula(form), data1)
      sdiff2 <- survival::survdiff(as.formula(form), data[data[[var.time]] >= cut.landmark, ])
      pvalue <- sapply(list(sdiff1, sdiff2), function(x){pchisq(x$chisq,length(x$n) - 1,lower.tail = FALSE)})
      
      ## cluster option
      if (cluster.option == "cluster" & !is.null(cluster.var)){
        form.old <- as.character(form)
        form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + cluster(", cluster.var, ")", sep="")
        sdiff1 <- survival::coxph(as.formula(form.new), data = data1, model = T, robust = T)
        sdiff2 <- survival::coxph(as.formula(form.new), data = data[data[[var.time]] >= cut.landmark, ], model = T, robust = T)
        pvalue <- sapply(list(sdiff1, sdiff2), function(x){summary(x)$robscore["pvalue"]})
      } else if (cluster.option == "frailty" & !is.null(cluster.var)){
        form.old <- as.character(form)
        form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + frailty(", cluster.var, ")", sep="")
        sdiff1 <- survival::coxph(as.formula(form.new), data = data1, model = T)
        sdiff2 <- survival::coxph(as.formula(form.new), data = data[data[[var.time]] >= cut.landmark, ], model = T)
        pvalue <- sapply(list(sdiff1, sdiff2), function(x){summary(x)$logtest["pvalue"]})
      }
      
      pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
      
      if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
      
      if (is.null(pval.coord)){
        p <- p + annotate("text",x = c(as.integer(max(sfit$time)/10), as.integer(max(sfit$time)/10) + cut.landmark), y = 0.1 + ylims[1],label = pvaltxt, size  = pval.size)
      } else{
        p <- p + annotate("text",x = c(pval.coord[1], pval.coord[1] + cut.landmark), y = pval.coord[2], label = pvaltxt, size  = pval.size)
      }
    }
    
  
  }
  
  ###################################################

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R	411	263	0	148	63.99%
Project Totals (2 files)	411	263	0	148	63.99%

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85	85		}
86	86		}
87	87
88		-	if (class(sfit) == "svykmlist"){
89		-	if(is.null(ystrataname)) ystrataname <- as.character(formula(sfit)[[3]])
90		-	if (is.null(ci)){
	88	+	if (is.null(ci)){
	89	+	if (class(sfit) == "svykmlist"){
91	90		ci <- "varlog" %in% names(sfit[[1]])
	91	+	} else if (class(sfit) == "svykm"){
	92	+	ci <- "varlog" %in% names(sfit)
92	93		}
	94	+	}
	95	+
	96	+
	97	+	if (ci & !is.null(cut.landmark)){
	98	+	if (is.null(design)){
	99	+	design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
	100	+	if ("error" %in% class(design)){
	101	+	stop("'pval' option requires design object. please input 'design' option")
	102	+	}
	103	+	}
	104	+	var.time <- as.character(formula(sfit)[[2]][[2]])
	105	+	var.event <- as.character(formula(sfit)[[2]][[3]])
	106	+	if (length(var.event) > 1){
	107	+	var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
	108	+	var.event <- var.event[sapply(var.event, function(x) {"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))})]
	109	+	}
	110	+	design1 <- design
	111	+	design1$variables[[var.event]][design1$variables[[var.time]] >= cut.landmark] <- 0
	112	+	design1$variables[[var.time]][design1$variables[[var.time]] >= cut.landmark] <- cut.landmark
	113	+
	114	+	sfit2 <- survey::svykm(formula(sfit), design = subset(design, get(var.time) >= cut.landmark), se = T)
	115	+	}
	116	+
	117	+
	118	+
	119	+
	120	+	if (class(sfit) == "svykmlist"){
	121	+	if(is.null(ystrataname)) ystrataname <- as.character(formula(sfit)[[3]])
	122	+
93	123		if (ci){
94	124		if ("varlog" %in% names(sfit[[1]])){
95		-	df <- Reduce(rbind, lapply(names(sfit), function(x){data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv, "lower" = pmax(0, exp(log(sfit[[x]]$surv) - 1.96 * sqrt(sfit[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit[[x]]$surv) + 1.96 * sqrt(sfit[[x]]$varlog))))}))
	125	+	df <- do.call(rbind, lapply(names(sfit), function(x){data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv, "lower" = pmax(0, exp(log(sfit[[x]]$surv) - 1.96 * sqrt(sfit[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit[[x]]$surv) + 1.96 * sqrt(sfit[[x]]$varlog))))}))
	126	+	if (!is.null(cut.landmark)){
	127	+	df2 <- do.call(rbind, lapply(names(sfit2), function(x){data.frame("strata" = x, "time" = sfit2[[x]]$time, "surv" = sfit2[[x]]$surv, "lower" = pmax(0, exp(log(sfit2[[x]]$surv) - 1.96 * sqrt(sfit2[[x]]$varlog))), "upper" = pmin(1, exp(log(sfit2[[x]]$surv) + 1.96 * sqrt(sfit2[[x]]$varlog))))}))
	128	+	df <- rbind(df[df$time < cut.landmark, ], data.frame("strata" = unique(df$strata), "time" = cut.landmark, "surv" = 1, "lower" = 1, "upper" = 1), df2)
	129	+	}
	130	+
96	131		} else{
97	132		stop("No CI information in svykmlist object. please run svykm with se = T option.")
98	133		}
99	134		} else{
100		-	df <- Reduce(rbind, lapply(names(sfit), function(x){data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv)}))
	135	+	df <- do.call(rbind, lapply(names(sfit), function(x){data.frame("strata" = x, "time" = sfit[[x]]$time, "surv" = sfit[[x]]$surv)}))
	136	+	if (!is.null(cut.landmark)){
	137	+	for (v in unique(df$strata)){
	138	+	if (nrow(subset(df, time == cut.landmark & strata == v)) == 0){
	139	+	df <- rbind(df, data.frame(strata = v, time = cut.landmark, surv = 1))
	140	+	} else{
	141	+	df[df$time == cut.landmark & df$strata == v, "surv"] <- 1
	142	+	}
	143	+
	144	+	df[df$time > cut.landmark & df$strata == v, "surv"] <- df[df$time > cut.landmark & df$strata == v, "surv"]/min(df[df$time < cut.landmark & df$strata == v, "surv"])
	145	+	}
	146	+	}
101	147		}
102	148
103	149		df$strata <- as.factor(df$strata)

111	157
112	158		} else if(class(sfit) == "svykm"){
113	159		if(is.null(ystrataname)) ystrataname <- "Strata"
114		-	if (is.null(ci)){
115		-	ci <- "varlog" %in% names(sfit)
116		-	}
	160	+
117	161		if (ci){
118	162		if ("varlog" %in% names(sfit)){
119	163		df <- data.frame("strata" = "All", "time" = sfit$time, "surv" = sfit$surv, "lower" = pmax(0, exp(log(sfit$surv) - 1.96 * sqrt(sfit$varlog))), "upper" = pmax(0, exp(log(sfit$surv) + 1.96 * sqrt(sfit$varlog))))
	164	+	if (!is.null(cut.landmark)){
	165	+	df2 <- data.frame("strata" = "All", "time" = sfit2$time, "surv" = sfit2$surv, "lower" = pmax(0, exp(log(sfit2$surv) - 1.96 * sqrt(sfit2$varlog))), "upper" = pmax(0, exp(log(sfit2$surv) + 1.96 * sqrt(sfit2$varlog))))
	166	+	df <- rbind(df[df$time < cut.landmark, ], data.frame("strata" = "All", "time" = cut.landmark, "surv" = 1, "lower" = 1, "upper" = 1), df2)
	167	+	}
120	168		} else{
121	169		stop("No CI information in svykm object. please run svykm with se = T option.")
122	170		}
123	171		} else{
124	172		df <- data.frame("strata" = "All", "time" = sfit$time, "surv" = sfit$surv)
	173	+	if (!is.null(cut.landmark)){
	174	+	if (nrow(subset(df, time == cut.landmark)) == 0){
	175	+	df <- rbind(df, data.frame(strata = "All", time = cut.landmark, surv = 1))
	176	+	} else{
	177	+	df[df$time == cut.landmark, "surv"] <- 1
	178	+	}
	179	+
	180	+	df[df$time > cut.landmark, "surv"] <- df[df$time > cut.landmark, "surv"]/min(df[df$time < cut.landmark, "surv"])
	181	+	}
125	182		}
126	183
127	184		times <- seq(0, max(sfit$time), by = timeby)

220	277		scale_colour_brewer(name = ystrataname, palette=linecols)
221	278
222	279		#Add 95% CI to plot
223		-	if(ci == TRUE){
	280	+	if(ci){
224	281		if (linecols2 == "black"){
225	282		p <- p + geom_ribbon(data=df, aes(ymin = lower, ymax = upper), alpha=0.25, colour=NA)
226	283		} else{

228	285		}
229	286		}
230	287
	288	+	if (!is.null(cut.landmark)){
	289	+	p <- p + geom_vline(xintercept = cut.landmark, lty = 2)
	290	+	}
	291	+
231	292		## p-value
232	293		if(class(sfit) == "svykm") pval <- FALSE
233	294		#if(is.null(design)) pval <- FALSE
234	295
235		-	if(pval == TRUE) {
236		-	if(is.null(design)){
237		-	sdiff <- survey::svylogrank(formula(sfit), design = get(as.character(attr(sfit, "call")$design)))
238		-	} else{
239		-	sdiff <- survey::svylogrank(formula(sfit), design = design)
	296	+	if(pval) {
	297	+	if (is.null(design)){
	298	+	design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
	299	+	if ("error" %in% class(design)){
	300	+	stop("'pval' option requires design object. please input 'design' option")
	301	+	}
240	302		}
241		-	pvalue <- sdiff[[2]][2]
242	303
243		-	pvaltxt <- ifelse(pvalue < 0.001,"p < 0.001",paste("p =", round(pvalue, 3)))
244		-	if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
245		-
246		-	# MOVE P-VALUE LEGEND HERE BELOW [set x and y]
247		-	if (is.null(pval.coord)){
248		-	p <- p + annotate("text",x = (as.integer(max(sapply(sfit, function(x){max(x$time)/5})))), y = 0.1 + ylims[1],label = pvaltxt, size = pval.size)
	304	+	if (is.null(cut.landmark)){
	305	+	sdiff <- survey::svylogrank(formula(sfit), design = design)
	306	+	pvalue <- sdiff[[2]][2]
	307	+
	308	+	pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
	309	+	if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
	310	+
	311	+	# MOVE P-VALUE LEGEND HERE BELOW [set x and y]
	312	+	if (is.null(pval.coord)){
	313	+	p <- p + annotate("text",x = as.integer(max(sapply(sfit, function(x){max(x$time)/10}))), y = 0.1 + ylims[1],label = pvaltxt, size = pval.size)
	314	+	} else{
	315	+	p <- p + annotate("text",x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size = pval.size)
	316	+	}
249	317		} else{
250		-	p <- p + annotate("text",x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size = pval.size)
	318	+	if (is.null(design)){
	319	+	design <- tryCatch(get(as.character(attr(sfit, "call")$design)), error = function(e) e)
	320	+	if ("error" %in% class(design)){
	321	+	stop("'pval' option requires design object. please input 'design' option")
	322	+	}
	323	+	}
	324	+	var.time <- as.character(formula(sfit)[[2]][[2]])
	325	+	var.event <- as.character(formula(sfit)[[2]][[3]])
	326	+	if (length(var.event) > 1){
	327	+	var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
	328	+	var.event <- var.event[sapply(var.event, function(x) {"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))})]
	329	+	}
	330	+	design1 <- design
	331	+	design1$variables[[var.event]][design1$variables[[var.time]] >= cut.landmark] <- 0
	332	+	design1$variables[[var.time]][design1$variables[[var.time]] >= cut.landmark] <- cut.landmark
	333	+
	334	+	sdiff1 <- survey::svylogrank(formula(sfit), design = design1)
	335	+	sdiff2 <- survey::svylogrank(formula(sfit), design = subset(design, get(var.time) >= cut.landmark))
	336	+	pvalue <- sapply(list(sdiff1, sdiff2), function(x){x[[2]][2]})
	337	+
	338	+	pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
	339	+	if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
	340	+
	341	+	if (is.null(pval.coord)){
	342	+	p <- p + annotate("text",x = c(as.integer(max(sapply(sfit, function(x){max(x$time)/10}))), as.integer(max(sapply(sfit, function(x){max(x$time)/10}))) + cut.landmark), y = 0.1 + ylims[1],label = pvaltxt, size = pval.size)
	343	+	} else{
	344	+	p <- p + annotate("text",x = c(pval.coord[1], pval.coord[1] + cut.landmark), y = pval.coord[2], label = pvaltxt, size = pval.size)
	345	+	}
	346	+
251	347		}
	348	+
252	349		}
253	350
254	351		## Create a blank plot for place-holding

185	185		upper = sfit$upper[subs2],
186	186		lower = sfit$lower[subs2]
187	187		)
	188	+
	189	+	form <- sfit$call$formula
188	190
189	191		if (!is.null(cut.landmark)){
190	192		if (is.null(data)){
191		-	stop("Landmark analysis requires data object. please check 'data' option")
	193	+	data <- tryCatch(eval(sfit$call$data), error = function(e) e)
	194	+	if ("error" %in% class(data)){
	195	+	stop("Landmark analysis requires data object. please input 'data' option")
	196	+	}
192	197		}
193	198
194		-	var.time <- as.character(sfit$call$formula[[2]][[2]])
195		-	var.event <- as.character(sfit$call$formula[[2]][[3]])
	199	+	var.time <- as.character(form[[2]][[2]])
	200	+	var.event <- as.character(form[[2]][[3]])
	201	+	if (length(var.event) > 1){
	202	+	var.event <- setdiff(var.event, as.character(as.symbol(var.event)))
	203	+	var.event <- var.event[sapply(var.event, function(x) {"warning" %in% class(tryCatch(as.numeric(x), warning = function(w) w))})]
	204	+	}
196	205		data1 <- data
197	206		data1[[var.event]][data1[[var.time]] >= cut.landmark] <- 0
198	207		data1[[var.time]][data1[[var.time]] >= cut.landmark] <- cut.landmark
199	208
200		-	sfit1 <- survfit(as.formula(sfit$call$formula), data1)
201		-	sfit2 <- survfit(as.formula(sfit$call$formula), data[data[[var.time]] >= cut.landmark, ])
	209	+	sfit1 <- survfit(as.formula(form), data1)
	210	+	sfit2 <- survfit(as.formula(form), data[data[[var.time]] >= cut.landmark, ])
202	211
203		-	if (levels(Factor) == "All"){
	212	+	if (length(levels(Factor)) == 1){
204	213		df2 <- merge(subset(df, time >= cut.landmark)[, c("time", "n.risk", "n.event", "n.censor", "strata")],
205	214		data.frame(time = sfit2$time, surv = sfit2$surv, strata = "All", upper = sfit2$upper, lower = sfit2$lower),
206	215		by = c("time", "strata"))

228	237
229	238		#Final changes to data for survival plot
230	239		levels(df$strata) <- ystratalabs
231		-	zeros <- data.frame(time = 0, surv = 1,
	240	+	zeros <- data.frame(time = 0, n.risk = NA, n.event = NA, n.censor = NA, surv = 1,
232	241		strata = factor(ystratalabs, levels=levels(df$strata)),
233	242		upper = 1, lower = 1)
234	243		if (cumhaz){

322	331		#####################a
323	332
324	333		if(length(levels(summary(sfit)$strata)) == 0) pval <- F
325		-	if(!is.null(cut.landmark)) pval <- F
	334	+	#if(!is.null(cut.landmark)) pval <- F
326	335
327	336		if(pval == TRUE) {
328	337		if (is.null(data)){
329		-	data = eval(sfit$call$data)
330		-	}
331		-
332		-	sdiff <- survival::survdiff(as.formula(sfit$call$formula), data = data)
333		-	pvalue <- pchisq(sdiff$chisq,length(sdiff$n) - 1,lower.tail = FALSE)
334		-
335		-	## cluster option
336		-	if (cluster.option == "cluster" & !is.null(cluster.var)){
337		-	form.old <- as.character(sfit$call$formula)
338		-	form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + cluster(", cluster.var, ")", sep="")
339		-	sdiff <- survival::coxph(as.formula(form.new), data = data, model = T, robust = T)
340		-	pvalue <- summary(sdiff)$robscore["pvalue"]
341		-	} else if (cluster.option == "frailty" & !is.null(cluster.var)){
342		-	form.old <- as.character(sfit$call$formula)
343		-	form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + frailty(", cluster.var, ")", sep="")
344		-	sdiff <- survival::coxph(as.formula(form.new), data =data, model = T)
345		-	pvalue <- summary(sdiff)$logtest["pvalue"]
	338	+	data <- tryCatch(eval(sfit$call$data), error = function(e) e)
	339	+	if ("error" %in% class(data)){
	340	+	stop("'pval' option requires data object. please input 'data' option")
	341	+	}
346	342		}
347	343
348		-	pvaltxt <- ifelse(pvalue < 0.001,"p < 0.001",paste("p =", round(pvalue, 3)))
349		-
350		-	if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
351		-
352		-	# MOVE P-VALUE LEGEND HERE BELOW [set x and y]
353		-	if (is.null(pval.coord)){
354		-	p <- p + annotate("text",x = (as.integer(max(sfit$time)/5)), y = 0.1 + ylims[1],label = pvaltxt, size = pval.size)
355		-	} else{
356		-	p <- p + annotate("text",x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size = pval.size)
	344	+	if (is.null(cut.landmark)){
	345	+	sdiff <- survival::survdiff(as.formula(form), data = data)
	346	+	pvalue <- pchisq(sdiff$chisq,length(sdiff$n) - 1,lower.tail = FALSE)
	347	+
	348	+	## cluster option
	349	+	if (cluster.option == "cluster" & !is.null(cluster.var)){
	350	+	form.old <- as.character(form)
	351	+	form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + cluster(", cluster.var, ")", sep="")
	352	+	sdiff <- survival::coxph(as.formula(form.new), data = data, model = T, robust = T)
	353	+	pvalue <- summary(sdiff)$robscore["pvalue"]
	354	+	} else if (cluster.option == "frailty" & !is.null(cluster.var)){
	355	+	form.old <- as.character(form)
	356	+	form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + frailty(", cluster.var, ")", sep="")
	357	+	sdiff <- survival::coxph(as.formula(form.new), data =data, model = T)
	358	+	pvalue <- summary(sdiff)$logtest["pvalue"]
	359	+	}
	360	+
	361	+	pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
	362	+	if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
	363	+
	364	+	# MOVE P-VALUE LEGEND HERE BELOW [set x and y]
	365	+	if (is.null(pval.coord)){
	366	+	p <- p + annotate("text",x = (as.integer(max(sfit$time)/5)), y = 0.1 + ylims[1],label = pvaltxt, size = pval.size)
	367	+	} else{
	368	+	p <- p + annotate("text",x = pval.coord[1], y = pval.coord[2], label = pvaltxt, size = pval.size)
	369	+	}
	370	+	} else {
	371	+	sdiff1 <- survival::survdiff(as.formula(form), data1)
	372	+	sdiff2 <- survival::survdiff(as.formula(form), data[data[[var.time]] >= cut.landmark, ])
	373	+	pvalue <- sapply(list(sdiff1, sdiff2), function(x){pchisq(x$chisq,length(x$n) - 1,lower.tail = FALSE)})
	374	+
	375	+	## cluster option
	376	+	if (cluster.option == "cluster" & !is.null(cluster.var)){
	377	+	form.old <- as.character(form)
	378	+	form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + cluster(", cluster.var, ")", sep="")
	379	+	sdiff1 <- survival::coxph(as.formula(form.new), data = data1, model = T, robust = T)
	380	+	sdiff2 <- survival::coxph(as.formula(form.new), data = data[data[[var.time]] >= cut.landmark, ], model = T, robust = T)
	381	+	pvalue <- sapply(list(sdiff1, sdiff2), function(x){summary(x)$robscore["pvalue"]})
	382	+	} else if (cluster.option == "frailty" & !is.null(cluster.var)){
	383	+	form.old <- as.character(form)
	384	+	form.new <- paste(form.old[2], form.old[1], " + ", form.old[3], " + frailty(", cluster.var, ")", sep="")
	385	+	sdiff1 <- survival::coxph(as.formula(form.new), data = data1, model = T)
	386	+	sdiff2 <- survival::coxph(as.formula(form.new), data = data[data[[var.time]] >= cut.landmark, ], model = T)
	387	+	pvalue <- sapply(list(sdiff1, sdiff2), function(x){summary(x)$logtest["pvalue"]})
	388	+	}
	389	+
	390	+	pvaltxt <- ifelse(pvalue < 0.001, "p < 0.001", paste("p =", round(pvalue, 3)))
	391	+
	392	+	if (pval.testname) pvaltxt <- paste0(pvaltxt, " (Log-rank)")
	393	+
	394	+	if (is.null(pval.coord)){
	395	+	p <- p + annotate("text",x = c(as.integer(max(sfit$time)/10), as.integer(max(sfit$time)/10) + cut.landmark), y = 0.1 + ylims[1],label = pvaltxt, size = pval.size)
	396	+	} else{
	397	+	p <- p + annotate("text",x = c(pval.coord[1], pval.coord[1] + cut.landmark), y = pval.coord[2], label = pvaltxt, size = pval.size)
	398	+	}
357	399		}
358		-
	400	+
359	401		}
360	402
361	403		###################################################

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