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Closes #271 surv_cnsr: allow CSNR > 1 #272

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Merged
ddsjoberg merged 2 commits into from
Mar 2, 2026
Merged

Closes #271 surv_cnsr: allow CSNR > 1 #272

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#271 surv_cnsr: allow CSNR > 1
bundfussr Feb 27, 2026
1741964
#271 surv_cnsr: refine argument check
bundfussr Mar 2, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: ggsurvfit
Title: Flexible Time-to-Event Figures
Version: 1.2.0.9000
Version: 1.2.0.9001
Authors@R: c(
person("Daniel D.", "Sjoberg", , "danield.sjoberg@gmail.com", role = c("aut", "cre", "cph"),
comment = c(ORCID = "0000-0003-0862-2018")),
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3 changes: 3 additions & 0 deletions NEWS.md
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@@ -1,5 +1,8 @@
# ggsurvfit (development version)

* `Surv_CNSR()` updated to accept values `>= 1` as censoring values (according
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@ddsjoberg ddsjoberg Feb 27, 2026

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Feel free to add your @bundfussr if you'd like.

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@bundfussr bundfussr Mar 2, 2026

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good idea, done

to CDISC recommendation). (#271, @bundfussr)

# ggsurvfit 1.2.0

* Updates to account for changes in ggplot2 v4.0.0. (#241)
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15 changes: 6 additions & 9 deletions R/Surv_CNSR.R
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Expand Up @@ -12,7 +12,7 @@
#' [survival](https://cran.r-project.org/package=survival) package.
#'
#' The `AVAL` and `CNSR` arguments are passed to
#' `survival::Surv(time = AVAL, event = 1 - CNSR, type = "right", origin = 0)`.
#' `survival::Surv(time = AVAL, event = CNSR == 0, type = "right", origin = 0)`.
#'
#' @section Details:
#'
Expand All @@ -29,11 +29,11 @@
#'
#' The CDISC ADaM ADTTE data model adopts a different coding convention for
#' the event/status indicator. Using this convention, the event/status variable
#' is named `'CNSR'` and uses the following coding: `censor = 1`, `status/event = 0`.
#' is named `'CNSR'` and uses the following coding: `censor >= 1`, `status/event = 0`.
#'
#' @param AVAL The follow-up time. The follow-up time is assumed to originate from zero.
#' When no argument is passed, the default value is a column/vector named `AVAL`.
#' @param CNSR The censoring indicator where `1=censored` and `0=death/event`.
#' @param CNSR The censoring indicator where `>=1=censored` and `0=death/event`.
#' When no argument is passed, the default value is a column/vector named `CNSR`.
#'
#' @return Object of class 'Surv'
Expand Down Expand Up @@ -68,17 +68,14 @@ Surv_CNSR <- function(AVAL, CNSR) {
stop("Expecting arguments 'AVAL' and 'CNSR' to be numeric.")
}

if (stats::na.omit(CNSR) %>% setdiff(c(0, 1)) %>%
{
!rlang::is_empty(.)
}) {
stop("Expecting 'CNSR' argument to be binary with values `0/1`.")
if (any(!rlang::is_integerish(CNSR)) || any(stats::na.omit(CNSR) < 0)) {
stop("Expecting 'CNSR' argument to be non-negative integer (>=0).")
}

if (any(AVAL < 0)) {
warning("Values of 'AVAL' are less than zero, which is likely a data error.")
}

# pass args to `survival::Surv()` --------------------------------------------
survival::Surv(time = AVAL, event = 1 - CNSR, type = "right", origin = 0)
survival::Surv(time = AVAL, event = CNSR == 0, type = "right", origin = 0)
}
2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -100,7 +100,7 @@ The package also includes gems for those using the [CDISC ADaM ADTTE v1.0](https

If columns `"PARAM"` or `"PARAMCD"` are present in the data frame passed to `survfit2()`, their values will be used to construct default labels in the `ggsurvfit()` figure.

The event indicator in ADTTE data sets is named `"CNSR"` and is coded in the opposite way the survival package expects outcomes---`1 = 'censored'` and `0 = 'event'`.
The event indicator in ADTTE data sets is named `"CNSR"` and is coded in the opposite way the survival package expects outcomes---`>=1 = 'censored'` and `0 = 'event'`.
This difference creates an opportunity for errors to be introduced in an analysis.
The **ggsurvfit** package exports a function called `Surv_CNSR()` to resolve this concern.
The function creates a survival object (e.g. `survival::Surv()`) that uses CDISC ADaM ADTTE coding conventions as the default values.
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20 changes: 10 additions & 10 deletions README.md
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Expand Up @@ -92,7 +92,7 @@ p +
)
```

<img src="man/figures/README-unnamed-chunk-2-1.png" width="100%" />
<img src="man/figures/README-unnamed-chunk-2-1.png" alt="" width="100%" />

## `survfit2()` vs `survfit()`

Expand Down Expand Up @@ -120,14 +120,14 @@ to `survfit2()`, their values will be used to construct default labels
in the `ggsurvfit()` figure.

The event indicator in ADTTE data sets is named `"CNSR"` and is coded in
the opposite way the survival package expects outcomes—`1 = 'censored'`
and `0 = 'event'`. This difference creates an opportunity for errors to
be introduced in an analysis. The **ggsurvfit** package exports a
function called `Surv_CNSR()` to resolve this concern. The function
creates a survival object (e.g. `survival::Surv()`) that uses CDISC ADaM
ADTTE coding conventions as the default values. The function can be used
in **ggsurvfit** as well as any other package that uses
`survival::Surv()`.
the opposite way the survival package expects
outcomes—`>=1 = 'censored'` and `0 = 'event'`. This difference creates
an opportunity for errors to be introduced in an analysis. The
**ggsurvfit** package exports a function called `Surv_CNSR()` to resolve
this concern. The function creates a survival object
(e.g. `survival::Surv()`) that uses CDISC ADaM ADTTE coding conventions
as the default values. The function can be used in **ggsurvfit** as well
as any other package that uses `survival::Surv()`.

``` r
survfit(Surv_CNSR() ~ 1, adtte)
Expand All @@ -139,4 +139,4 @@ survfit(Surv_CNSR() ~ 1, adtte)

## Related Packages

<img src="man/figures/README-gt-related-pkgs.png" width="100%" />
<img src="man/figures/README-gt-related-pkgs.png" alt="" width="100%" />
6 changes: 3 additions & 3 deletions man/Surv_CNSR.Rd
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13 changes: 8 additions & 5 deletions tests/testthat/test-Surv_CNSR.R
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Expand Up @@ -23,16 +23,16 @@ test_that("The function is compatible with the survival package", {
test_that("The results of the estimation match between Surv_CNSR and Surv with inverted censoring", {
expect_equal(
with(adtte, Surv_CNSR()),
with(adtte, Surv(AVAL, 1 - CNSR))
with(adtte, Surv(AVAL, CNSR == 0))
)

km1 <- survfit2(formula = Surv_CNSR() ~ 1, data = adtte)
km2 <- survfit2(formula = Surv(AVAL, 1 - CNSR) ~ 1, data = adtte)
km2 <- survfit2(formula = Surv(AVAL, CNSR == 0) ~ 1, data = adtte)
km1$call <- km2$call <- km1$.Environment <- km2$.Environment <- NULL
expect_equal(km1, km2)

km1 <- survfit2(formula = Surv_CNSR() ~ STR01, data = adtte)
km2 <- survfit2(formula = Surv(AVAL, 1 - CNSR) ~ STR01, data = adtte)
km2 <- survfit2(formula = Surv(AVAL, CNSR == 0) ~ STR01, data = adtte)
km1$call <- km2$call <- km1$.Environment <- km2$.Environment <- NULL
expect_equal(km1, km2)
})
Expand Down Expand Up @@ -74,6 +74,9 @@ test_that("An error when the column name specified through CNSR in the environme
expect_error(survfit(Surv_CDISC(AVAL = time) ~ 1, data = survival::lung %>% dplyr::mutate(CNSR = as.character(status))))
})

test_that("An error when the column name specified through CNSR is not coded as 0/1", {
expect_error(survfit(Surv_CNSR(time, status) ~ 1, data = survival::lung))
test_that("An error when the column name specified through CNSR < 0", {
expect_error(survfit(
Surv_CNSR(time, status) ~ 1,
data = survival::lung %>% dplyr::mutate(status = status - 2)
))
})