Commit ⋅ jinseob2kim/jskm

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84.08% 100.00% +0.21%

R/svyjskm.R changed.

71.60% 25.00% -9.09%

R/jskm.R changed.

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DESCRIPTION has changed.

man/jskm.Rd has changed.

man/svyjskm.Rd has changed.

NEWS.md has changed.

@@ -25,6 +25,7 @@

#' @param table logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
#' @param label.nrisk Numbers at risk label. Default = "Numbers at risk"
#' @param size.label.nrisk Font size of label.nrisk. Default = 10
#' @param cut.landmark cut-off for landmark analysis, Default = NULL
#' @param ... PARAM_DESCRIPTION
#' @return plot
#' @details DETAILS

@@ -69,6 +70,7 @@

                    table = F,
                    label.nrisk = "Numbers at risk",
                    size.label.nrisk = 10,
                    cut.landmark = NULL,
                    ...) {
  
  surv <- strata <- lower <- upper <- NULL

@@ -140,8 +142,10 @@

  if (cumhaz){
    df$surv <- 1 - df$surv
    if (ci){
      df$lower <- 1 - df$upper
      df$upper <- 1 - df$lower
      upper.new <- 1 - df$lower
      lower.new <- 1 - df$upper
      df$lower = lower.new
      df$upper = upper.new
    }
    }
  

@@ -29,7 +29,8 @@

#' @param cumhaz Show cumulaive hazard function, Default: F
#' @param cluster.option Cluster option for p value, Option: "None", "cluster", "frailty", Default: "None"
#' @param cluster.var Cluster variable
#' @param data select specific data - for reactive input. Default = NULL
#' @param data select specific data - for reactive input, Default = NULL
#' @param cut.landmark cut-off for landmark analysis, Default = NULL
#' @param ... PARAM_DESCRIPTION
#' @return Plot
#' @details DETAILS

@@ -104,6 +105,7 @@

                 cluster.option = "None",
                 cluster.var = NULL,
                 data = NULL,
                 cut.landmark = NULL,
                 ...) {
  
  

@@ -183,11 +185,44 @@

183	185		upper = sfit$upper[subs2],
184	186		lower = sfit$lower[subs2]
185	187		)
	188	+
	189	+	if (!is.null(cut.landmark)){
	190	+	if (is.null(data)){
	191	+	stop("Landmark analysis requires data object. please check 'data' option")
	192	+	}
	193	+
	194	+	var.time <- as.character(sfit$call$formula[[2]][[2]])
	195	+	var.event <- as.character(sfit$call$formula[[2]][[3]])
	196	+	data1 <- data
	197	+	data1[[var.event]][data1[[var.time]] >= cut.landmark] <- 0
	198	+	data1[[var.time]][data1[[var.time]] >= cut.landmark] <- cut.landmark
	199	+
	200	+	sfit1 <- survfit(as.formula(sfit$call$formula), data1)
	201	+	sfit2 <- survfit(as.formula(sfit$call$formula), data[data[[var.time]] >= cut.landmark, ])
	202	+
	203	+	if (levels(Factor) == "All"){
	204	+	df2 <- merge(subset(df, time >= cut.landmark)[, c("time", "n.risk", "n.event", "n.censor", "strata")],
	205	+	data.frame(time = sfit2$time, surv = sfit2$surv, strata = "All", upper = sfit2$upper, lower = sfit2$lower),
	206	+	by = c("time", "strata"))
	207	+	} else{
	208	+	df2 <- merge(subset(df, time >= cut.landmark)[, c("time", "n.risk", "n.event", "n.censor", "strata")],
	209	+	data.frame(time = sfit2$time, surv = sfit2$surv, strata = rep(names(sfit2$strata), sfit2$strata), upper = sfit2$upper, lower = sfit2$lower),
	210	+	by = c("time", "strata"))
	211	+	}
	212	+
	213	+
	214	+
	215	+	df11 <- rbind(subset(df, time < cut.landmark), df2)
	216	+	df <- rbind(df11, data.frame(time = cut.landmark, n.risk = summary(sfit, times = cut.landmark)$n.risk, n.event = 0, n.censor = 0, surv = 1, strata = factor(ystratalabs, levels = levels(df$strata)), upper = 1, lower = 1))
	217	+	}
	218	+
186	219
187	220		if (cumhaz){
188		-	df$surv = 1 - sfit$surv[subs2]
189		-	df$lower = 1 - sfit$upper[subs2]
190		-	df$upper = 1 - sfit$lower[subs2]
	221	+	upper.new <- 1 - df$lower
	222	+	lower.new <- 1 - df$upper
	223	+	df$surv = 1 - df$surv
	224	+	df$lower = lower.new
	225	+	df$upper = upper.new
191	226
192	227		}
193	228

@@ -270,6 +305,10 @@

    } 
  }
  
  if (!is.null(cut.landmark)){
    p <- p + geom_vline(xintercept = cut.landmark, lty = 2)
  }
  
  ## Create a blank plot for place-holding
  blank.pic <- ggplot(df, aes(time, surv)) +
    geom_blank() + theme_void() +             ## Remove gray color

@@ -282,7 +321,8 @@

  # p-value placement #
  #####################a
  
  if(length(levels(summary(sfit)$strata)) == 0) pval <- FALSE
  if(length(levels(summary(sfit)$strata)) == 0) pval <- F
  if(!is.null(cut.landmark)) pval <- F
  
  if(pval == TRUE) {
    if (is.null(data)){

Files		•	•	•	Coverage
R	326	253	0	73	77.61%
Project Totals (2 files)	326	253	0	73	77.61%

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140	142		if (cumhaz){
141	143		df$surv <- 1 - df$surv
142	144		if (ci){
143		-	df$lower <- 1 - df$upper
144		-	df$upper <- 1 - df$lower
	145	+	upper.new <- 1 - df$lower
	146	+	lower.new <- 1 - df$upper
	147	+	df$lower = lower.new
	148	+	df$upper = upper.new
145	149		}
146	150		}
147	151

104	105		cluster.option = "None",
105	106		cluster.var = NULL,
106	107		data = NULL,
	108	+	cut.landmark = NULL,
107	109		...) {
108	110
109	111

270	305		}
271	306		}
272	307
	308	+	if (!is.null(cut.landmark)){
	309	+	p <- p + geom_vline(xintercept = cut.landmark, lty = 2)
	310	+	}
	311	+
273	312		## Create a blank plot for place-holding
274	313		blank.pic <- ggplot(df, aes(time, surv)) +
275	314		geom_blank() + theme_void() + ## Remove gray color

282	321		# p-value placement #
283	322		#####################a
284	323
285		-	if(length(levels(summary(sfit)$strata)) == 0) pval <- FALSE
	324	+	if(length(levels(summary(sfit)$strata)) == 0) pval <- F
	325	+	if(!is.null(cut.landmark)) pval <- F
286	326
287	327		if(pval == TRUE) {
288	328		if (is.null(data)){

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25	25		#' @param table logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
26	26		#' @param label.nrisk Numbers at risk label. Default = "Numbers at risk"
27	27		#' @param size.label.nrisk Font size of label.nrisk. Default = 10
	28	+	#' @param cut.landmark cut-off for landmark analysis, Default = NULL
28	29		#' @param ... PARAM_DESCRIPTION
29	30		#' @return plot
30	31		#' @details DETAILS

69	70		table = F,
70	71		label.nrisk = "Numbers at risk",
71	72		size.label.nrisk = 10,
	73	+	cut.landmark = NULL,
72	74		...) {
73	75
74	76		surv <- strata <- lower <- upper <- NULL

29	29		#' @param cumhaz Show cumulaive hazard function, Default: F
30	30		#' @param cluster.option Cluster option for p value, Option: "None", "cluster", "frailty", Default: "None"
31	31		#' @param cluster.var Cluster variable
32		-	#' @param data select specific data - for reactive input. Default = NULL
	32	+	#' @param data select specific data - for reactive input, Default = NULL
	33	+	#' @param cut.landmark cut-off for landmark analysis, Default = NULL
33	34		#' @param ... PARAM_DESCRIPTION
34	35		#' @return Plot
35	36		#' @details DETAILS