---
title: "jskm"
author: "Jinseob Kim"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{jskm}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(jskm)
```


## Install
```r
install.packages("devtools")
library(devtools)
install_github("jinseob2kim/jskm")
library(jskm)
```

## Example

### Survival probability
```{r}
# Load dataset
library(survival)
data(colon)
fit <- survfit(Surv(time, status) ~ rx, data = colon)

# Plot the data
jskm(fit)
jskm(fit,
  table = T, pval = T, label.nrisk = "No. at risk", size.label.nrisk = 8,
  xlabs = "Time(Day)", ylabs = "Survival", ystratalabs = c("Obs", "Lev", "Lev + 5FU"), ystrataname = "rx",
  marks = F, timeby = 365, xlims = c(0, 3000), ylims = c(0.25, 1), showpercent = T
)
```

### Cumulative incidence: 1- Survival probability
```{r}
jskm(fit, ci = T, cumhaz = T, mark = F, ylab = "Cumulative incidence (%)", surv.scale = "percent", pval = T, pval.size = 6, pval.coord = c(300, 0.7))
```

### Landmark analysis 

```{r}
jskm(fit, mark = F, surv.scale = "percent", pval = T, table = T, cut.landmark = 500, showpercent = T)
```

### Competing risk analysis

`status2` variable: 0 - censoring, 1 - event, 2 - competing risk
```{r}
## Make competing risk variable, Not real
colon$status2 <- colon$status
colon$status2[1:400] <- 2
colon$status2 <- factor(colon$status2)
fit2 <- survfit(Surv(time, status2) ~ rx, data = colon)
jskm(fit2, mark = F, surv.scale = "percent", table = T, status.cmprsk = "1")
jskm(fit2, mark = F, surv.scale = "percent", table = T, status.cmprsk = "1", showpercent = T, cut.landmark = 500)
```

### Theme Jama

```{r}
jskm(fit, theme = "jama", cumhaz = T, table = T, mark = F, ylab = "Cumulative incidence (%)", surv.scale = "percent", pval = T, pval.size = 6, pval.coord = c(300, 0.7))
```

### Theme Nejmoa

```{r}
jskm(fit, theme = "nejm", nejm.infigure.ratiow = 0.6, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0, 0.7), cumhaz = T, table = T, mark = F, ylab = "Cumulative incidence (%)", surv.scale = "percent", pval = T, pval.size = 6, pval.coord = c(300, 0.7))
```

### Weighted Kaplan-Meier plot - `svykm.object` in **survey** package

```{r}
library(survey)
data(pbc, package = "survival")
pbc$randomized <- with(pbc, !is.na(trt) & trt > 0)
biasmodel <- glm(randomized ~ age * edema, data = pbc)
pbc$randprob <- fitted(biasmodel)

dpbc <- svydesign(id = ~1, prob = ~randprob, strata = ~edema, data = subset(pbc, randomized))

s1 <- svykm(Surv(time, status > 0) ~ 1, design = dpbc)
s2 <- svykm(Surv(time, status > 0) ~ sex, design = dpbc)

svyjskm(s1)
svyjskm(s2)
svyjskm(s2, cumhaz = T, ylab = "Cumulative incidence(%)", surv.scale = "percent", showpercent = T)
```

If you want to get **confidence interval**, you should apply `se = T` option to `svykm` object.

```{r}
s3 <- svykm(Surv(time, status > 0) ~ sex, design = dpbc, se = T)
svyjskm(s3)
svyjskm(s3, ci = F, showpercent = T)
svyjskm(s3, ci = F, surv.scale = "percent", pval = T, table = T, cut.landmark = 1000)
```

### Theme 

#### JAMA

```{r}
svyjskm(s2, theme = "jama", pval = T, table = T, design = dpbc)
```

#### NEJM

```{r}
svyjskm(s2, theme = "nejm", nejm.infigure.ratiow = 0.4, nejm.infigure.ratioh = 0.4, nejm.infigure.ylim = c(0.2, 1), pval = T, table = T, design = dpbc)
```