Adds support for flexsurvspline engine for survival_reg model spec

NEWS.md

@@ -1,5 +1,7 @@
 # parsnip (development version)
 
+* Adds support for `flexsurvspline` engine for the `survival_reg()` model specification from the `censored` package (#831)
+
 * The matrix interface for fitting `fit_xy()` now works for the `"censored regression"` mode (#829).
 
 # parsnip 1.0.2

R/surv_reg_flexsurvspline.R

@@ -0,0 +1,11 @@
+#' Flexible parametric survival regression
+#'
+#' [flexsurv::flexsurvspline()] fits a flexible parametric survival model.
+#'
+#' @includeRmd man/rmd/surv_reg_flexsurvspline.md details
+#'
+#' @name details_surv_reg_flexsurvspline
+#' @keywords internal
+NULL
+
+# See inst/README-DOCS.md for a description of how these files are processed

R/survival_reg_flexsurvspline.R

@@ -0,0 +1,11 @@
+#' Flexible parametric survival regression
+#'
+#' [flexsurv::flexsurvspline()] fits a flexible parametric survival model.
+#'
+#' @includeRmd man/rmd/survival_reg_flexsurvspline.md details
+#'
+#' @name details_survival_reg_flexsurvspline
+#' @keywords internal
+NULL
+
+# See inst/README-DOCS.md for a description of how these files are processed

R/tunable.R

@@ -190,6 +190,17 @@ brulee_multinomial_engine_args <-
   brulee_mlp_engine_args %>%
   dplyr::filter(name %in% c("momentum", "batch_size", "stop_iter", "class_weights"))
 
+flexsurvspline_engine_args <-
+  tibble::tibble(
+    name = c("num_knots"),
+    call_info = list(
+      list(pkg = "dials", fun = "num_knots")
+    ),
+    source = "model_spec",
+    component = "survival_reg",
+    component_id = "engine"
+  )
+
 # ------------------------------------------------------------------------------
 
 # Lazily registered in .onLoad()
@@ -310,5 +321,16 @@ tunable_mlp <- function(x, ...) {
   res
 }
 
+# Lazily registered in .onLoad()
+tunable_survival_reg <- function(x, ...) {
+  res <- NextMethod()
+  if (x$engine == "flexsurvspline") {
+    res <- add_engine_parameters(res, flexsurvspline_engine_args)
+  }
+  res
+}
+
+tunable_surv_reg <- tunable_survival_reg
+
 # nocov end
 

man/rmd/surv_reg_flexsurvspline.Rmd

@@ -0,0 +1,55 @@
+```{r, child = "aaa.Rmd", include = FALSE}
+```
+
+`r descr_models("surv_reg", "flexsurvspline")`
+
+## Tuning Parameters
+
+```{r flexsurvspline-param-info, echo = FALSE}
+defaults <- 
+  tibble::tibble(parsnip = c("num_knots"), default = 1L)
+
+param <-
+  surv_reg() %>%
+  set_engine("flexsurvspline") %>%
+  set_mode("censored regression") %>%
+  make_parameter_list(defaults)
+```
+
+This model has `r nrow(param)` tuning parameters:
+
+```{r flexsurvspline-param-list, echo = FALSE, results = "asis"}
+param$item
+```
+
+## Translation from parsnip to the original package
+
+`r uses_extension("surv_reg", "flexsurvspline", "censored regression")`
+
+```{r flexsurvspline-creg}
+library(censored)
+
+surv_reg() %>% 
+  set_engine("flexsurvspline", num_knots = 1L) %>% 
+  set_mode("censored regression") %>% 
+  translate()
+```
+
+## Other details
+
+The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
+
+For this engine, stratification cannot be specified via [`strata()`], please see [flexsurv::flexsurvspline()] for alternative specifications.
+
+```{r child = "template-survival-mean.Rmd"}
+```
+
+## Saving fitted model objects
+
+```{r child = "template-butcher.Rmd"}
+```
+
+
+## References
+
+- Jackson, C. 2016. `flexsurv`: A Platform for Parametric Survival  Modeling in R. _Journal of Statistical Software_, 70(8), 1 - 33.

man/rmd/survival_reg_flexsurvspline.Rmd

@@ -0,0 +1,55 @@
+```{r, child = "aaa.Rmd", include = FALSE}
+```
+
+`r descr_models("survival_reg", "flexsurvspline")`
+
+## Tuning Parameters
+
+```{r flexsurvspline-param-info, echo = FALSE}
+defaults <- 
+  tibble::tibble(parsnip = c("num_knots"), default = 1L)
+
+param <-
+  survival_reg() %>%
+  set_engine("flexsurvspline") %>%
+  set_mode("censored regression") %>%
+  make_parameter_list(defaults)
+```
+
+This model has `r nrow(param)` tuning parameters:
+
+```{r flexsurvspline-param-list, echo = FALSE, results = "asis"}
+param$item
+```
+
+## Translation from parsnip to the original package
+
+`r uses_extension("survival_reg", "flexsurvspline", "censored regression")`
+
+```{r flexsurvspline-creg}
+library(censored)
+
+survival_reg() %>% 
+  set_engine("flexsurvspline", num_knots = 1L) %>% 
+  set_mode("censored regression") %>% 
+  translate()
+```
+
+## Other details
+
+The main interface for this model uses the formula method since the model specification typically involved the use of [survival::Surv()]. 
+
+For this engine, stratification cannot be specified via [`strata()`], please see [flexsurv::flexsurvspline()] for alternative specifications.
+
+```{r child = "template-survival-mean.Rmd"}
+```
+
+## Saving fitted model objects
+
+```{r child = "template-butcher.Rmd"}
+```
+
+
+## References
+
+- Jackson, C. 2016. `flexsurv`: A Platform for Parametric Survival  Modeling in R. _Journal of Statistical Software_, 70(8), 1 - 33.