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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# tidycmprsk <a href="https://mskcc-epi-bio.github.io/tidycmprsk/"><img src="man/figures/logo.png" align="right" height="138" /></a>
<!-- badges: start -->
[](https://github.com/MSKCC-Epi-Bio/tidycmprsk/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/MSKCC-Epi-Bio/tidycmprsk?branch=main)
[](https://cran.r-project.org/package=tidycmprsk)
[](https://cran.r-project.org/package=tidycmprsk)
<!-- badges: end -->
The `tidycmprsk` package provides an intuitive interface for working with the competing risk endpoints.
The package wraps the `cmprsk` package, and exports functions for univariate cumulative incidence estimates with `cuminc()` and competing risk regression with `crr()`.
The package also includes broom-style tidiers: `tidy()`, `augment()`, and `glance()`.
## Installation
You can install {tidycmprsk} with the following code.
``` r
install.packages("tidycmprsk")
```
Install the development version of {tidycmprsk} with:
``` r
# install.packages("devtools")
devtools::install_github("MSKCC-Epi-Bio/tidycmprsk")
```
## Competing Risk Regression
Fit a Fine and Gray competing risks regression model using the the example data, `trial`.
```{r example}
library(tidycmprsk)
crr_mod <- crr(Surv(ttdeath, death_cr) ~ age + trt, trial)
crr_mod
```
The `tidycmprsk` plays well with other packages, such as `gtsummary`.
```{r gtsummary, message = FALSE}
tbl <-
crr_mod %>%
gtsummary::tbl_regression(exponentiate = TRUE) %>%
gtsummary::add_global_p() %>%
add_n(location = "level")
```
```{r gtsummary_print, include = FALSE}
# Had to manually save images in temp file, not sure if better way.
gt::gtsave(gtsummary::as_gt(tbl), file = "man/figures/README-gtsummary-crr.png")
```
```{r out.width = "50%", echo = FALSE}
# Have to do this workaround since the README needs markdown format for GitHub page but a different format for the website.
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
tbl
} else {
knitr::include_graphics("man/figures/README-gtsummary-crr.png")
}
```
```{r}
gtsummary::inline_text(tbl, variable = age)
```
## Cumulative Incidence
```{r}
cuminc(Surv(ttdeath, death_cr) ~ 1, trial)
```
Plot risks using using the {ggsurvfit} package.
```{r}
library(ggsurvfit)
cuminc(Surv(ttdeath, death_cr) ~ trt, trial) %>%
ggcuminc() +
add_confidence_interval() +
add_risktable() +
scale_ggsurvfit(x_scales = list(breaks = seq(0, 24, by = 6)))
```
Summary table
```{r tbl_cuminc}
tbl <-
cuminc(Surv(ttdeath, death_cr) ~ trt, trial) %>%
tbl_cuminc(times = c(12, 24), label_header = "**Month {time}**") %>%
add_p() %>%
add_n()
```
```{r gtsummary_print2, include = FALSE}
# Had to manually save images in temp file, not sure if better way.
gt::gtsave(gtsummary::as_gt(tbl), file = "man/figures/README-gtsummary-cuminc.png")
```
```{r out.width = "70%", echo = FALSE}
# Have to do this workaround since the README needs markdown format for GitHub page but a different format for the website.
if (identical(Sys.getenv("IN_PKGDOWN"), "true")) {
tbl
} else {
knitr::include_graphics("man/figures/README-gtsummary-cuminc.png")
}
```
## Contributing
Please note that the {tidycmprsk} project is released with a [Contributor Code of Conduct](https://mskcc-epi-bio.github.io/tidycmprsk/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms. Thank you to all contributors!
`r usethis::use_tidy_thanks("mskcc-epi-bio/tidycmprsk", from = "2018-01-01") %>% {glue::glue("[@{.}](https://github.com/{.})")} %>% glue::glue_collapse(sep = ", ", last = ", and ")`
#### Limitations
The `tidycmprsk` package implements most features (and more) available in `cmprsk`.
However, the time interaction features available in `cmprsk::crr()` is not available in `tidycmprsk`.